Starting phenix.real_space_refine on Mon Aug 25 01:23:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tza_41739/08_2025/8tza_41739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tza_41739/08_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_41739/08_2025/8tza_41739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tza_41739/08_2025/8tza_41739.map" model { file = "/net/cci-nas-00/data/ceres_data/8tza_41739/08_2025/8tza_41739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tza_41739/08_2025/8tza_41739_trim.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} 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: 3.91, per 1000 atoms: 0.16 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: 1.49 Conformation dependent library (CDL) restraints added in 656.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 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: 0.46 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: 5.12 Time building geometry restraints manager: 2.10 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: 0.01 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.170 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.001 0.000 ARG A 355 TYR 0.007 0.001 TYR A 216 PHE 0.011 0.001 PHE C 269 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00868 (12564) covalent geometry : angle 0.50849 (17118) hydrogen bonds : bond 0.14007 ( 979) hydrogen bonds : angle 4.66609 ( 2901) *********************** 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 : 0.458 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: 0.8663 (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: 0.7538 (t80) REVERT: C 130 ASN cc_start: 0.6308 (t0) cc_final: 0.5984 (m-40) REVERT: C 428 MET cc_start: 0.8759 (mmt) cc_final: 0.8374 (mmt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1988 time to fit residues: 101.4809 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 : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.139407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113955 restraints weight = 55893.620| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.21 r_work: 0.3345 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12564 Z= 0.127 Angle : 0.480 5.094 17118 Z= 0.261 Chirality : 0.035 0.124 1986 Planarity : 0.004 0.059 2082 Dihedral : 6.947 91.564 1764 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.96 % Allowed : 9.62 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.98 (0.21), residues: 1593 helix: 3.28 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.92 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 589 TYR 0.013 0.001 TYR A 119 PHE 0.012 0.001 PHE B 259 TRP 0.013 0.001 TRP C 184 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00261 (12564) covalent geometry : angle 0.48030 (17118) hydrogen bonds : bond 0.04868 ( 979) hydrogen bonds : angle 4.04882 ( 2901) *********************** 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 212 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.525 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 182 VAL cc_start: 0.9123 (t) cc_final: 0.8854 (t) REVERT: B 186 CYS cc_start: 0.8403 (m) cc_final: 0.7974 (m) REVERT: B 206 GLN cc_start: 0.8880 (mp10) cc_final: 0.8498 (mp10) REVERT: B 325 MET cc_start: 0.8241 (mtt) cc_final: 0.8021 (mtm) REVERT: A 154 MET cc_start: 0.7803 (mmm) cc_final: 0.6682 (ttt) REVERT: A 497 MET cc_start: 0.8361 (tmt) cc_final: 0.8110 (tmm) REVERT: C 314 MET cc_start: 0.7798 (ttm) cc_final: 0.7240 (ttm) REVERT: C 428 MET cc_start: 0.8512 (mmt) cc_final: 0.7927 (mmt) outliers start: 12 outliers final: 9 residues processed: 209 average time/residue: 0.1736 time to fit residues: 57.7650 Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 423 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 42 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.132729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107581 restraints weight = 56204.090| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.11 r_work: 0.3256 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12564 Z= 0.160 Angle : 0.484 5.035 17118 Z= 0.269 Chirality : 0.035 0.121 1986 Planarity : 0.004 0.047 2082 Dihedral : 5.118 71.043 1764 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.84 % Allowed : 10.50 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.11 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 589 TYR 0.011 0.001 TYR A 519 PHE 0.013 0.001 PHE A 164 TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00355 (12564) covalent geometry : angle 0.48426 (17118) hydrogen bonds : bond 0.05342 ( 979) hydrogen bonds : angle 4.03487 ( 2901) *********************** 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 200 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.649 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: B 186 CYS cc_start: 0.8388 (m) cc_final: 0.7930 (m) REVERT: B 325 MET cc_start: 0.8242 (mtt) cc_final: 0.8010 (mtt) REVERT: A 154 MET cc_start: 0.7807 (mmm) cc_final: 0.6857 (mtp) REVERT: C 428 MET cc_start: 0.8523 (mmt) cc_final: 0.7916 (mmt) REVERT: C 555 SER cc_start: 0.7721 (m) cc_final: 0.7295 (p) outliers start: 23 outliers final: 16 residues processed: 196 average time/residue: 0.1771 time to fit residues: 54.6979 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 132 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110157 restraints weight = 56115.407| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.12 r_work: 0.3292 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12564 Z= 0.111 Angle : 0.430 4.582 17118 Z= 0.232 Chirality : 0.034 0.117 1986 Planarity : 0.003 0.043 2082 Dihedral : 4.853 64.751 1764 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.28 % Allowed : 11.46 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.76 (0.21), residues: 1593 helix: 3.14 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 589 TYR 0.013 0.001 TYR A 119 PHE 0.013 0.001 PHE A 164 TRP 0.005 0.001 TRP C 316 HIS 0.004 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00229 (12564) covalent geometry : angle 0.42985 (17118) hydrogen bonds : bond 0.04222 ( 979) hydrogen bonds : angle 3.74614 ( 2901) *********************** 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 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.444 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: B 158 GLU cc_start: 0.7988 (pp20) cc_final: 0.7450 (pm20) REVERT: B 186 CYS cc_start: 0.8411 (m) cc_final: 0.7930 (m) REVERT: A 154 MET cc_start: 0.7862 (mmm) cc_final: 0.6992 (mtp) REVERT: C 428 MET cc_start: 0.8606 (mmt) cc_final: 0.8048 (mmt) outliers start: 16 outliers final: 14 residues processed: 189 average time/residue: 0.1687 time to fit residues: 50.9643 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 578 VAL Chi-restraints excluded: chain A residue 145 ILE 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 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 ASP 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 2 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.128836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106537 restraints weight = 54910.465| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.53 r_work: 0.3211 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12564 Z= 0.152 Angle : 0.462 5.097 17118 Z= 0.256 Chirality : 0.035 0.118 1986 Planarity : 0.004 0.041 2082 Dihedral : 4.980 64.483 1764 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.76 % Allowed : 12.58 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.21), residues: 1593 helix: 2.94 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 589 TYR 0.010 0.001 TYR A 519 PHE 0.014 0.001 PHE A 164 TRP 0.006 0.001 TRP C 176 HIS 0.004 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00332 (12564) covalent geometry : angle 0.46240 (17118) hydrogen bonds : bond 0.05053 ( 979) hydrogen bonds : angle 3.91660 ( 2901) *********************** 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 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.634 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: 0.8656 (m) cc_final: 0.8195 (m) REVERT: A 154 MET cc_start: 0.8000 (mmm) cc_final: 0.7229 (mtp) REVERT: A 176 TRP cc_start: 0.7429 (t-100) cc_final: 0.6336 (t60) REVERT: C 428 MET cc_start: 0.8732 (mmt) cc_final: 0.8250 (mmt) REVERT: C 555 SER cc_start: 0.8120 (m) cc_final: 0.7872 (p) outliers start: 22 outliers final: 19 residues processed: 187 average time/residue: 0.1592 time to fit residues: 47.9069 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 440 GLU 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 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 423 ASN Chi-restraints excluded: chain C residue 482 ASP 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 107 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 125 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.131099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108929 restraints weight = 54785.555| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.54 r_work: 0.3246 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12564 Z= 0.111 Angle : 0.428 4.500 17118 Z= 0.232 Chirality : 0.034 0.116 1986 Planarity : 0.003 0.041 2082 Dihedral : 4.804 63.655 1764 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.68 % Allowed : 12.58 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.21), residues: 1593 helix: 3.06 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 589 TYR 0.007 0.001 TYR A 519 PHE 0.014 0.001 PHE A 164 TRP 0.006 0.001 TRP C 316 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00230 (12564) covalent geometry : angle 0.42832 (17118) hydrogen bonds : bond 0.04353 ( 979) hydrogen bonds : angle 3.72799 ( 2901) *********************** 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 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.658 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: 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: 0.7928 (pp20) cc_final: 0.7448 (pt0) REVERT: B 186 CYS cc_start: 0.8614 (m) cc_final: 0.8132 (m) REVERT: A 154 MET cc_start: 0.7834 (mmm) cc_final: 0.7230 (mtp) REVERT: A 176 TRP cc_start: 0.7382 (t-100) cc_final: 0.6319 (t60) REVERT: C 428 MET cc_start: 0.8744 (mmt) cc_final: 0.8286 (mmt) REVERT: C 555 SER cc_start: 0.7996 (m) cc_final: 0.7740 (p) outliers start: 21 outliers final: 17 residues processed: 186 average time/residue: 0.1630 time to fit residues: 49.1548 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 222 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 482 ASP 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 128 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.132905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110897 restraints weight = 54369.391| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.53 r_work: 0.3274 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12564 Z= 0.097 Angle : 0.414 4.975 17118 Z= 0.221 Chirality : 0.033 0.127 1986 Planarity : 0.003 0.041 2082 Dihedral : 4.621 63.614 1764 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.52 % Allowed : 12.42 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.82 (0.21), residues: 1593 helix: 3.23 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 589 TYR 0.005 0.001 TYR A 519 PHE 0.014 0.001 PHE A 164 TRP 0.006 0.000 TRP C 316 HIS 0.004 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00199 (12564) covalent geometry : angle 0.41412 (17118) hydrogen bonds : bond 0.03818 ( 979) hydrogen bonds : angle 3.58041 ( 2901) *********************** 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 192 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.525 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: B 158 GLU cc_start: 0.7912 (pp20) cc_final: 0.7424 (pt0) REVERT: B 186 CYS cc_start: 0.8630 (m) cc_final: 0.8412 (m) REVERT: A 154 MET cc_start: 0.7827 (mmm) cc_final: 0.7230 (mtp) REVERT: A 176 TRP cc_start: 0.7357 (t-100) cc_final: 0.6398 (t60) REVERT: C 428 MET cc_start: 0.8743 (mmt) cc_final: 0.8389 (mmt) REVERT: C 555 SER cc_start: 0.7948 (m) cc_final: 0.7665 (p) outliers start: 19 outliers final: 17 residues processed: 188 average time/residue: 0.1520 time to fit residues: 46.4430 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 571 ASN 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 482 ASP 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 139 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 GLN C 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105862 restraints weight = 55284.821| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.52 r_work: 0.3204 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4578 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= 0.160 Angle : 0.467 4.857 17118 Z= 0.258 Chirality : 0.035 0.116 1986 Planarity : 0.003 0.040 2082 Dihedral : 4.914 63.202 1764 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 13.30 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -1.00 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.014 0.001 TYR A 119 PHE 0.015 0.001 PHE A 164 TRP 0.006 0.001 TRP B 178 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00357 (12564) covalent geometry : angle 0.46714 (17118) hydrogen bonds : bond 0.05000 ( 979) hydrogen bonds : angle 3.87820 ( 2901) *********************** 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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.622 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: 0.8052 (pp20) cc_final: 0.7593 (pt0) REVERT: B 186 CYS cc_start: 0.8645 (m) cc_final: 0.8187 (m) REVERT: A 154 MET cc_start: 0.7859 (mmm) cc_final: 0.7316 (mtp) REVERT: A 176 TRP cc_start: 0.7338 (t-100) cc_final: 0.7101 (t-100) REVERT: A 305 MET cc_start: 0.8509 (tpp) cc_final: 0.8087 (mmp) REVERT: C 428 MET cc_start: 0.8709 (mmt) cc_final: 0.8266 (mmt) REVERT: C 555 SER cc_start: 0.8233 (m) cc_final: 0.7994 (p) outliers start: 24 outliers final: 19 residues processed: 179 average time/residue: 0.1516 time to fit residues: 43.8758 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 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 423 ASN Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 554 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 6 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 45 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 = 0.3553 r_free = 0.3553 target = 0.125961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103892 restraints weight = 55872.653| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.53 r_work: 0.3173 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4728 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= 0.208 Angle : 0.499 4.875 17118 Z= 0.280 Chirality : 0.036 0.120 1986 Planarity : 0.004 0.041 2082 Dihedral : 5.082 64.224 1764 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.60 % Allowed : 14.02 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.21), residues: 1593 helix: 2.74 (0.14), residues: 1293 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 589 TYR 0.011 0.001 TYR A 519 PHE 0.015 0.001 PHE A 164 TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00472 (12564) covalent geometry : angle 0.49897 (17118) hydrogen bonds : bond 0.05412 ( 979) hydrogen bonds : angle 4.02388 ( 2901) *********************** 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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.605 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: 0.8043 (pp20) cc_final: 0.7544 (pt0) REVERT: B 186 CYS cc_start: 0.8634 (m) cc_final: 0.8181 (m) REVERT: A 154 MET cc_start: 0.7821 (mmm) cc_final: 0.7331 (mtp) REVERT: A 305 MET cc_start: 0.8628 (tpp) cc_final: 0.8189 (mmp) REVERT: C 349 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 428 MET cc_start: 0.8750 (mmt) cc_final: 0.8320 (mmt) REVERT: C 555 SER cc_start: 0.8328 (m) cc_final: 0.8110 (p) outliers start: 20 outliers final: 17 residues processed: 177 average time/residue: 0.1582 time to fit residues: 45.1408 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 C residue 127 CYS Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 423 ASN Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 554 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 94 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 ASN C 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109035 restraints weight = 54525.041| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.45 r_work: 0.3252 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12564 Z= 0.109 Angle : 0.430 4.360 17118 Z= 0.232 Chirality : 0.034 0.116 1986 Planarity : 0.003 0.043 2082 Dihedral : 4.748 62.395 1764 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1299 sheet: None (None), residues: 0 loop : -0.92 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 589 TYR 0.007 0.001 TYR B 385 PHE 0.016 0.001 PHE A 164 TRP 0.024 0.001 TRP A 181 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00228 (12564) covalent geometry : angle 0.42985 (17118) hydrogen bonds : bond 0.04119 ( 979) hydrogen bonds : angle 3.65926 ( 2901) ********************** 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.525 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: 0.8047 (pp20) cc_final: 0.7549 (pt0) REVERT: B 186 CYS cc_start: 0.8612 (m) cc_final: 0.8163 (m) REVERT: B 440 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6006 (mm-30) REVERT: A 154 MET cc_start: 0.7806 (mmm) cc_final: 0.7314 (mtp) REVERT: A 305 MET cc_start: 0.8527 (tpp) cc_final: 0.8150 (mmp) REVERT: C 349 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7208 (tm-30) REVERT: C 428 MET cc_start: 0.8691 (mmt) cc_final: 0.8301 (mmt) REVERT: C 555 SER cc_start: 0.8080 (m) cc_final: 0.7774 (p) outliers start: 16 outliers final: 14 residues processed: 179 average time/residue: 0.1506 time to fit residues: 43.7371 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 418 GLU Chi-restraints excluded: chain A residue 571 ASN 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 Chi-restraints excluded: chain C residue 554 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.128777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106931 restraints weight = 55357.947| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.53 r_work: 0.3219 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12564 Z= 0.134 Angle : 0.444 4.434 17118 Z= 0.242 Chirality : 0.034 0.117 1986 Planarity : 0.003 0.043 2082 Dihedral : 4.761 60.199 1764 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.28 % Allowed : 14.26 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.21), residues: 1593 helix: 2.97 (0.14), residues: 1299 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 589 TYR 0.013 0.001 TYR A 119 PHE 0.015 0.001 PHE A 164 TRP 0.017 0.001 TRP A 181 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00294 (12564) covalent geometry : angle 0.44403 (17118) hydrogen bonds : bond 0.04480 ( 979) hydrogen bonds : angle 3.74048 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5105.58 seconds wall clock time: 87 minutes 6.27 seconds (5226.27 seconds total)