Starting phenix.real_space_refine on Thu Aug 6 12:20:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxk_18730/08_2026/8qxk_18730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxk_18730/08_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_18730/08_2026/8qxk_18730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxk_18730/08_2026/8qxk_18730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qxk_18730/08_2026/8qxk_18730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxk_18730/08_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-2.2rc3-6140/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, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 4.61, per 1000 atoms: 0.30 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: 1.37 Conformation dependent library (CDL) restraints added in 985.7 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: 0.64 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: 2.57 Time building geometry restraints manager: 1.88 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: 2.790 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.800 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- 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 : 0.636 Fit side-chains REVERT: A 311 ASP cc_start: 0.8353 (t0) cc_final: 0.8120 (t0) REVERT: A 461 GLN cc_start: 0.7502 (tt0) cc_final: 0.7125 (tt0) REVERT: B 311 ASP cc_start: 0.8356 (t0) cc_final: 0.8068 (t0) REVERT: B 372 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7127 (mtm180) REVERT: D 311 ASP cc_start: 0.8433 (t0) cc_final: 0.8226 (t0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.7848 time to fit residues: 195.9564 Evaluate side-chains 179 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.164009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135048 restraints weight = 15862.409| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.19 r_work: 0.3248 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1062 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 : 0.626 7.924 21250 Z= 0.330 Chirality : 0.046 0.194 2241 Planarity : 0.005 0.044 2688 Dihedral : 15.933 172.014 2334 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 1.05 % Allowed : 7.99 % Favored : 90.95 % 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: 0.12 (0.20), residues: 1817 helix: 0.94 (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 A 451 TYR 0.033 0.002 TYR B 315 PHE 0.016 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 0.00339 / 0.15 (15680) covalent geometry : angle 0.62592 / 0.33 (21250) hydrogen bonds : bond 0.06565 / 4.58 ( 704) hydrogen bonds : angle 4.62947 / 3.17 ( 1908) Misc. bond : bond 0.00141 / 0.07 ( 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 196 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.527 Fit side-chains REVERT: A 251 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8168 (mmtp) REVERT: A 461 GLN cc_start: 0.7386 (tt0) cc_final: 0.6981 (tt0) REVERT: A 494 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7597 (tmmm) REVERT: C 134 ARG cc_start: 0.8439 (tpt-90) cc_final: 0.8177 (tpt90) REVERT: C 494 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7559 (tmmm) REVERT: B 494 LYS cc_start: 0.8118 (mppt) cc_final: 0.7486 (mmtm) REVERT: D 494 LYS cc_start: 0.7780 (mtpp) cc_final: 0.6959 (tttt) outliers start: 17 outliers final: 6 residues processed: 193 average time/residue: 0.7386 time to fit residues: 154.8260 Evaluate side-chains 177 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 365 THR 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 B residue 533 THR 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: 0.0170 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 133 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 215 HIS D 527 ASN D 535 ASN D 548 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.166159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.138901 restraints weight = 17924.217| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.32 r_work: 0.3277 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1306 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= 0.116 Angle : 0.542 7.136 21250 Z= 0.284 Chirality : 0.044 0.149 2241 Planarity : 0.004 0.038 2688 Dihedral : 14.706 179.618 2334 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.18 % Allowed : 9.54 % 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: 0.61 (0.20), residues: 1817 helix: 1.39 (0.19), residues: 880 sheet: 1.59 (0.47), residues: 120 loop : -0.88 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 470 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 0.00238 / 0.12 (15680) covalent geometry : angle 0.54235 / 0.28 (21250) hydrogen bonds : bond 0.05073 / 3.53 ( 704) hydrogen bonds : angle 4.34733 / 2.97 ( 1908) Misc. bond : bond 0.00091 / 0.05 ( 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 206 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.593 Fit side-chains REVERT: A 185 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6540 (ttpt) REVERT: A 242 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: A 372 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7722 (mtm180) REVERT: A 461 GLN cc_start: 0.7445 (tt0) cc_final: 0.7043 (tt0) REVERT: A 475 SER cc_start: 0.7488 (OUTLIER) cc_final: 0.6703 (t) REVERT: A 478 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7242 (mttt) REVERT: A 494 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7640 (tmmm) REVERT: C 134 ARG cc_start: 0.8446 (tpt-90) cc_final: 0.8182 (tpt90) REVERT: C 494 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7596 (tmmm) REVERT: B 251 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (mmtp) REVERT: B 311 ASP cc_start: 0.8698 (t0) cc_final: 0.8284 (t0) REVERT: B 429 GLU cc_start: 0.8320 (tt0) cc_final: 0.8096 (tm-30) REVERT: B 478 LYS cc_start: 0.7508 (mtmm) cc_final: 0.7241 (mttt) REVERT: B 494 LYS cc_start: 0.8218 (mppt) cc_final: 0.7550 (mmtm) REVERT: B 501 ASP cc_start: 0.7883 (t70) cc_final: 0.7646 (t70) REVERT: D 429 GLU cc_start: 0.8411 (tt0) cc_final: 0.8090 (tm-30) REVERT: D 494 LYS cc_start: 0.7779 (mtpp) cc_final: 0.6982 (ttpt) outliers start: 19 outliers final: 5 residues processed: 201 average time/residue: 0.7511 time to fit residues: 163.9888 Evaluate side-chains 177 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 365 THR 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 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: 2.9990 chunk 122 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 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: 3.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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 215 HIS D 527 ASN D 535 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.159499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131213 restraints weight = 16050.138| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.28 r_work: 0.3212 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15682 Z= 0.214 Angle : 0.697 9.638 21250 Z= 0.364 Chirality : 0.048 0.182 2241 Planarity : 0.005 0.042 2688 Dihedral : 15.750 179.875 2334 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 2.17 % Allowed : 10.22 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1817 helix: 0.83 (0.18), residues: 900 sheet: 1.55 (0.48), residues: 120 loop : -1.10 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 164 TYR 0.030 0.003 TYR B 315 PHE 0.016 0.002 PHE C 363 TRP 0.005 0.001 TRP B 572 HIS 0.008 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (15680) covalent geometry : angle 0.69727 / 0.36 (21250) hydrogen bonds : bond 0.07826 / 5.51 ( 704) hydrogen bonds : angle 4.62777 / 3.19 ( 1908) Misc. bond : bond 0.00248 / 0.13 ( 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 211 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.690 Fit side-chains REVERT: A 475 SER cc_start: 0.7534 (OUTLIER) cc_final: 0.6731 (t) REVERT: A 478 LYS cc_start: 0.7555 (mtmm) cc_final: 0.7233 (mttt) REVERT: A 494 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7641 (tmmm) REVERT: A 575 ASP cc_start: 0.7627 (t0) cc_final: 0.7264 (m-30) REVERT: C 134 ARG cc_start: 0.8393 (tpt-90) cc_final: 0.8124 (tpt90) REVERT: C 494 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7630 (tmmm) REVERT: B 429 GLU cc_start: 0.8368 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 478 LYS cc_start: 0.7518 (mtmm) cc_final: 0.7230 (mttt) REVERT: B 494 LYS cc_start: 0.8228 (mppt) cc_final: 0.7599 (mmtm) REVERT: D 429 GLU cc_start: 0.8417 (tt0) cc_final: 0.8082 (tm-30) REVERT: D 494 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7062 (tttt) outliers start: 35 outliers final: 17 residues processed: 206 average time/residue: 0.6850 time to fit residues: 153.7462 Evaluate side-chains 185 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR 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 A residue 549 LEU 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 365 THR Chi-restraints excluded: chain D residue 533 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: 0.9990 chunk 148 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 110 optimal weight: 0.0870 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 536 GLN C 527 ASN C 535 ASN C 536 GLN C 539 GLN B 345 ASN B 527 ASN B 536 GLN D 527 ASN D 535 ASN D 536 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.165324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138566 restraints weight = 16208.668| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.27 r_work: 0.3230 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1482 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= 0.120 Angle : 0.545 7.459 21250 Z= 0.285 Chirality : 0.044 0.144 2241 Planarity : 0.004 0.038 2688 Dihedral : 14.527 169.909 2334 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.61 % Allowed : 11.46 % Favored : 86.93 % 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: 0.55 (0.20), residues: 1817 helix: 1.33 (0.18), residues: 876 sheet: 1.57 (0.48), residues: 120 loop : -0.89 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 339 TYR 0.026 0.001 TYR B 315 PHE 0.016 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 0.00249 / 0.12 (15680) covalent geometry : angle 0.54529 / 0.28 (21250) hydrogen bonds : bond 0.05130 / 3.58 ( 704) hydrogen bonds : angle 4.32291 / 2.96 ( 1908) Misc. bond : bond 0.00063 / 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 208 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.596 Fit side-chains REVERT: A 242 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: A 262 GLU cc_start: 0.6631 (mp0) cc_final: 0.6399 (pm20) REVERT: A 461 GLN cc_start: 0.7507 (tt0) cc_final: 0.7136 (tt0) REVERT: A 475 SER cc_start: 0.7531 (OUTLIER) cc_final: 0.6759 (t) REVERT: A 478 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7255 (mttt) REVERT: A 494 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7674 (tmmm) REVERT: A 575 ASP cc_start: 0.7616 (t0) cc_final: 0.7300 (m-30) REVERT: C 429 GLU cc_start: 0.8575 (tt0) cc_final: 0.8339 (tm-30) REVERT: C 494 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7639 (tmmm) REVERT: B 429 GLU cc_start: 0.8400 (tt0) cc_final: 0.8137 (tm-30) REVERT: B 478 LYS cc_start: 0.7489 (mtmm) cc_final: 0.7240 (mttt) REVERT: B 494 LYS cc_start: 0.8233 (mppt) cc_final: 0.7634 (mmmm) REVERT: D 429 GLU cc_start: 0.8503 (tt0) cc_final: 0.8204 (tm-30) REVERT: D 494 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7098 (ttpt) outliers start: 26 outliers final: 9 residues processed: 205 average time/residue: 0.6723 time to fit residues: 150.8014 Evaluate side-chains 184 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 463 THR Chi-restraints excluded: chain A residue 475 SER 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 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: 3.9990 chunk 98 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.160256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.132287 restraints weight = 17758.337| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.33 r_work: 0.3207 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15682 Z= 0.194 Angle : 0.668 9.640 21250 Z= 0.347 Chirality : 0.047 0.172 2241 Planarity : 0.005 0.040 2688 Dihedral : 15.329 164.289 2334 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.03 % Rotamer: Outliers : 1.67 % Allowed : 12.52 % Favored : 85.81 % 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: 0.24 (0.19), residues: 1817 helix: 1.03 (0.18), residues: 876 sheet: 1.57 (0.48), residues: 120 loop : -1.02 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 143 TYR 0.029 0.002 TYR B 315 PHE 0.015 0.002 PHE A 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 0.00446 / 0.19 (15680) covalent geometry : angle 0.66770 / 0.35 (21250) hydrogen bonds : bond 0.07340 / 5.17 ( 704) hydrogen bonds : angle 4.54730 / 3.13 ( 1908) Misc. bond : bond 0.00187 / 0.09 ( 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 200 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.606 Fit side-chains REVERT: A 242 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: A 262 GLU cc_start: 0.6593 (mp0) cc_final: 0.6382 (pm20) REVERT: A 372 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7734 (ttp80) REVERT: A 478 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7255 (mttt) REVERT: A 494 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7704 (tmmm) REVERT: A 575 ASP cc_start: 0.7569 (t0) cc_final: 0.7301 (m-30) REVERT: C 429 GLU cc_start: 0.8506 (tt0) cc_final: 0.8274 (tm-30) REVERT: C 494 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7656 (tmmm) REVERT: B 429 GLU cc_start: 0.8404 (tt0) cc_final: 0.8078 (tm-30) REVERT: B 478 LYS cc_start: 0.7529 (mtmm) cc_final: 0.7236 (mttt) REVERT: B 494 LYS cc_start: 0.8235 (mppt) cc_final: 0.7640 (mmmm) REVERT: B 502 VAL cc_start: 0.8386 (m) cc_final: 0.8070 (t) REVERT: D 429 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: D 494 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7057 (ttpt) outliers start: 27 outliers final: 19 residues processed: 196 average time/residue: 0.6762 time to fit residues: 144.9456 Evaluate side-chains 191 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 489 LEU 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 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 533 THR 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: 0.3980 chunk 162 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 82 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 328 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN 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 = 0.3784 r_free = 0.3784 target = 0.164551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.137461 restraints weight = 20486.524| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.38 r_work: 0.3206 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15682 Z= 0.117 Angle : 0.541 7.659 21250 Z= 0.282 Chirality : 0.044 0.139 2241 Planarity : 0.004 0.037 2688 Dihedral : 14.197 158.177 2334 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.49 % Allowed : 12.95 % Favored : 85.56 % 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: 0.62 (0.20), residues: 1817 helix: 1.36 (0.18), residues: 876 sheet: 1.67 (0.48), residues: 120 loop : -0.83 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 164 TYR 0.024 0.001 TYR B 315 PHE 0.015 0.001 PHE B 165 TRP 0.005 0.001 TRP D 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (15680) covalent geometry : angle 0.54133 / 0.28 (21250) hydrogen bonds : bond 0.05049 / 3.52 ( 704) hydrogen bonds : angle 4.31413 / 2.95 ( 1908) Misc. bond : bond 0.00059 / 0.03 ( 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 211 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.587 Fit side-chains REVERT: A 242 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: A 262 GLU cc_start: 0.6657 (mp0) cc_final: 0.6430 (pm20) REVERT: A 461 GLN cc_start: 0.7475 (tt0) cc_final: 0.7098 (tt0) REVERT: A 475 SER cc_start: 0.7509 (OUTLIER) cc_final: 0.6744 (t) REVERT: A 478 LYS cc_start: 0.7565 (mtmm) cc_final: 0.7278 (mttt) REVERT: A 494 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7737 (tmmm) REVERT: A 575 ASP cc_start: 0.7621 (t0) cc_final: 0.7336 (m-30) REVERT: C 429 GLU cc_start: 0.8642 (tt0) cc_final: 0.8424 (tm-30) REVERT: C 494 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7690 (tmmm) REVERT: B 429 GLU cc_start: 0.8497 (tt0) cc_final: 0.8227 (tm-30) REVERT: B 478 LYS cc_start: 0.7467 (mtmm) cc_final: 0.7226 (mttt) REVERT: B 494 LYS cc_start: 0.8199 (mppt) cc_final: 0.7617 (mmmm) REVERT: B 502 VAL cc_start: 0.8224 (m) cc_final: 0.7938 (t) REVERT: D 429 GLU cc_start: 0.8559 (tt0) cc_final: 0.8269 (tm-30) REVERT: D 494 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7126 (ttpt) REVERT: D 539 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8459 (mm-40) outliers start: 24 outliers final: 12 residues processed: 209 average time/residue: 0.6616 time to fit residues: 151.5121 Evaluate side-chains 190 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 0.0040 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131991 restraints weight = 21660.508| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.43 r_work: 0.3140 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15682 Z= 0.231 Angle : 0.714 10.180 21250 Z= 0.370 Chirality : 0.049 0.201 2241 Planarity : 0.005 0.044 2688 Dihedral : 15.441 161.863 2334 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 2.17 % Allowed : 12.52 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1817 helix: 0.77 (0.18), residues: 900 sheet: 1.58 (0.48), residues: 120 loop : -1.05 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 451 TYR 0.028 0.003 TYR B 315 PHE 0.017 0.002 PHE A 363 TRP 0.005 0.001 TRP C 313 HIS 0.009 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (15680) covalent geometry : angle 0.71371 / 0.37 (21250) hydrogen bonds : bond 0.07988 / 5.63 ( 704) hydrogen bonds : angle 4.61180 / 3.18 ( 1908) Misc. bond : bond 0.00281 / 0.14 ( 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: 35 poor density : 176 time to evaluate : 0.629 Fit side-chains REVERT: A 242 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: A 478 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7334 (mttt) REVERT: C 429 GLU cc_start: 0.8443 (tt0) cc_final: 0.8203 (tm-30) REVERT: C 494 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7683 (tmmm) REVERT: B 429 GLU cc_start: 0.8330 (tt0) cc_final: 0.8003 (tm-30) REVERT: B 478 LYS cc_start: 0.7518 (mtmm) cc_final: 0.7227 (mttt) REVERT: B 494 LYS cc_start: 0.8251 (mppt) cc_final: 0.7641 (mmmm) REVERT: B 502 VAL cc_start: 0.8474 (m) cc_final: 0.8105 (t) REVERT: B 510 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6074 (mp10) REVERT: D 429 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: D 494 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7173 (ttpt) outliers start: 35 outliers final: 19 residues processed: 203 average time/residue: 0.6806 time to fit residues: 150.3986 Evaluate side-chains 197 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 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 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 533 THR 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: 3.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 328 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 = 0.162473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136469 restraints weight = 16351.991| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.21 r_work: 0.3231 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1620 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= 0.140 Angle : 0.584 8.356 21250 Z= 0.304 Chirality : 0.045 0.147 2241 Planarity : 0.004 0.039 2688 Dihedral : 14.694 159.618 2334 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 1.61 % Allowed : 13.51 % Favored : 84.88 % 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: 0.40 (0.19), residues: 1817 helix: 1.16 (0.18), residues: 876 sheet: 1.58 (0.48), residues: 120 loop : -0.92 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.026 0.002 TYR A 331 PHE 0.015 0.002 PHE B 165 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 0.00303 / 0.14 (15680) covalent geometry : angle 0.58355 / 0.30 (21250) hydrogen bonds : bond 0.05874 / 4.12 ( 704) hydrogen bonds : angle 4.41602 / 3.03 ( 1908) Misc. bond : bond 0.00100 / 0.05 ( 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 206 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.647 Fit side-chains REVERT: A 242 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: A 429 GLU cc_start: 0.8505 (tt0) cc_final: 0.8283 (tm-30) REVERT: A 470 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6659 (tpp-160) REVERT: A 478 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7336 (mttt) REVERT: A 494 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7679 (tmmm) REVERT: C 429 GLU cc_start: 0.8522 (tt0) cc_final: 0.8292 (tm-30) REVERT: C 494 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7666 (tmmm) REVERT: B 429 GLU cc_start: 0.8431 (tt0) cc_final: 0.8109 (tm-30) REVERT: B 478 LYS cc_start: 0.7498 (mtmm) cc_final: 0.7231 (mttt) REVERT: B 494 LYS cc_start: 0.8169 (mppt) cc_final: 0.7606 (mmmm) REVERT: B 502 VAL cc_start: 0.8409 (m) cc_final: 0.8039 (t) REVERT: D 429 GLU cc_start: 0.8505 (tt0) cc_final: 0.8189 (tm-30) REVERT: D 494 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7159 (ttpt) REVERT: D 539 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8401 (mm-40) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.6294 time to fit residues: 138.5594 Evaluate side-chains 200 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 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 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 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 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 463 THR 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: 6.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 145 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN C 328 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 = 0.3779 r_free = 0.3779 target = 0.164000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.137142 restraints weight = 14729.074| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.26 r_work: 0.3244 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15682 Z= 0.132 Angle : 0.567 8.033 21250 Z= 0.295 Chirality : 0.044 0.139 2241 Planarity : 0.004 0.038 2688 Dihedral : 13.979 160.359 2334 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 13.69 % Favored : 84.70 % 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: 0.57 (0.20), residues: 1817 helix: 1.31 (0.18), residues: 876 sheet: 1.68 (0.48), residues: 120 loop : -0.84 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 164 TYR 0.028 0.002 TYR A 331 PHE 0.014 0.001 PHE B 165 TRP 0.005 0.001 TRP C 285 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15680) covalent geometry : angle 0.56701 / 0.30 (21250) hydrogen bonds : bond 0.05524 / 3.86 ( 704) hydrogen bonds : angle 4.32668 / 2.97 ( 1908) Misc. bond : bond 0.00083 / 0.04 ( 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 214 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.743 Fit side-chains REVERT: A 242 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: A 429 GLU cc_start: 0.8466 (tt0) cc_final: 0.8226 (tm-30) REVERT: A 461 GLN cc_start: 0.7401 (tt0) cc_final: 0.6997 (tt0) REVERT: A 470 ARG cc_start: 0.6985 (mmm160) cc_final: 0.6605 (tpp-160) REVERT: A 478 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7215 (mttt) REVERT: A 494 LYS cc_start: 0.7881 (ttpt) cc_final: 0.7621 (tmmm) REVERT: C 429 GLU cc_start: 0.8485 (tt0) cc_final: 0.8253 (tm-30) REVERT: C 494 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7703 (tmmm) REVERT: B 311 ASP cc_start: 0.8800 (t0) cc_final: 0.8587 (t0) REVERT: B 429 GLU cc_start: 0.8392 (tt0) cc_final: 0.8055 (tm-30) REVERT: B 478 LYS cc_start: 0.7415 (mtmm) cc_final: 0.7178 (mttt) REVERT: B 494 LYS cc_start: 0.8148 (mppt) cc_final: 0.7612 (mmmm) REVERT: B 502 VAL cc_start: 0.8302 (m) cc_final: 0.7946 (t) REVERT: D 429 GLU cc_start: 0.8424 (tt0) cc_final: 0.8093 (tm-30) REVERT: D 494 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7203 (ttpt) REVERT: D 539 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8370 (mm-40) outliers start: 26 outliers final: 21 residues processed: 210 average time/residue: 0.6140 time to fit residues: 141.7119 Evaluate side-chains 203 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 A residue 549 LEU 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 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 463 THR Chi-restraints excluded: chain D residue 549 LEU 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: 0.8980 chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 153 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.162546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.136428 restraints weight = 15959.581| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.20 r_work: 0.3206 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.34 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: 0.8482 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15682 Z= 0.155 Angle : 0.608 8.655 21250 Z= 0.317 Chirality : 0.046 0.151 2241 Planarity : 0.005 0.039 2688 Dihedral : 14.136 160.898 2334 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 1.61 % Allowed : 13.57 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.20), residues: 1817 helix: 1.18 (0.18), residues: 876 sheet: 1.64 (0.48), residues: 120 loop : -0.91 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 164 TYR 0.027 0.002 TYR A 331 PHE 0.013 0.002 PHE B 165 TRP 0.006 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (15680) covalent geometry : angle 0.60814 / 0.32 (21250) hydrogen bonds : bond 0.06311 / 4.43 ( 704) hydrogen bonds : angle 4.42193 / 3.04 ( 1908) Misc. bond : bond 0.00119 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5488.81 seconds wall clock time: 94 minutes 6.27 seconds (5646.27 seconds total)