Starting phenix.real_space_refine on Fri Jul 3 17:10:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxk_18730/07_2026/8qxk_18730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxk_18730/07_2026/8qxk_18730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qxk_18730/07_2026/8qxk_18730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxk_18730/07_2026/8qxk_18730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qxk_18730/07_2026/8qxk_18730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxk_18730/07_2026/8qxk_18730.map" } resolution = 2.66 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= 0.003 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 36 5.49 5 Mg 12 5.21 5 S 80 5.16 5 C 9694 2.51 5 N 2646 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15323 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3738 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3729 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 3742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3734 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 458, 3734 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3813 Chain: "D" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3738 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Time building chain proxies: 4.10, per 1000 atoms: 0.27 Number of scatterers: 15323 At special positions: 0 Unit cell: (119.88, 104.76, 93.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 80 16.00 P 36 15.00 Mg 12 11.99 O 2851 8.00 N 2646 7.00 C 9694 6.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 794.4 milliseconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 16 sheets defined 60.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 removed outlier: 3.518A pdb=" N ILE A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.766A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.000A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.524A pdb=" N GLN A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 214 through 220 removed outlier: 4.146A pdb=" N ASP A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.598A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.574A pdb=" N TYR A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.113A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.856A pdb=" N SER A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.683A pdb=" N TRP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.200A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.131A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.911A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.716A pdb=" N VAL A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.541A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 removed outlier: 3.517A pdb=" N ILE C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.765A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 3.998A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.653A pdb=" N GLN C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 214 through 220 removed outlier: 4.189A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.590A pdb=" N LEU C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 248 Processing helix chain 'C' and resid 250 through 257 removed outlier: 3.590A pdb=" N TYR C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.233A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.906A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.681A pdb=" N TRP C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.615A pdb=" N ALA C 412 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 413 " --> pdb=" O SER C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 423 No H-bonds generated for 'chain 'C' and resid 421 through 423' Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.123A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.656A pdb=" N VAL C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 574 removed outlier: 3.635A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 removed outlier: 3.514A pdb=" N ILE B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.766A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.997A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.618A pdb=" N GLN B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.180A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.601A pdb=" N LEU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 248 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.567A pdb=" N TYR B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.148A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.884A pdb=" N SER B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.699A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.628A pdb=" N ALA B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.124A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 469 through 474 removed outlier: 4.107A pdb=" N TYR B 473 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.684A pdb=" N VAL B 537 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 removed outlier: 3.516A pdb=" N ILE D 147 " --> pdb=" O LEU D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 147' Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.761A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 3.996A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.551A pdb=" N GLN D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.129A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.602A pdb=" N LEU D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 248 Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.578A pdb=" N TYR D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 removed outlier: 4.309A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.882A pdb=" N SER D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.682A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 394 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 410 through 414 removed outlier: 4.171A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.135A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.947A pdb=" N TYR D 473 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.699A pdb=" N VAL D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 574 removed outlier: 3.650A pdb=" N ALA D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 342 removed outlier: 8.343A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.994A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 120 Processing sheet with id=AA6, first strand: chain 'C' and resid 339 through 342 removed outlier: 8.333A pdb=" N TYR C 521 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 351 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'C' and resid 455 through 459 removed outlier: 6.980A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 343 removed outlier: 8.342A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'B' and resid 455 through 459 removed outlier: 6.986A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 120 Processing sheet with id=AB5, first strand: chain 'D' and resid 339 through 342 removed outlier: 8.341A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 459 removed outlier: 6.975A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1908 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: 2.87 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4943 1.34 - 1.46: 3456 1.46 - 1.58: 7104 1.58 - 1.69: 57 1.69 - 1.81: 120 Bond restraints: 15680 Sorted by residual: bond pdb=" O3B DCP B 707 " pdb=" PG DCP B 707 " ideal model delta sigma weight residual 1.746 1.611 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" O3B DCP D 707 " pdb=" PG DCP D 707 " ideal model delta sigma weight residual 1.746 1.611 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" O3B DCP C 706 " pdb=" PG DCP C 706 " ideal model delta sigma weight residual 1.746 1.611 0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" O3B DCP A 706 " pdb=" PG DCP A 706 " ideal model delta sigma weight residual 1.746 1.611 0.135 2.00e-02 2.50e+03 4.52e+01 bond pdb=" O3A DCP C 706 " pdb=" PB DCP C 706 " ideal model delta sigma weight residual 1.672 1.610 0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 15675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 20947 2.45 - 4.90: 230 4.90 - 7.35: 55 7.35 - 9.79: 14 9.79 - 12.24: 4 Bond angle restraints: 21250 Sorted by residual: angle pdb=" O1A DCP D 707 " pdb=" PA DCP D 707 " pdb=" O2A DCP D 707 " ideal model delta sigma weight residual 121.40 109.16 12.24 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O1A DCP B 707 " pdb=" PA DCP B 707 " pdb=" O2A DCP B 707 " ideal model delta sigma weight residual 121.40 109.48 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O1A DCP A 706 " pdb=" PA DCP A 706 " pdb=" O2A DCP A 706 " ideal model delta sigma weight residual 121.40 109.48 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O1A DCP C 706 " pdb=" PA DCP C 706 " pdb=" O2A DCP C 706 " ideal model delta sigma weight residual 121.40 109.50 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" PA DCP C 706 " pdb=" O3A DCP C 706 " pdb=" PB DCP C 706 " ideal model delta sigma weight residual 132.21 122.46 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 21245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 9168 33.50 - 67.01: 299 67.01 - 100.51: 59 100.51 - 134.01: 4 134.01 - 167.51: 4 Dihedral angle restraints: 9534 sinusoidal: 4174 harmonic: 5360 Sorted by residual: dihedral pdb=" O3A GTP D 702 " pdb=" O3B GTP D 702 " pdb=" PB GTP D 702 " pdb=" PG GTP D 702 " ideal model delta sinusoidal sigma weight residual 303.79 136.28 167.51 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP B 702 " pdb=" O3B GTP B 702 " pdb=" PB GTP B 702 " pdb=" PG GTP B 702 " ideal model delta sinusoidal sigma weight residual 303.79 136.57 167.22 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP C 701 " pdb=" O3B GTP C 701 " pdb=" PB GTP C 701 " pdb=" PG GTP C 701 " ideal model delta sinusoidal sigma weight residual 303.79 136.99 166.80 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 9531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1764 0.048 - 0.096: 345 0.096 - 0.145: 113 0.145 - 0.193: 7 0.193 - 0.241: 12 Chirality restraints: 2241 Sorted by residual: chirality pdb=" C3' DTP D 701 " pdb=" C2' DTP D 701 " pdb=" C4' DTP D 701 " pdb=" O3' DTP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' DTP C 707 " pdb=" C2' DTP C 707 " pdb=" C4' DTP C 707 " pdb=" O3' DTP C 707 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DTP B 701 " pdb=" C2' DTP B 701 " pdb=" C4' DTP B 701 " pdb=" O3' DTP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2238 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 707 " -0.017 2.00e-02 2.50e+03 6.56e-02 9.68e+01 pdb=" C2 DCP B 707 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DCP B 707 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DCP B 707 " -0.116 2.00e-02 2.50e+03 pdb=" C6 DCP B 707 " 0.061 2.00e-02 2.50e+03 pdb=" N1 DCP B 707 " 0.059 2.00e-02 2.50e+03 pdb=" N3 DCP B 707 " 0.098 2.00e-02 2.50e+03 pdb=" N4 DCP B 707 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DCP B 707 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP C 706 " 0.019 2.00e-02 2.50e+03 6.50e-02 9.50e+01 pdb=" C2 DCP C 706 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DCP C 706 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DCP C 706 " 0.115 2.00e-02 2.50e+03 pdb=" C6 DCP C 706 " -0.062 2.00e-02 2.50e+03 pdb=" N1 DCP C 706 " -0.059 2.00e-02 2.50e+03 pdb=" N3 DCP C 706 " -0.096 2.00e-02 2.50e+03 pdb=" N4 DCP C 706 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DCP C 706 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP A 706 " -0.016 2.00e-02 2.50e+03 6.49e-02 9.47e+01 pdb=" C2 DCP A 706 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DCP A 706 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DCP A 706 " -0.115 2.00e-02 2.50e+03 pdb=" C6 DCP A 706 " 0.059 2.00e-02 2.50e+03 pdb=" N1 DCP A 706 " 0.057 2.00e-02 2.50e+03 pdb=" N3 DCP A 706 " 0.098 2.00e-02 2.50e+03 pdb=" N4 DCP A 706 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DCP A 706 " -0.089 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 110 2.55 - 3.14: 11263 3.14 - 3.73: 22390 3.73 - 4.31: 33339 4.31 - 4.90: 55855 Nonbonded interactions: 122957 Sorted by model distance: nonbonded pdb=" O1B GTP C 701 " pdb="MG MG C 705 " model vdw 1.965 2.170 nonbonded pdb=" O1B GTP A 701 " pdb="MG MG A 705 " model vdw 1.968 2.170 nonbonded pdb=" O1B GTP D 702 " pdb="MG MG D 706 " model vdw 1.969 2.170 nonbonded pdb=" O1B GTP B 702 " pdb="MG MG B 706 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR B 463 " pdb=" OE1 GLN B 465 " model vdw 1.990 3.040 ... (remaining 122952 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 527 or resid 5 \ 29 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or resid 704 through 705)) selection = (chain 'B' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 527 or resid 529 through 576 o \ r (resid 577 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 78 or resid 704 through 705)) selection = (chain 'C' and (resid 114 through 483 or (resid 484 and (name N or name CA or na \ me C or name O or name CB )) or resid 485 through 527 or resid 529 through 578 o \ r resid 704 through 705)) selection = (chain 'D' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 527 or resid 5 \ 29 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or resid 704 through 705)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.380 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.900 15682 Z= 1.035 Angle : 0.733 12.243 21250 Z= 0.373 Chirality : 0.046 0.241 2241 Planarity : 0.005 0.066 2688 Dihedral : 17.414 167.514 6092 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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 are not related in a simple way. whole: -0.20 (0.20), residues: 1817 helix: 0.63 (0.19), residues: 896 sheet: 1.15 (0.48), residues: 120 loop : -1.20 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.021 0.002 TYR B 473 PHE 0.015 0.001 PHE B 165 TRP 0.005 0.001 TRP B 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (15680) covalent geometry : angle 0.73266 / 0.37 (21250) hydrogen bonds : bond 0.17575 / 11.84 ( 704) hydrogen bonds : angle 5.98286 / 4.10 ( 1908) Misc. bond : bond 0.89843 / 45.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.465 Fit side-chains REVERT: A 461 GLN cc_start: 0.7502 (tt0) cc_final: 0.7124 (tt0) REVERT: B 372 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7127 (mtm180) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.7663 time to fit residues: 191.2197 Evaluate side-chains 178 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 293 ASN A 527 ASN A 548 GLN C 293 ASN C 527 ASN B 293 ASN B 527 ASN D 215 HIS D 293 ASN D 527 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.134331 restraints weight = 15867.931| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.20 r_work: 0.3242 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15682 Z= 0.155 Angle : 0.627 8.120 21250 Z= 0.331 Chirality : 0.046 0.185 2241 Planarity : 0.005 0.043 2688 Dihedral : 15.798 172.251 2334 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.05 % Allowed : 7.93 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1817 helix: 0.93 (0.18), residues: 900 sheet: 1.50 (0.47), residues: 120 loop : -1.15 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 470 TYR 0.034 0.002 TYR B 315 PHE 0.015 0.002 PHE B 165 TRP 0.007 0.001 TRP B 572 HIS 0.006 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (15680) covalent geometry : angle 0.62707 / 0.33 (21250) hydrogen bonds : bond 0.06509 / 4.54 ( 704) hydrogen bonds : angle 4.61422 / 3.16 ( 1908) Misc. bond : bond 0.00067 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.616 Fit side-chains REVERT: A 251 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (mmtp) REVERT: A 311 ASP cc_start: 0.8737 (t0) cc_final: 0.8532 (t0) REVERT: A 461 GLN cc_start: 0.7383 (tt0) cc_final: 0.6976 (tt0) REVERT: A 475 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.6605 (t) REVERT: A 494 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7586 (tmmm) REVERT: C 134 ARG cc_start: 0.8431 (tpt-90) cc_final: 0.8169 (tpt90) REVERT: C 494 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7579 (tmmm) REVERT: B 494 LYS cc_start: 0.8125 (mppt) cc_final: 0.7504 (mmtm) REVERT: D 494 LYS cc_start: 0.7781 (mtpp) cc_final: 0.6970 (tttt) outliers start: 17 outliers final: 5 residues processed: 192 average time/residue: 0.7272 time to fit residues: 151.2656 Evaluate side-chains 178 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 535 ASN C 527 ASN C 535 ASN B 345 ASN B 527 ASN D 527 ASN D 535 ASN D 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.165079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137350 restraints weight = 17951.624| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.33 r_work: 0.3258 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15682 Z= 0.121 Angle : 0.552 7.327 21250 Z= 0.289 Chirality : 0.044 0.153 2241 Planarity : 0.004 0.038 2688 Dihedral : 14.717 178.309 2334 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.24 % Allowed : 9.48 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1817 helix: 1.32 (0.19), residues: 880 sheet: 1.56 (0.47), residues: 120 loop : -0.91 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 164 TYR 0.031 0.001 TYR B 315 PHE 0.015 0.001 PHE B 165 TRP 0.006 0.001 TRP B 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15680) covalent geometry : angle 0.55190 / 0.29 (21250) hydrogen bonds : bond 0.05315 / 3.71 ( 704) hydrogen bonds : angle 4.39675 / 3.01 ( 1908) Misc. bond : bond 0.00086 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.551 Fit side-chains REVERT: A 242 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: A 372 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6969 (mtp180) REVERT: A 461 GLN cc_start: 0.7463 (tt0) cc_final: 0.7014 (tt0) REVERT: A 475 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.6698 (t) REVERT: A 478 LYS cc_start: 0.7535 (mtmm) cc_final: 0.7232 (mttt) REVERT: A 494 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7613 (tmmm) REVERT: C 134 ARG cc_start: 0.8454 (tpt-90) cc_final: 0.8192 (tpt90) REVERT: C 494 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7554 (tmmm) REVERT: B 251 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8118 (mmtp) REVERT: B 429 GLU cc_start: 0.8375 (tt0) cc_final: 0.8152 (tm-30) REVERT: B 478 LYS cc_start: 0.7528 (mtmm) cc_final: 0.7262 (mttt) REVERT: B 494 LYS cc_start: 0.8225 (mppt) cc_final: 0.7561 (mmtm) REVERT: D 429 GLU cc_start: 0.8475 (tt0) cc_final: 0.8163 (tm-30) REVERT: D 494 LYS cc_start: 0.7773 (mtpp) cc_final: 0.6991 (tttt) outliers start: 20 outliers final: 6 residues processed: 201 average time/residue: 0.7265 time to fit residues: 158.8669 Evaluate side-chains 180 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN D 527 ASN D 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135704 restraints weight = 16068.661| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.20 r_work: 0.3219 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15682 Z= 0.164 Angle : 0.626 8.809 21250 Z= 0.327 Chirality : 0.046 0.166 2241 Planarity : 0.005 0.037 2688 Dihedral : 14.912 179.344 2334 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 2.04 % Allowed : 10.22 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1817 helix: 1.11 (0.18), residues: 880 sheet: 1.56 (0.48), residues: 120 loop : -0.97 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.029 0.002 TYR B 315 PHE 0.014 0.002 PHE B 165 TRP 0.005 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15680) covalent geometry : angle 0.62633 / 0.33 (21250) hydrogen bonds : bond 0.06718 / 4.72 ( 704) hydrogen bonds : angle 4.51450 / 3.10 ( 1908) Misc. bond : bond 0.00166 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.538 Fit side-chains REVERT: A 372 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6828 (mtp180) REVERT: A 461 GLN cc_start: 0.7517 (tt0) cc_final: 0.7120 (tt0) REVERT: A 475 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.6773 (t) REVERT: A 478 LYS cc_start: 0.7567 (mtmm) cc_final: 0.7263 (mttt) REVERT: A 494 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7658 (tmmm) REVERT: A 575 ASP cc_start: 0.7581 (t0) cc_final: 0.7298 (m-30) REVERT: C 494 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7648 (tmmm) REVERT: B 251 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8166 (mmtp) REVERT: B 429 GLU cc_start: 0.8427 (tt0) cc_final: 0.8129 (tm-30) REVERT: B 478 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7263 (mttt) REVERT: B 494 LYS cc_start: 0.8246 (mppt) cc_final: 0.7650 (mmtm) REVERT: D 429 GLU cc_start: 0.8474 (tt0) cc_final: 0.8164 (tm-30) REVERT: D 494 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7073 (ttpt) outliers start: 33 outliers final: 12 residues processed: 201 average time/residue: 0.7199 time to fit residues: 157.6239 Evaluate side-chains 183 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 110 optimal weight: 0.0040 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 536 GLN C 527 ASN C 535 ASN C 539 GLN B 345 ASN B 527 ASN B 536 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.164797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135722 restraints weight = 16250.382| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.24 r_work: 0.3225 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15682 Z= 0.117 Angle : 0.539 7.562 21250 Z= 0.281 Chirality : 0.044 0.145 2241 Planarity : 0.004 0.036 2688 Dihedral : 13.733 171.169 2334 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.80 % Allowed : 10.90 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1817 helix: 1.36 (0.18), residues: 880 sheet: 1.56 (0.48), residues: 120 loop : -0.84 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 470 TYR 0.026 0.001 TYR B 315 PHE 0.015 0.001 PHE B 165 TRP 0.005 0.001 TRP C 572 HIS 0.006 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (15680) covalent geometry : angle 0.53919 / 0.28 (21250) hydrogen bonds : bond 0.05028 / 3.51 ( 704) hydrogen bonds : angle 4.29819 / 2.94 ( 1908) Misc. bond : bond 0.00070 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.655 Fit side-chains REVERT: A 185 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6655 (ttpt) REVERT: A 242 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: A 262 GLU cc_start: 0.6623 (mp0) cc_final: 0.6377 (pm20) REVERT: A 372 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6724 (mtp180) REVERT: A 461 GLN cc_start: 0.7474 (tt0) cc_final: 0.7021 (tt0) REVERT: A 475 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.6693 (t) REVERT: A 494 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7571 (tmmm) REVERT: A 575 ASP cc_start: 0.7590 (t0) cc_final: 0.7319 (m-30) REVERT: C 429 GLU cc_start: 0.8506 (tt0) cc_final: 0.8208 (tm-30) REVERT: C 494 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7572 (tmmm) REVERT: B 251 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8073 (mmtp) REVERT: B 429 GLU cc_start: 0.8470 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 478 LYS cc_start: 0.7456 (mtmm) cc_final: 0.7193 (mttt) REVERT: B 494 LYS cc_start: 0.8185 (mppt) cc_final: 0.7559 (mmtm) REVERT: B 539 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8415 (mm-40) REVERT: D 429 GLU cc_start: 0.8555 (tt0) cc_final: 0.8252 (tm-30) REVERT: D 494 LYS cc_start: 0.7792 (mtpp) cc_final: 0.6998 (ttpt) outliers start: 29 outliers final: 12 residues processed: 217 average time/residue: 0.6868 time to fit residues: 162.8313 Evaluate side-chains 192 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN D 527 ASN D 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.161407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.131840 restraints weight = 17800.753| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.28 r_work: 0.3215 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15682 Z= 0.175 Angle : 0.637 9.241 21250 Z= 0.332 Chirality : 0.046 0.166 2241 Planarity : 0.005 0.038 2688 Dihedral : 14.241 166.355 2334 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.23 % Allowed : 11.34 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1817 helix: 1.10 (0.18), residues: 880 sheet: 1.57 (0.48), residues: 120 loop : -0.92 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.028 0.002 TYR B 315 PHE 0.013 0.002 PHE C 363 TRP 0.005 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (15680) covalent geometry : angle 0.63719 / 0.33 (21250) hydrogen bonds : bond 0.06794 / 4.78 ( 704) hydrogen bonds : angle 4.49723 / 3.09 ( 1908) Misc. bond : bond 0.00151 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.629 Fit side-chains REVERT: A 262 GLU cc_start: 0.6594 (mp0) cc_final: 0.6359 (pm20) REVERT: A 372 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6818 (mtp180) REVERT: A 461 GLN cc_start: 0.7388 (tt0) cc_final: 0.6997 (tt0) REVERT: A 475 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.6708 (t) REVERT: A 478 LYS cc_start: 0.7518 (mtmm) cc_final: 0.7216 (mttt) REVERT: A 494 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7635 (tmmm) REVERT: A 575 ASP cc_start: 0.7562 (t0) cc_final: 0.7264 (m-30) REVERT: C 429 GLU cc_start: 0.8428 (tt0) cc_final: 0.8092 (tm-30) REVERT: C 494 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7629 (tmmm) REVERT: B 251 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8164 (mmtp) REVERT: B 429 GLU cc_start: 0.8381 (tt0) cc_final: 0.8047 (tm-30) REVERT: B 478 LYS cc_start: 0.7483 (mtmm) cc_final: 0.7207 (mttt) REVERT: B 494 LYS cc_start: 0.8232 (mppt) cc_final: 0.7644 (mmmm) REVERT: D 429 GLU cc_start: 0.8464 (tt0) cc_final: 0.8135 (tm-30) REVERT: D 475 SER cc_start: 0.7243 (m) cc_final: 0.6926 (t) REVERT: D 494 LYS cc_start: 0.7806 (mtpp) cc_final: 0.7016 (ttpt) outliers start: 36 outliers final: 20 residues processed: 201 average time/residue: 0.6727 time to fit residues: 148.2007 Evaluate side-chains 196 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN D 527 ASN D 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.163488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135834 restraints weight = 20566.458| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.39 r_work: 0.3196 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15682 Z= 0.134 Angle : 0.570 8.286 21250 Z= 0.297 Chirality : 0.044 0.146 2241 Planarity : 0.004 0.037 2688 Dihedral : 13.490 160.140 2334 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 12.14 % 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 are not related in a simple way. whole: 0.53 (0.20), residues: 1817 helix: 1.25 (0.18), residues: 880 sheet: 1.61 (0.48), residues: 120 loop : -0.83 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.025 0.002 TYR B 315 PHE 0.015 0.001 PHE B 165 TRP 0.005 0.001 TRP B 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15680) covalent geometry : angle 0.56966 / 0.30 (21250) hydrogen bonds : bond 0.05591 / 3.91 ( 704) hydrogen bonds : angle 4.37085 / 2.99 ( 1908) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.624 Fit side-chains REVERT: A 242 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: A 262 GLU cc_start: 0.6617 (mp0) cc_final: 0.6367 (pm20) REVERT: A 372 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6779 (mtp180) REVERT: A 461 GLN cc_start: 0.7424 (tt0) cc_final: 0.7052 (tt0) REVERT: A 475 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.6733 (t) REVERT: A 478 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7278 (mttt) REVERT: A 494 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7685 (tmmm) REVERT: A 575 ASP cc_start: 0.7602 (t0) cc_final: 0.7336 (m-30) REVERT: C 311 ASP cc_start: 0.8887 (t0) cc_final: 0.8678 (t0) REVERT: C 429 GLU cc_start: 0.8557 (tt0) cc_final: 0.8264 (tm-30) REVERT: C 494 LYS cc_start: 0.8000 (ttpt) cc_final: 0.7674 (tmmm) REVERT: B 429 GLU cc_start: 0.8462 (tt0) cc_final: 0.8151 (tm-30) REVERT: B 478 LYS cc_start: 0.7456 (mtmm) cc_final: 0.7216 (mttt) REVERT: B 494 LYS cc_start: 0.8162 (mppt) cc_final: 0.7638 (mmmm) REVERT: B 502 VAL cc_start: 0.8270 (m) cc_final: 0.7933 (t) REVERT: D 429 GLU cc_start: 0.8551 (tt0) cc_final: 0.8250 (tm-30) REVERT: D 494 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7104 (ttpt) REVERT: D 539 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8444 (mm-40) outliers start: 29 outliers final: 16 residues processed: 208 average time/residue: 0.6764 time to fit residues: 153.8700 Evaluate side-chains 197 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 142 optimal weight: 0.0010 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 overall best weight: 1.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.161528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135372 restraints weight = 21742.915| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.59 r_work: 0.3172 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15682 Z= 0.177 Angle : 0.639 9.437 21250 Z= 0.332 Chirality : 0.046 0.159 2241 Planarity : 0.005 0.040 2688 Dihedral : 13.884 160.030 2334 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 2.11 % Allowed : 12.21 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1817 helix: 1.06 (0.18), residues: 880 sheet: 1.58 (0.48), residues: 120 loop : -0.89 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.027 0.002 TYR B 315 PHE 0.013 0.002 PHE C 363 TRP 0.005 0.001 TRP D 572 HIS 0.007 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (15680) covalent geometry : angle 0.63862 / 0.33 (21250) hydrogen bonds : bond 0.06884 / 4.84 ( 704) hydrogen bonds : angle 4.51151 / 3.10 ( 1908) Misc. bond : bond 0.00158 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.616 Fit side-chains REVERT: A 242 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: A 372 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6845 (mtp180) REVERT: A 461 GLN cc_start: 0.7482 (tt0) cc_final: 0.7105 (tt0) REVERT: A 478 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7254 (mttt) REVERT: A 575 ASP cc_start: 0.7525 (t0) cc_final: 0.7260 (m-30) REVERT: C 429 GLU cc_start: 0.8537 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 494 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7679 (tmmm) REVERT: B 429 GLU cc_start: 0.8521 (tt0) cc_final: 0.8203 (tm-30) REVERT: B 478 LYS cc_start: 0.7511 (mtmm) cc_final: 0.7226 (mttt) REVERT: B 494 LYS cc_start: 0.8242 (mppt) cc_final: 0.7681 (mmmm) REVERT: B 502 VAL cc_start: 0.8381 (m) cc_final: 0.8016 (t) REVERT: B 510 GLN cc_start: 0.6260 (OUTLIER) cc_final: 0.5947 (mp10) REVERT: D 429 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: D 494 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7136 (ttpt) REVERT: D 539 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8415 (mm-40) outliers start: 34 outliers final: 19 residues processed: 205 average time/residue: 0.6823 time to fit residues: 152.9872 Evaluate side-chains 197 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 30 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 527 ASN C 535 ASN C 536 GLN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.133981 restraints weight = 16363.737| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.17 r_work: 0.3179 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15682 Z= 0.217 Angle : 0.699 9.769 21250 Z= 0.365 Chirality : 0.049 0.174 2241 Planarity : 0.005 0.042 2688 Dihedral : 14.672 161.286 2334 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 1.92 % Allowed : 12.39 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1817 helix: 0.71 (0.18), residues: 904 sheet: 1.52 (0.47), residues: 120 loop : -1.02 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 442 TYR 0.028 0.003 TYR B 315 PHE 0.017 0.002 PHE C 363 TRP 0.005 0.001 TRP C 313 HIS 0.008 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (15680) covalent geometry : angle 0.69947 / 0.37 (21250) hydrogen bonds : bond 0.07842 / 5.52 ( 704) hydrogen bonds : angle 4.63111 / 3.19 ( 1908) Misc. bond : bond 0.00230 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.431 Fit side-chains REVERT: A 242 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: A 372 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6878 (mtp180) REVERT: A 429 GLU cc_start: 0.8552 (tt0) cc_final: 0.8343 (tm-30) REVERT: A 478 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7358 (mttt) REVERT: C 429 GLU cc_start: 0.8497 (tt0) cc_final: 0.8181 (tm-30) REVERT: B 429 GLU cc_start: 0.8470 (tt0) cc_final: 0.8152 (tm-30) REVERT: B 478 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7239 (mttt) REVERT: B 494 LYS cc_start: 0.8244 (mppt) cc_final: 0.7655 (mmmm) REVERT: B 502 VAL cc_start: 0.8434 (m) cc_final: 0.8088 (t) REVERT: D 429 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: D 494 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7190 (ttpt) outliers start: 31 outliers final: 21 residues processed: 196 average time/residue: 0.6589 time to fit residues: 140.8703 Evaluate side-chains 196 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 163 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 535 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.162419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135283 restraints weight = 14778.810| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.23 r_work: 0.3223 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15682 Z= 0.154 Angle : 0.605 8.733 21250 Z= 0.316 Chirality : 0.046 0.157 2241 Planarity : 0.004 0.039 2688 Dihedral : 14.017 159.572 2334 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 1.61 % Allowed : 13.14 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1817 helix: 1.04 (0.18), residues: 880 sheet: 1.53 (0.48), residues: 120 loop : -0.91 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.027 0.002 TYR A 331 PHE 0.014 0.002 PHE B 165 TRP 0.005 0.001 TRP D 572 HIS 0.006 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (15680) covalent geometry : angle 0.60464 / 0.32 (21250) hydrogen bonds : bond 0.06225 / 4.36 ( 704) hydrogen bonds : angle 4.47762 / 3.07 ( 1908) Misc. bond : bond 0.00117 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.436 Fit side-chains REVERT: A 242 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: A 372 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6813 (mtp180) REVERT: A 429 GLU cc_start: 0.8467 (tt0) cc_final: 0.8245 (tm-30) REVERT: A 461 GLN cc_start: 0.7419 (tt0) cc_final: 0.7011 (tt0) REVERT: A 470 ARG cc_start: 0.7066 (mmm160) cc_final: 0.6617 (tpp-160) REVERT: A 478 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7317 (mttt) REVERT: A 494 LYS cc_start: 0.7760 (ttpt) cc_final: 0.7539 (tmmm) REVERT: C 429 GLU cc_start: 0.8459 (tt0) cc_final: 0.8128 (tm-30) REVERT: B 429 GLU cc_start: 0.8365 (tt0) cc_final: 0.8031 (tm-30) REVERT: B 478 LYS cc_start: 0.7431 (mtmm) cc_final: 0.7173 (mttt) REVERT: B 494 LYS cc_start: 0.8108 (mppt) cc_final: 0.7234 (tmmm) REVERT: B 502 VAL cc_start: 0.8302 (m) cc_final: 0.8000 (t) REVERT: B 510 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.6076 (mp10) REVERT: D 429 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: D 494 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7165 (ttpt) REVERT: D 539 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8418 (mm-40) outliers start: 26 outliers final: 19 residues processed: 199 average time/residue: 0.6476 time to fit residues: 140.5609 Evaluate side-chains 192 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 535 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.160382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135016 restraints weight = 16019.120| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.21 r_work: 0.3169 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15682 Z= 0.177 Angle : 0.643 9.285 21250 Z= 0.335 Chirality : 0.047 0.178 2241 Planarity : 0.005 0.040 2688 Dihedral : 14.160 160.509 2334 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 1.92 % Allowed : 12.95 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1817 helix: 0.97 (0.18), residues: 880 sheet: 1.55 (0.48), residues: 120 loop : -0.95 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 164 TYR 0.028 0.002 TYR A 331 PHE 0.015 0.002 PHE D 363 TRP 0.005 0.001 TRP D 572 HIS 0.007 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (15680) covalent geometry : angle 0.64323 / 0.34 (21250) hydrogen bonds : bond 0.06874 / 4.83 ( 704) hydrogen bonds : angle 4.53112 / 3.11 ( 1908) Misc. bond : bond 0.00157 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5608.09 seconds wall clock time: 96 minutes 11.24 seconds (5771.24 seconds total)