Starting phenix.real_space_refine on Fri May 23 14:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tza_41739/05_2025/8tza_41739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tza_41739/05_2025/8tza_41739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tza_41739/05_2025/8tza_41739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tza_41739/05_2025/8tza_41739.map" model { file = "/net/cci-nas-00/data/ceres_data/8tza_41739/05_2025/8tza_41739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tza_41739/05_2025/8tza_41739_trim.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.061 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: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 8103 2.51 5 N 1923 2.21 5 O 2115 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24297 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.33, per 1000 atoms: 0.47 Number of scatterers: 24297 At special positions: 0 Unit cell: (128.52, 126.36, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 2115 8.00 N 1923 7.00 C 8103 6.00 H 12069 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: 5.81 Conformation dependent library (CDL) restraints added in 1.9 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 88.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'B' and resid 90 through 130 removed outlier: 5.678A pdb=" N THR B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.669A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 4.018A pdb=" N PHE B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.412A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.526A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.544A pdb=" N PHE B 281 " --> pdb=" O ALA B 277 " (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 293 through 312 Processing helix chain 'B' and resid 313 through 329 Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.817A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.582A 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: 3.633A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 4.030A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.064A 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 481 removed outlier: 3.783A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.587A 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: 4.259A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 4.095A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.921A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.521A pdb=" N THR B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 130 removed outlier: 5.638A pdb=" N THR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.733A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.831A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.463A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 277 removed outlier: 3.523A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.789A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 3.567A 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 375 Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.997A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.170A 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 481 removed outlier: 3.613A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.566A 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: 4.290A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 4.033A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.798A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 596 through 619 removed outlier: 3.761A pdb=" N ALA A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 130 removed outlier: 5.661A pdb=" N THR C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.705A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.949A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.438A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 3.681A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 313 through 329 Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.819A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 361 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: 3.683A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.033A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.137A 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 481 removed outlier: 3.713A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.577A 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: 4.284A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.962A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 586 removed outlier: 4.489A pdb=" N GLY C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.644A pdb=" N GLY C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 597 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.17 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12051 1.03 - 1.23: 24 1.23 - 1.42: 5331 1.42 - 1.61: 7068 1.61 - 1.81: 159 Bond restraints: 24633 Sorted by residual: bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.680 -0.282 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.678 -0.280 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.674 -0.276 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C10 XMO C 801 " pdb=" C11 XMO C 801 " ideal model delta sigma weight residual 1.534 1.287 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C10 XMO A 801 " pdb=" C11 XMO A 801 " ideal model delta sigma weight residual 1.534 1.291 0.243 2.00e-02 2.50e+03 1.47e+02 ... (remaining 24628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 44117 1.75 - 3.51: 250 3.51 - 5.26: 59 5.26 - 7.02: 7 7.02 - 8.77: 3 Bond angle restraints: 44436 Sorted by residual: angle pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O06 XMO A 801 " ideal model delta sigma weight residual 111.45 120.22 -8.77 3.00e+00 1.11e-01 8.55e+00 angle pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sigma weight residual 111.45 120.20 -8.75 3.00e+00 1.11e-01 8.51e+00 angle pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sigma weight residual 111.45 119.76 -8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 105.39 2.80 1.29e+00 6.01e-01 4.70e+00 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 105.46 2.73 1.29e+00 6.01e-01 4.49e+00 ... (remaining 44431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 11351 28.63 - 57.25: 351 57.25 - 85.88: 27 85.88 - 114.50: 3 114.50 - 143.13: 13 Dihedral angle restraints: 11745 sinusoidal: 6015 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO A 801 " pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O05 XMO A 801 " ideal model delta sinusoidal sigma weight residual 116.78 -26.35 143.13 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C01 XMO A 801 " pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O06 XMO A 801 " ideal model delta sinusoidal sigma weight residual 296.92 153.91 143.01 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C03 XMO A 801 " pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O05 XMO A 801 " ideal model delta sinusoidal sigma weight residual -7.58 -150.48 142.90 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 11742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1863 0.072 - 0.145: 120 0.145 - 0.217: 0 0.217 - 0.289: 0 0.289 - 0.362: 3 Chirality restraints: 1986 Sorted by residual: chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.38 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1983 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO B 296 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO C 296 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO A 296 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.036 5.00e-02 4.00e+02 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 614 2.16 - 2.77: 45117 2.77 - 3.38: 69148 3.38 - 3.99: 84175 3.99 - 4.60: 136522 Nonbonded interactions: 335576 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" HG1 THR A 199 " model vdw 1.547 2.450 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.596 2.450 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.598 2.450 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU A 525 " pdb=" H GLU A 525 " model vdw 1.624 2.450 ... (remaining 335571 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.470 Extract box with map and model: 0.780 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 48.120 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.009 0.282 12564 Z= 0.433 Angle : 0.508 8.771 17118 Z= 0.262 Chirality : 0.038 0.362 1986 Planarity : 0.004 0.068 2082 Dihedral : 13.217 143.131 4275 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.21), residues: 1593 helix: 3.45 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 288 PHE 0.011 0.001 PHE C 269 TYR 0.007 0.001 TYR A 216 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.14007 ( 979) hydrogen bonds : angle 4.66609 ( 2901) covalent geometry : bond 0.00868 (12564) covalent geometry : angle 0.50849 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 342 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 VAL cc_start: 0.9102 (t) cc_final: 0.8664 (t) REVERT: B 186 CYS cc_start: 0.8040 (m) cc_final: 0.7645 (m) REVERT: B 370 MET cc_start: 0.7923 (mtp) cc_final: 0.7623 (mtm) REVERT: A 154 MET cc_start: 0.7706 (mmm) cc_final: 0.6835 (mtp) REVERT: A 176 TRP cc_start: 0.7178 (t-100) cc_final: 0.6904 (t-100) REVERT: A 497 MET cc_start: 0.7754 (tmt) cc_final: 0.7552 (tmm) REVERT: C 119 TYR cc_start: 0.7805 (t80) cc_final: 0.7540 (t80) REVERT: C 130 ASN cc_start: 0.6308 (t0) cc_final: 0.5985 (m-40) REVERT: C 428 MET cc_start: 0.8759 (mmt) cc_final: 0.8385 (mmt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.4595 time to fit residues: 231.8918 Evaluate side-chains 201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113749 restraints weight = 55721.604| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.20 r_work: 0.3340 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12564 Z= 0.128 Angle : 0.480 4.860 17118 Z= 0.262 Chirality : 0.035 0.125 1986 Planarity : 0.004 0.060 2082 Dihedral : 6.982 91.966 1764 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.88 % Allowed : 9.62 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.21), residues: 1593 helix: 3.27 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.92 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 184 HIS 0.003 0.001 HIS A 288 PHE 0.013 0.001 PHE B 259 TYR 0.013 0.001 TYR A 119 ARG 0.005 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 979) hydrogen bonds : angle 4.05503 ( 2901) covalent geometry : bond 0.00265 (12564) covalent geometry : angle 0.47992 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 210 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8402 (m) cc_final: 0.7977 (m) REVERT: B 206 GLN cc_start: 0.8887 (mp10) cc_final: 0.8496 (mp10) REVERT: B 325 MET cc_start: 0.8243 (mtt) cc_final: 0.8024 (mtm) REVERT: B 503 MET cc_start: 0.9025 (mtm) cc_final: 0.8824 (mtm) REVERT: A 154 MET cc_start: 0.7802 (mmm) cc_final: 0.6682 (ttt) REVERT: A 497 MET cc_start: 0.8360 (tmt) cc_final: 0.8132 (tmm) REVERT: C 314 MET cc_start: 0.7809 (ttm) cc_final: 0.7254 (ttm) REVERT: C 509 ASP cc_start: 0.8741 (m-30) cc_final: 0.8418 (m-30) outliers start: 11 outliers final: 8 residues processed: 207 average time/residue: 0.3921 time to fit residues: 127.4098 Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 33 optimal weight: 0.0000 chunk 158 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106646 restraints weight = 55139.608| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.11 r_work: 0.3237 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12564 Z= 0.174 Angle : 0.502 5.162 17118 Z= 0.280 Chirality : 0.036 0.121 1986 Planarity : 0.004 0.046 2082 Dihedral : 5.263 72.734 1764 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.76 % Allowed : 10.42 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.21), residues: 1593 helix: 2.90 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.10 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.003 0.001 HIS B 175 PHE 0.014 0.001 PHE A 164 TYR 0.013 0.001 TYR A 519 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.05608 ( 979) hydrogen bonds : angle 4.09759 ( 2901) covalent geometry : bond 0.00390 (12564) covalent geometry : angle 0.50177 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8392 (m) cc_final: 0.7935 (m) REVERT: B 349 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 503 MET cc_start: 0.9104 (mtm) cc_final: 0.8897 (mtm) REVERT: A 154 MET cc_start: 0.7768 (mmm) cc_final: 0.6869 (mtp) REVERT: C 555 SER cc_start: 0.7873 (m) cc_final: 0.7452 (p) outliers start: 22 outliers final: 17 residues processed: 198 average time/residue: 0.4085 time to fit residues: 126.4690 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 550 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102968 restraints weight = 57568.982| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.11 r_work: 0.3195 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12564 Z= 0.210 Angle : 0.518 4.844 17118 Z= 0.292 Chirality : 0.037 0.121 1986 Planarity : 0.004 0.047 2082 Dihedral : 5.499 64.644 1764 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.48 % Allowed : 11.62 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.90 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS A 226 PHE 0.014 0.001 PHE A 413 TYR 0.013 0.001 TYR A 519 ARG 0.003 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.05819 ( 979) hydrogen bonds : angle 4.22373 ( 2901) covalent geometry : bond 0.00477 (12564) covalent geometry : angle 0.51763 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 GLU cc_start: 0.8082 (pp20) cc_final: 0.7632 (pt0) REVERT: B 186 CYS cc_start: 0.8415 (m) cc_final: 0.7934 (m) REVERT: B 349 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 154 MET cc_start: 0.7969 (mmm) cc_final: 0.7117 (mtp) REVERT: C 555 SER cc_start: 0.8162 (m) cc_final: 0.7782 (p) outliers start: 31 outliers final: 22 residues processed: 190 average time/residue: 0.3864 time to fit residues: 116.9865 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106375 restraints weight = 55076.910| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.52 r_work: 0.3207 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12564 Z= 0.131 Angle : 0.448 4.572 17118 Z= 0.246 Chirality : 0.034 0.119 1986 Planarity : 0.004 0.045 2082 Dihedral : 5.072 65.040 1764 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.32 % Allowed : 12.58 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -0.97 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.004 0.001 HIS B 175 PHE 0.013 0.001 PHE A 164 TYR 0.008 0.001 TYR A 519 ARG 0.001 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 979) hydrogen bonds : angle 3.91501 ( 2901) covalent geometry : bond 0.00282 (12564) covalent geometry : angle 0.44836 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8646 (m) cc_final: 0.8208 (m) REVERT: B 440 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6058 (mm-30) REVERT: A 154 MET cc_start: 0.8065 (mmm) cc_final: 0.7258 (mtp) REVERT: C 555 SER cc_start: 0.8138 (m) cc_final: 0.7932 (p) outliers start: 29 outliers final: 18 residues processed: 184 average time/residue: 0.3983 time to fit residues: 116.6326 Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104911 restraints weight = 55365.345| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.53 r_work: 0.3187 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12564 Z= 0.163 Angle : 0.470 4.863 17118 Z= 0.260 Chirality : 0.035 0.123 1986 Planarity : 0.004 0.045 2082 Dihedral : 5.103 63.399 1764 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 13.54 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.21), residues: 1593 helix: 2.75 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.93 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 316 HIS 0.005 0.001 HIS B 175 PHE 0.014 0.001 PHE A 164 TYR 0.014 0.001 TYR A 119 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 979) hydrogen bonds : angle 3.99480 ( 2901) covalent geometry : bond 0.00363 (12564) covalent geometry : angle 0.47009 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 GLU cc_start: 0.8140 (pp20) cc_final: 0.7598 (pt0) REVERT: B 186 CYS cc_start: 0.8595 (m) cc_final: 0.8128 (m) REVERT: B 440 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6147 (mm-30) REVERT: A 154 MET cc_start: 0.8079 (mmm) cc_final: 0.7302 (mtp) REVERT: A 305 MET cc_start: 0.8843 (tpp) cc_final: 0.8387 (mmp) REVERT: C 555 SER cc_start: 0.8192 (m) cc_final: 0.7954 (p) outliers start: 23 outliers final: 20 residues processed: 172 average time/residue: 0.3794 time to fit residues: 104.4039 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 140 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105982 restraints weight = 55359.008| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.53 r_work: 0.3203 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12564 Z= 0.138 Angle : 0.448 4.520 17118 Z= 0.245 Chirality : 0.034 0.118 1986 Planarity : 0.003 0.043 2082 Dihedral : 4.946 60.751 1764 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 13.78 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 178 HIS 0.002 0.001 HIS B 394 PHE 0.015 0.001 PHE A 164 TYR 0.007 0.001 TYR A 519 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 979) hydrogen bonds : angle 3.87680 ( 2901) covalent geometry : bond 0.00302 (12564) covalent geometry : angle 0.44771 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 GLU cc_start: 0.8101 (pp20) cc_final: 0.7594 (pt0) REVERT: B 186 CYS cc_start: 0.8615 (m) cc_final: 0.8168 (m) REVERT: B 440 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6090 (mm-30) REVERT: A 154 MET cc_start: 0.7831 (mmm) cc_final: 0.7326 (mtp) REVERT: C 555 SER cc_start: 0.8190 (m) cc_final: 0.7949 (p) outliers start: 24 outliers final: 21 residues processed: 178 average time/residue: 0.3772 time to fit residues: 107.4794 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102793 restraints weight = 56015.854| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.57 r_work: 0.3155 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12564 Z= 0.209 Angle : 0.504 4.659 17118 Z= 0.283 Chirality : 0.036 0.130 1986 Planarity : 0.004 0.044 2082 Dihedral : 5.158 63.610 1764 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.00 % Allowed : 14.02 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.21), residues: 1593 helix: 2.59 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 181 HIS 0.003 0.001 HIS B 175 PHE 0.015 0.001 PHE A 164 TYR 0.013 0.001 TYR A 119 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 979) hydrogen bonds : angle 4.10807 ( 2901) covalent geometry : bond 0.00475 (12564) covalent geometry : angle 0.50353 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8562 (m) cc_final: 0.8099 (m) REVERT: B 440 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: A 154 MET cc_start: 0.7874 (mmm) cc_final: 0.7354 (mtp) REVERT: A 305 MET cc_start: 0.8866 (tpp) cc_final: 0.8450 (mmp) REVERT: C 555 SER cc_start: 0.8369 (m) cc_final: 0.8129 (p) outliers start: 25 outliers final: 21 residues processed: 172 average time/residue: 0.4042 time to fit residues: 110.9280 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103792 restraints weight = 55731.601| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.53 r_work: 0.3171 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12564 Z= 0.175 Angle : 0.479 4.698 17118 Z= 0.267 Chirality : 0.035 0.119 1986 Planarity : 0.004 0.045 2082 Dihedral : 5.090 62.857 1764 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.76 % Allowed : 14.74 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.21), residues: 1593 helix: 2.61 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 150 HIS 0.003 0.001 HIS B 152 PHE 0.015 0.001 PHE A 164 TYR 0.008 0.001 TYR A 519 ARG 0.002 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 979) hydrogen bonds : angle 4.02847 ( 2901) covalent geometry : bond 0.00393 (12564) covalent geometry : angle 0.47923 (17118) *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8585 (m) cc_final: 0.8143 (m) REVERT: B 440 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6255 (mm-30) REVERT: A 154 MET cc_start: 0.7882 (mmm) cc_final: 0.7418 (mtp) REVERT: A 305 MET cc_start: 0.8832 (tpp) cc_final: 0.8376 (mmp) REVERT: C 169 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7514 (pt0) REVERT: C 555 SER cc_start: 0.8337 (m) cc_final: 0.8112 (p) outliers start: 22 outliers final: 21 residues processed: 166 average time/residue: 0.3911 time to fit residues: 103.5684 Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104228 restraints weight = 55653.643| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.53 r_work: 0.3175 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 12564 Z= 0.180 Angle : 0.749 59.195 17118 Z= 0.445 Chirality : 0.035 0.118 1986 Planarity : 0.004 0.045 2082 Dihedral : 5.095 62.869 1764 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.76 % Allowed : 14.74 % Favored : 83.49 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.21), residues: 1593 helix: 2.62 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 150 HIS 0.003 0.001 HIS B 175 PHE 0.015 0.001 PHE A 164 TYR 0.008 0.001 TYR A 519 ARG 0.001 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 979) hydrogen bonds : angle 4.02098 ( 2901) covalent geometry : bond 0.00389 (12564) covalent geometry : angle 0.74860 (17118) ********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8584 (m) cc_final: 0.8139 (m) REVERT: B 440 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6239 (mm-30) REVERT: A 154 MET cc_start: 0.7807 (mmm) cc_final: 0.7406 (mtp) REVERT: A 305 MET cc_start: 0.8818 (tpp) cc_final: 0.8357 (mmp) REVERT: C 169 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7513 (pt0) REVERT: C 555 SER cc_start: 0.8328 (m) cc_final: 0.8103 (p) outliers start: 22 outliers final: 20 residues processed: 163 average time/residue: 0.3834 time to fit residues: 100.3430 Evaluate side-chains 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104174 restraints weight = 55377.941| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.53 r_work: 0.3174 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 12564 Z= 0.180 Angle : 0.749 59.195 17118 Z= 0.445 Chirality : 0.035 0.118 1986 Planarity : 0.004 0.045 2082 Dihedral : 5.095 62.869 1764 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.68 % Allowed : 14.82 % Favored : 83.49 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.21), residues: 1593 helix: 2.62 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 150 HIS 0.003 0.001 HIS B 175 PHE 0.015 0.001 PHE A 164 TYR 0.008 0.001 TYR A 519 ARG 0.001 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 979) hydrogen bonds : angle 4.02098 ( 2901) covalent geometry : bond 0.00389 (12564) covalent geometry : angle 0.74860 (17118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11391.73 seconds wall clock time: 195 minutes 43.95 seconds (11743.95 seconds total)