Starting phenix.real_space_refine on Thu Aug 6 14:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxj_18729/08_2026/8qxj_18729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxj_18729/08_2026/8qxj_18729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qxj_18729/08_2026/8qxj_18729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxj_18729/08_2026/8qxj_18729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qxj_18729/08_2026/8qxj_18729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxj_18729/08_2026/8qxj_18729.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.151 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 9945 2.51 5 N 2733 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 15953 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3895 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3881 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 477, 3881 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3957 Chain: "B" Number of atoms: 3856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3844 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 477, 3844 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3922 Chain: "C" Number of atoms: 3804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3798 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 477, 3798 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 3883 Chain: "D" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3800 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 23, 'TRANS': 453} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 96 Unusual residues: {' FE': 1, ' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 96 Unusual residues: {' FE': 1, ' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 96 Unusual residues: {' FE': 1, ' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 96 Unusual residues: {' FE': 1, ' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS A 484 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 484 " occ=0.50 Time building chain proxies: 5.04, per 1000 atoms: 0.32 Number of scatterers: 15953 At special positions: 0 Unit cell: (106.92, 117.72, 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 3143 8.00 N 2733 7.00 C 9945 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=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 16 sheets defined 59.2% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 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: 3.641A 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: 3.603A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 3.946A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 4.008A 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: 3.967A pdb=" N ASP A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.760A 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 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.855A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 6.071A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.678A pdb=" N TRP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.732A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) 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 411 through 414 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: 4.030A 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: 3.535A 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 537 removed outlier: 3.558A pdb=" N VAL A 537 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.953A pdb=" N TYR A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.665A pdb=" N ILE A 587 " --> pdb=" O ASP A 583 " (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: 3.713A 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: 3.645A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.939A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.966A 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: 3.830A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.754A 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 Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.910A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 5.645A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.664A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.772A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 411 through 414 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: 4.033A 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 473 removed outlier: 3.512A pdb=" N TYR B 473 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 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 removed outlier: 3.508A pdb=" N VAL B 518 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.515A pdb=" N VAL B 537 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 removed outlier: 4.110A pdb=" N TYR B 563 " --> pdb=" O ARG B 559 " (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: 3.640A 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: 3.608A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 3.952A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.909A 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: 3.992A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.763A 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 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.902A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.613A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.671A pdb=" N TRP C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.768A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 411 through 414 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: 4.028A 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 469 through 473 Processing helix chain 'C' and resid 475 through 483 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 537 removed outlier: 3.596A pdb=" N VAL C 537 " --> pdb=" O LYS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 576 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: 3.646A 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: 3.598A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 3.970A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.768A 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: 3.990A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.766A 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: 3.530A pdb=" N TYR D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 3.942A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.635A pdb=" N SER D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.641A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 3.768A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) 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 411 through 414 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: 4.029A 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 Processing helix chain 'D' and resid 475 through 483 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 537 removed outlier: 3.528A pdb=" N VAL D 537 " --> pdb=" O LYS D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 576 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: 8.402A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.785A 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 460 removed outlier: 6.640A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342 removed outlier: 8.475A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.659A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 342 removed outlier: 8.452A pdb=" N TYR C 521 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA C 351 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'C' and resid 455 through 460 removed outlier: 6.665A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 119 Processing sheet with id=AB5, first strand: chain 'D' and resid 339 through 343 removed outlier: 8.423A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.709A 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 460 removed outlier: 6.655A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 1947 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: 2.14 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5125 1.34 - 1.46: 3081 1.46 - 1.58: 7718 1.58 - 1.69: 68 1.69 - 1.81: 128 Bond restraints: 16120 Sorted by residual: bond pdb=" C1' DZ4 A 701 " pdb=" C2' DZ4 A 701 " ideal model delta sigma weight residual 1.522 1.314 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C1' DZ4 B 702 " pdb=" C2' DZ4 B 702 " ideal model delta sigma weight residual 1.522 1.314 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C1' DZ4 C 702 " pdb=" C2' DZ4 C 702 " ideal model delta sigma weight residual 1.522 1.314 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C1' DZ4 D 703 " pdb=" C2' DZ4 D 703 " ideal model delta sigma weight residual 1.522 1.315 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C1' DZ4 D 701 " pdb=" C2' DZ4 D 701 " ideal model delta sigma weight residual 1.522 1.319 0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 16115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 21549 3.11 - 6.22: 251 6.22 - 9.33: 79 9.33 - 12.44: 9 12.44 - 15.55: 15 Bond angle restraints: 21903 Sorted by residual: angle pdb=" PA DZ4 D 701 " pdb=" N3A DZ4 D 701 " pdb=" PB DZ4 D 701 " ideal model delta sigma weight residual 135.12 119.57 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" PA DZ4 A 707 " pdb=" N3A DZ4 A 707 " pdb=" PB DZ4 A 707 " ideal model delta sigma weight residual 135.12 120.58 14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" PA DZ4 B 707 " pdb=" N3A DZ4 B 707 " pdb=" PB DZ4 B 707 " ideal model delta sigma weight residual 135.12 120.60 14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" PA DZ4 C 701 " pdb=" N3A DZ4 C 701 " pdb=" PB DZ4 C 701 " ideal model delta sigma weight residual 135.12 120.64 14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" PA DZ4 C 702 " pdb=" N3A DZ4 C 702 " pdb=" PB DZ4 C 702 " ideal model delta sigma weight residual 135.12 120.85 14.27 3.00e+00 1.11e-01 2.26e+01 ... (remaining 21898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 9505 35.62 - 71.25: 236 71.25 - 106.87: 53 106.87 - 142.50: 3 142.50 - 178.12: 15 Dihedral angle restraints: 9812 sinusoidal: 4212 harmonic: 5600 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 -56.21 107.89 -164.10 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O3A GTP A 706 " pdb=" O3B GTP A 706 " pdb=" PB GTP A 706 " pdb=" PG GTP A 706 " ideal model delta sinusoidal sigma weight residual -56.21 107.29 -163.50 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O3A GTP C 707 " pdb=" O3B GTP C 707 " pdb=" PB GTP C 707 " pdb=" PG GTP C 707 " ideal model delta sinusoidal sigma weight residual -56.21 107.16 -163.37 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 9809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1357 0.030 - 0.060: 655 0.060 - 0.091: 158 0.091 - 0.121: 130 0.121 - 0.151: 27 Chirality restraints: 2327 Sorted by residual: chirality pdb=" C4' DZ4 A 707 " pdb=" C3' DZ4 A 707 " pdb=" C5' DZ4 A 707 " pdb=" O4' DZ4 A 707 " both_signs ideal model delta sigma weight residual False -2.38 -2.54 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" C4' DZ4 B 707 " pdb=" C3' DZ4 B 707 " pdb=" C5' DZ4 B 707 " pdb=" O4' DZ4 B 707 " both_signs ideal model delta sigma weight residual False -2.38 -2.54 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA GLU A 511 " pdb=" N GLU A 511 " pdb=" C GLU A 511 " pdb=" CB GLU A 511 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 2324 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BLYS A 484 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO A 485 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALYS A 484 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 485 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 278 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO B 279 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 279 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 279 " -0.033 5.00e-02 4.00e+02 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 115 2.50 - 3.10: 11219 3.10 - 3.70: 23628 3.70 - 4.30: 36935 4.30 - 4.90: 59943 Nonbonded interactions: 131840 Sorted by model distance: nonbonded pdb="MG MG C 706 " pdb=" O1B GTP D 702 " model vdw 1.904 2.170 nonbonded pdb=" O1A DZ4 A 701 " pdb="FE FE A 702 " model vdw 1.907 2.260 nonbonded pdb=" O1B GTP C 707 " pdb="MG MG D 707 " model vdw 1.909 2.170 nonbonded pdb=" O1B GTP A 706 " pdb="MG MG B 706 " model vdw 1.914 2.170 nonbonded pdb=" O1A DZ4 B 702 " pdb="FE FE B 703 " model vdw 1.925 2.260 ... (remaining 131835 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 113 through 229 or (resid 230 and (name N or name CA or na \ me C or name O or name CB )) or resid 231 through 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 291 or (resid \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 throug \ h 303 or (resid 304 through 305 and (name N or name CA or name C or name O or na \ me CB )) or resid 306 through 341 or (resid 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 397 or (resid 398 and (name N or n \ ame CA or name C or name O or name CB )) or resid 399 through 434 or (resid 435 \ and (name N or name CA or name C or name O or name CB )) or resid 436 or (resid \ 437 and (name N or name CA or name C or name O or name CB )) or resid 438 throug \ h 451 or resid 453 through 464 or (resid 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 through 468 or (resid 469 and (name N or name \ CA or name C or name O or name CB )) or resid 470 through 473 or (resid 474 and \ (name N or name CA or name C or name O or name CB )) or resid 475 through 477 o \ r (resid 478 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 79 through 483 or resid 485 or (resid 486 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 or resid 493 or (resid 494 through 4 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 542 or (resid 543 through 544 and (name N or name CA or name C or name O or nam \ e CB )) or resid 545 through 558 or (resid 559 through 560 and (name N or name C \ A or name C or name O or name CB )) or resid 561 through 589 or resid 705)) selection = (chain 'B' and (resid 113 through 229 or (resid 230 and (name N or name CA or na \ me C or name O or name CB )) or resid 231 through 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 291 or (resid \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 throug \ h 303 or (resid 304 through 305 and (name N or name CA or name C or name O or na \ me CB )) or resid 306 through 341 or (resid 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 397 or (resid 398 and (name N or n \ ame CA or name C or name O or name CB )) or resid 399 through 434 or (resid 435 \ and (name N or name CA or name C or name O or name CB )) or resid 436 or (resid \ 437 and (name N or name CA or name C or name O or name CB )) or resid 438 throug \ h 451 or resid 453 through 477 or (resid 478 and (name N or name CA or name C or \ name O or name CB )) or resid 479 through 483 or resid 485 through 486 or (resi \ d 487 through 490 and (name N or name CA or name C or name O or name CB )) or re \ sid 491 or resid 493 or (resid 494 through 496 and (name N or name CA or name C \ or name O or name CB )) or resid 497 through 559 or (resid 560 and (name N or na \ me CA or name C or name O or name CB )) or resid 561 through 589 or resid 705)) selection = (chain 'C' and (resid 113 through 451 or resid 453 through 468 or (resid 469 and \ (name N or name CA or name C or name O or name CB )) or resid 470 through 483 o \ r resid 485 through 491 or resid 493 or (resid 494 through 496 and (name N or na \ me CA or name C or name O or name CB )) or resid 497 through 589 or resid 705)) selection = (chain 'D' and (resid 113 through 229 or (resid 230 and (name N or name CA or na \ me C or name O or name CB )) or resid 231 through 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 451 or resid 4 \ 53 through 468 or (resid 469 and (name N or name CA or name C or name O or name \ CB )) or resid 470 through 483 or resid 485 through 486 or (resid 487 through 49 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 491 or resid \ 493 through 589 or resid 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.330 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.208 16120 Z= 0.465 Angle : 0.977 15.555 21903 Z= 0.442 Chirality : 0.043 0.151 2327 Planarity : 0.005 0.063 2787 Dihedral : 18.522 178.119 6218 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.58 % Favored : 96.16 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.63 % 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: -0.32 (0.19), residues: 1907 helix: 0.61 (0.19), residues: 900 sheet: 0.91 (0.44), residues: 132 loop : -1.25 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 451 TYR 0.018 0.001 TYR B 315 PHE 0.015 0.001 PHE D 165 TRP 0.007 0.001 TRP B 313 HIS 0.004 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.46 (16120) covalent geometry : angle 0.97655 / 0.44 (21903) hydrogen bonds : bond 0.17227 / 11.54 ( 725) hydrogen bonds : angle 6.21997 / 4.57 ( 1947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7757 (mtm) cc_final: 0.7512 (mtp) REVERT: B 239 MET cc_start: 0.7797 (mtm) cc_final: 0.7537 (mtp) REVERT: C 239 MET cc_start: 0.7776 (mtm) cc_final: 0.7551 (mtp) REVERT: D 239 MET cc_start: 0.7836 (mtm) cc_final: 0.7538 (mtp) REVERT: D 385 MET cc_start: 0.8500 (mtp) cc_final: 0.8074 (mtp) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.7470 time to fit residues: 219.4805 Evaluate side-chains 159 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 ASN A 536 GLN B 306 ASN B 328 ASN B 527 ASN B 536 GLN B 567 GLN B 577 ASN C 328 ASN C 447 GLN D 328 ASN D 447 GLN D 535 ASN D 536 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.148726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109402 restraints weight = 46426.681| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.32 r_work: 0.3377 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16120 Z= 0.127 Angle : 0.601 8.791 21903 Z= 0.305 Chirality : 0.047 0.178 2327 Planarity : 0.005 0.048 2787 Dihedral : 18.893 176.139 2437 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.47 % Favored : 97.26 % Rotamer: Outliers : 1.34 % Allowed : 9.33 % Favored : 89.32 % 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: 0.60 (0.20), residues: 1907 helix: 1.51 (0.19), residues: 885 sheet: 1.01 (0.44), residues: 140 loop : -0.88 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 566 TYR 0.033 0.001 TYR D 315 PHE 0.017 0.002 PHE B 165 TRP 0.007 0.001 TRP B 572 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16120) covalent geometry : angle 0.60113 / 0.31 (21903) hydrogen bonds : bond 0.04968 / 3.41 ( 725) hydrogen bonds : angle 4.16888 / 3.06 ( 1947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7933 (mtm) cc_final: 0.7583 (mtp) REVERT: A 346 GLU cc_start: 0.6848 (tp30) cc_final: 0.6367 (tt0) REVERT: A 474 GLU cc_start: 0.7612 (pm20) cc_final: 0.7305 (mp0) REVERT: A 494 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6422 (ttpp) REVERT: A 528 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7337 (ptt90) REVERT: A 544 LYS cc_start: 0.7739 (mttp) cc_final: 0.7440 (mttm) REVERT: B 239 MET cc_start: 0.7915 (mtm) cc_final: 0.7567 (mtp) REVERT: B 330 ASP cc_start: 0.8001 (t0) cc_final: 0.7790 (t70) REVERT: B 344 ASP cc_start: 0.8080 (p0) cc_final: 0.7846 (p0) REVERT: B 348 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.6836 (mtt180) REVERT: B 494 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7473 (ttpt) REVERT: B 497 ASP cc_start: 0.6334 (m-30) cc_final: 0.6023 (m-30) REVERT: B 528 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7558 (ptt90) REVERT: C 185 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6769 (mtmm) REVERT: C 239 MET cc_start: 0.7965 (mtm) cc_final: 0.7609 (mtp) REVERT: C 566 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6312 (tpp-160) REVERT: D 239 MET cc_start: 0.7960 (mtm) cc_final: 0.7654 (mtp) REVERT: D 408 ARG cc_start: 0.7253 (mtt180) cc_final: 0.6859 (mtp85) REVERT: D 528 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7452 (ptt90) outliers start: 20 outliers final: 8 residues processed: 171 average time/residue: 0.6756 time to fit residues: 125.8637 Evaluate side-chains 150 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 309 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 123 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN A 536 GLN B 328 ASN B 577 ASN C 246 ASN C 328 ASN D 328 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 = 0.3724 r_free = 0.3724 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101862 restraints weight = 48964.311| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.36 r_work: 0.3237 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16120 Z= 0.196 Angle : 0.653 7.185 21903 Z= 0.336 Chirality : 0.050 0.199 2327 Planarity : 0.005 0.042 2787 Dihedral : 18.702 173.050 2437 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.32 % Favored : 97.42 % Rotamer: Outliers : 1.65 % Allowed : 9.70 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1907 helix: 1.29 (0.18), residues: 893 sheet: 1.20 (0.46), residues: 132 loop : -1.06 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 408 TYR 0.035 0.002 TYR B 315 PHE 0.014 0.002 PHE A 427 TRP 0.010 0.001 TRP B 572 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (16120) covalent geometry : angle 0.65348 / 0.34 (21903) hydrogen bonds : bond 0.06682 / 4.61 ( 725) hydrogen bonds : angle 4.18284 / 3.06 ( 1947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7897 (mtm) cc_final: 0.7552 (mtp) REVERT: A 346 GLU cc_start: 0.6767 (tp30) cc_final: 0.6133 (tt0) REVERT: A 439 LYS cc_start: 0.7097 (ttpp) cc_final: 0.6776 (ttmm) REVERT: A 459 GLU cc_start: 0.8455 (tt0) cc_final: 0.7642 (tp30) REVERT: A 494 LYS cc_start: 0.7591 (ttmm) cc_final: 0.6588 (ttpp) REVERT: A 497 ASP cc_start: 0.6462 (m-30) cc_final: 0.6220 (m-30) REVERT: A 528 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7147 (ptt90) REVERT: A 544 LYS cc_start: 0.7830 (mttp) cc_final: 0.7464 (mttm) REVERT: B 239 MET cc_start: 0.7925 (mtm) cc_final: 0.7558 (mtp) REVERT: B 330 ASP cc_start: 0.7816 (t0) cc_final: 0.7609 (t70) REVERT: B 344 ASP cc_start: 0.8236 (p0) cc_final: 0.8029 (p0) REVERT: B 348 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.6615 (mtt180) REVERT: B 494 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7538 (ttpt) REVERT: B 497 ASP cc_start: 0.6364 (m-30) cc_final: 0.6097 (m-30) REVERT: C 239 MET cc_start: 0.7878 (mtm) cc_final: 0.7478 (mtp) REVERT: C 408 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6897 (mtp85) REVERT: C 535 ASN cc_start: 0.7881 (m-40) cc_final: 0.7539 (p0) REVERT: C 566 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6384 (tpp-160) REVERT: D 239 MET cc_start: 0.7868 (mtm) cc_final: 0.7473 (mtp) REVERT: D 348 ARG cc_start: 0.6844 (mtp180) cc_final: 0.6122 (mtp85) REVERT: D 408 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6785 (mtp85) REVERT: D 528 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7436 (ttp-170) outliers start: 25 outliers final: 5 residues processed: 171 average time/residue: 0.6675 time to fit residues: 124.1214 Evaluate side-chains 158 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 309 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 139 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 246 ASN B 328 ASN C 328 ASN D 186 GLN D 328 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 = 0.3692 r_free = 0.3692 target = 0.138254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099497 restraints weight = 43148.774| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.16 r_work: 0.3211 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 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 = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 16120 Z= 0.275 Angle : 0.733 7.482 21903 Z= 0.377 Chirality : 0.053 0.215 2327 Planarity : 0.006 0.047 2787 Dihedral : 19.155 177.696 2437 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.79 % Favored : 96.95 % Rotamer: Outliers : 1.83 % Allowed : 10.92 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1907 helix: 1.03 (0.18), residues: 893 sheet: 1.13 (0.47), residues: 132 loop : -1.13 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 408 TYR 0.037 0.003 TYR C 315 PHE 0.017 0.003 PHE B 427 TRP 0.014 0.002 TRP A 572 HIS 0.012 0.003 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.27 (16120) covalent geometry : angle 0.73295 / 0.38 (21903) hydrogen bonds : bond 0.07905 / 5.46 ( 725) hydrogen bonds : angle 4.27932 / 3.13 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.645 Fit side-chains REVERT: A 239 MET cc_start: 0.7978 (mtm) cc_final: 0.7609 (mtp) REVERT: A 348 ARG cc_start: 0.6878 (ptm160) cc_final: 0.6630 (ptp-170) REVERT: A 439 LYS cc_start: 0.7166 (ttpp) cc_final: 0.6842 (ttmm) REVERT: A 466 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7564 (pt) REVERT: A 494 LYS cc_start: 0.7881 (ttmm) cc_final: 0.6817 (ttpp) REVERT: A 497 ASP cc_start: 0.6526 (m-30) cc_final: 0.6318 (m-30) REVERT: A 528 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7304 (ttp-170) REVERT: A 544 LYS cc_start: 0.8132 (mttp) cc_final: 0.7749 (mttm) REVERT: B 239 MET cc_start: 0.8001 (mtm) cc_final: 0.7565 (mtp) REVERT: B 326 GLN cc_start: 0.7624 (tp40) cc_final: 0.7312 (tp40) REVERT: B 348 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.6648 (mtt180) REVERT: B 497 ASP cc_start: 0.6524 (m-30) cc_final: 0.6275 (m-30) REVERT: B 528 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7278 (ptt90) REVERT: C 239 MET cc_start: 0.7973 (mtm) cc_final: 0.7548 (mtp) REVERT: C 344 ASP cc_start: 0.8440 (p0) cc_final: 0.8031 (p0) REVERT: C 348 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6304 (mtt180) REVERT: C 408 ARG cc_start: 0.7265 (mtt180) cc_final: 0.6950 (mtp85) REVERT: C 497 ASP cc_start: 0.6484 (m-30) cc_final: 0.6258 (m-30) REVERT: C 535 ASN cc_start: 0.7781 (m-40) cc_final: 0.7465 (p0) REVERT: D 239 MET cc_start: 0.7995 (mtm) cc_final: 0.7574 (mtp) REVERT: D 326 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6503 (mp-120) REVERT: D 348 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6286 (mtp85) REVERT: D 408 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6994 (mtp85) REVERT: D 528 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7304 (ttp-170) outliers start: 28 outliers final: 10 residues processed: 168 average time/residue: 0.7783 time to fit residues: 142.0114 Evaluate side-chains 154 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 326 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN C 328 ASN D 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105801 restraints weight = 40105.409| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.08 r_work: 0.3336 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16120 Z= 0.115 Angle : 0.547 7.390 21903 Z= 0.280 Chirality : 0.046 0.189 2327 Planarity : 0.005 0.042 2787 Dihedral : 18.277 179.729 2437 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.63 % Favored : 97.11 % Rotamer: Outliers : 1.28 % Allowed : 11.78 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1907 helix: 1.55 (0.18), residues: 885 sheet: 1.78 (0.49), residues: 112 loop : -0.69 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 408 TYR 0.030 0.001 TYR A 315 PHE 0.014 0.001 PHE C 165 TRP 0.007 0.001 TRP B 572 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16120) covalent geometry : angle 0.54738 / 0.28 (21903) hydrogen bonds : bond 0.04563 / 3.16 ( 725) hydrogen bonds : angle 3.86177 / 2.83 ( 1947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.749 Fit side-chains REVERT: A 239 MET cc_start: 0.7932 (mtm) cc_final: 0.7531 (mtp) REVERT: A 326 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: A 342 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 348 ARG cc_start: 0.6932 (ptm160) cc_final: 0.6678 (ptp-170) REVERT: A 439 LYS cc_start: 0.7264 (ttpp) cc_final: 0.6984 (tttm) REVERT: A 497 ASP cc_start: 0.6470 (m-30) cc_final: 0.6247 (m-30) REVERT: A 528 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7237 (ptt-90) REVERT: A 544 LYS cc_start: 0.8098 (mttp) cc_final: 0.7750 (mttm) REVERT: B 239 MET cc_start: 0.8063 (mtm) cc_final: 0.7651 (mtp) REVERT: B 326 GLN cc_start: 0.7731 (tp40) cc_final: 0.7462 (tp40) REVERT: B 330 ASP cc_start: 0.7868 (t0) cc_final: 0.7660 (t70) REVERT: B 342 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 348 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.6793 (mtt180) REVERT: B 528 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7442 (ptt90) REVERT: C 185 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6485 (mtmm) REVERT: C 239 MET cc_start: 0.7971 (mtm) cc_final: 0.7575 (mtp) REVERT: C 348 ARG cc_start: 0.7339 (mtp180) cc_final: 0.6483 (mtt180) REVERT: C 459 GLU cc_start: 0.8432 (tt0) cc_final: 0.8200 (tt0) REVERT: C 535 ASN cc_start: 0.7765 (m-40) cc_final: 0.7527 (p0) REVERT: C 566 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6448 (tpp-160) REVERT: D 239 MET cc_start: 0.7949 (mtm) cc_final: 0.7563 (mtp) REVERT: D 348 ARG cc_start: 0.7001 (mtp180) cc_final: 0.6338 (mtp85) REVERT: D 408 ARG cc_start: 0.7450 (mtt180) cc_final: 0.7056 (mtp85) REVERT: D 497 ASP cc_start: 0.6724 (m-30) cc_final: 0.6507 (m-30) REVERT: D 528 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7247 (ttp-170) REVERT: D 531 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7700 (mmm160) outliers start: 18 outliers final: 8 residues processed: 163 average time/residue: 0.7840 time to fit residues: 138.9997 Evaluate side-chains 153 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 509 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 181 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 82 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 ASN A 536 GLN B 328 ASN D 246 ASN D 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106874 restraints weight = 44478.721| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.28 r_work: 0.3315 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16120 Z= 0.103 Angle : 0.523 8.744 21903 Z= 0.266 Chirality : 0.045 0.210 2327 Planarity : 0.004 0.041 2787 Dihedral : 17.841 178.354 2437 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.58 % Favored : 97.16 % Rotamer: Outliers : 1.40 % Allowed : 11.84 % Favored : 86.76 % 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: 0.96 (0.19), residues: 1907 helix: 1.70 (0.18), residues: 893 sheet: 1.43 (0.47), residues: 120 loop : -0.56 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.028 0.001 TYR A 315 PHE 0.015 0.001 PHE B 165 TRP 0.005 0.001 TRP B 285 HIS 0.004 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (16120) covalent geometry : angle 0.52269 / 0.27 (21903) hydrogen bonds : bond 0.04154 / 2.88 ( 725) hydrogen bonds : angle 3.73502 / 2.73 ( 1947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.598 Fit side-chains REVERT: A 239 MET cc_start: 0.7624 (mtm) cc_final: 0.7234 (mtp) REVERT: A 342 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 348 ARG cc_start: 0.6977 (ptm160) cc_final: 0.6451 (ptp-170) REVERT: A 439 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6731 (tttm) REVERT: A 466 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7550 (pt) REVERT: A 497 ASP cc_start: 0.6346 (m-30) cc_final: 0.6131 (m-30) REVERT: A 528 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7245 (ptt90) REVERT: A 544 LYS cc_start: 0.7878 (mttp) cc_final: 0.7531 (mttm) REVERT: B 239 MET cc_start: 0.7706 (mtm) cc_final: 0.7325 (mtp) REVERT: B 326 GLN cc_start: 0.7587 (tp40) cc_final: 0.7085 (tp40) REVERT: B 342 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 348 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.6580 (mtt180) REVERT: B 497 ASP cc_start: 0.7140 (m-30) cc_final: 0.6835 (m-30) REVERT: B 528 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7301 (ptt90) REVERT: C 239 MET cc_start: 0.7645 (mtm) cc_final: 0.7262 (mtp) REVERT: C 344 ASP cc_start: 0.8405 (p0) cc_final: 0.8142 (p0) REVERT: C 348 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6209 (mtt180) REVERT: C 408 ARG cc_start: 0.7269 (mtt180) cc_final: 0.7007 (mtp85) REVERT: C 497 ASP cc_start: 0.7173 (m-30) cc_final: 0.6859 (m-30) REVERT: C 535 ASN cc_start: 0.7708 (m-40) cc_final: 0.7412 (p0) REVERT: C 566 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6283 (tpp-160) REVERT: D 239 MET cc_start: 0.7672 (mtm) cc_final: 0.7251 (mtp) REVERT: D 348 ARG cc_start: 0.6837 (mtp180) cc_final: 0.6131 (mtp85) REVERT: D 408 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6843 (mtp85) REVERT: D 497 ASP cc_start: 0.6636 (m-30) cc_final: 0.6406 (m-30) REVERT: D 528 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7246 (ttp-170) REVERT: D 531 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7616 (mmm160) outliers start: 20 outliers final: 8 residues processed: 162 average time/residue: 0.7285 time to fit residues: 128.4528 Evaluate side-chains 155 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 509 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 535 ASN C 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107591 restraints weight = 38484.287| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.07 r_work: 0.3325 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16120 Z= 0.104 Angle : 0.520 6.396 21903 Z= 0.265 Chirality : 0.045 0.161 2327 Planarity : 0.004 0.042 2787 Dihedral : 17.546 177.278 2437 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 1.22 % Allowed : 12.02 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1907 helix: 1.74 (0.18), residues: 901 sheet: 1.43 (0.47), residues: 120 loop : -0.46 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 408 TYR 0.027 0.001 TYR A 315 PHE 0.015 0.001 PHE C 165 TRP 0.007 0.001 TRP B 572 HIS 0.004 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (16120) covalent geometry : angle 0.52044 / 0.26 (21903) hydrogen bonds : bond 0.04194 / 2.91 ( 725) hydrogen bonds : angle 3.68380 / 2.69 ( 1947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.605 Fit side-chains REVERT: A 239 MET cc_start: 0.7659 (mtm) cc_final: 0.7271 (mtp) REVERT: A 342 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 348 ARG cc_start: 0.6947 (ptm160) cc_final: 0.6413 (ptp-170) REVERT: A 439 LYS cc_start: 0.7031 (ttpp) cc_final: 0.6801 (tttm) REVERT: A 466 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7642 (pt) REVERT: A 497 ASP cc_start: 0.6333 (m-30) cc_final: 0.6124 (m-30) REVERT: A 528 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7196 (ttp-170) REVERT: A 544 LYS cc_start: 0.7900 (mttp) cc_final: 0.7550 (mttm) REVERT: B 239 MET cc_start: 0.7692 (mtm) cc_final: 0.7300 (mtp) REVERT: B 326 GLN cc_start: 0.7571 (tp40) cc_final: 0.7221 (tp40) REVERT: B 342 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 348 ARG cc_start: 0.7281 (mtm-85) cc_final: 0.6543 (mtt180) REVERT: B 497 ASP cc_start: 0.7040 (m-30) cc_final: 0.6746 (m-30) REVERT: B 528 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7247 (ptt90) REVERT: C 239 MET cc_start: 0.7673 (mtm) cc_final: 0.7282 (mtp) REVERT: C 344 ASP cc_start: 0.8392 (p0) cc_final: 0.8131 (p0) REVERT: C 348 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6156 (mtt180) REVERT: C 408 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7078 (mtp85) REVERT: C 497 ASP cc_start: 0.7026 (m-30) cc_final: 0.6708 (m-30) REVERT: C 535 ASN cc_start: 0.7678 (m-40) cc_final: 0.7412 (p0) REVERT: C 566 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6301 (tpp-160) REVERT: D 239 MET cc_start: 0.7672 (mtm) cc_final: 0.7312 (mtp) REVERT: D 326 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6504 (mp-120) REVERT: D 348 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6138 (mtp85) REVERT: D 408 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6792 (mtp85) REVERT: D 497 ASP cc_start: 0.6632 (m-30) cc_final: 0.6408 (m-30) REVERT: D 528 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7141 (ttp-170) REVERT: D 531 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7606 (mmm160) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.7030 time to fit residues: 122.4793 Evaluate side-chains 163 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 509 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 34 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 328 ASN D 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101376 restraints weight = 47134.524| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.30 r_work: 0.3235 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16120 Z= 0.196 Angle : 0.640 8.041 21903 Z= 0.327 Chirality : 0.049 0.251 2327 Planarity : 0.005 0.044 2787 Dihedral : 18.242 178.087 2437 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.42 % Favored : 97.32 % Rotamer: Outliers : 1.46 % Allowed : 12.45 % Favored : 86.09 % 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: 0.70 (0.19), residues: 1907 helix: 1.49 (0.18), residues: 893 sheet: 1.09 (0.46), residues: 132 loop : -0.70 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 531 TYR 0.033 0.002 TYR C 315 PHE 0.014 0.002 PHE B 427 TRP 0.011 0.002 TRP C 572 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (16120) covalent geometry : angle 0.64016 / 0.33 (21903) hydrogen bonds : bond 0.06477 / 4.48 ( 725) hydrogen bonds : angle 3.98528 / 2.91 ( 1947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7870 (mtm) cc_final: 0.7426 (mtp) REVERT: A 342 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 346 GLU cc_start: 0.7051 (tp30) cc_final: 0.6165 (tt0) REVERT: A 408 ARG cc_start: 0.7263 (mtt-85) cc_final: 0.6784 (mtp85) REVERT: A 439 LYS cc_start: 0.7121 (ttpp) cc_final: 0.6860 (tttm) REVERT: A 466 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7655 (pt) REVERT: A 497 ASP cc_start: 0.6414 (m-30) cc_final: 0.6202 (m-30) REVERT: A 528 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7221 (ttp-170) REVERT: A 544 LYS cc_start: 0.7950 (mttp) cc_final: 0.7615 (mttm) REVERT: B 239 MET cc_start: 0.7891 (mtm) cc_final: 0.7420 (mtp) REVERT: B 326 GLN cc_start: 0.7602 (tp40) cc_final: 0.7185 (tp40) REVERT: B 342 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 348 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.6616 (mtt180) REVERT: B 497 ASP cc_start: 0.7040 (m-30) cc_final: 0.6738 (m-30) REVERT: B 528 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7154 (ttp-170) REVERT: C 239 MET cc_start: 0.7832 (mtm) cc_final: 0.7395 (mtp) REVERT: C 326 GLN cc_start: 0.7063 (mp-120) cc_final: 0.6858 (mp-120) REVERT: C 344 ASP cc_start: 0.8445 (p0) cc_final: 0.7969 (p0) REVERT: C 348 ARG cc_start: 0.7247 (mtp180) cc_final: 0.6324 (mtt180) REVERT: C 408 ARG cc_start: 0.7468 (mtt180) cc_final: 0.7109 (mtp85) REVERT: C 497 ASP cc_start: 0.7093 (m-30) cc_final: 0.6753 (m-30) REVERT: C 535 ASN cc_start: 0.7752 (m-40) cc_final: 0.7493 (p0) REVERT: C 566 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6367 (tpp-160) REVERT: D 239 MET cc_start: 0.7879 (mtm) cc_final: 0.7464 (mtp) REVERT: D 326 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6472 (mp-120) REVERT: D 348 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6236 (mtp85) REVERT: D 408 ARG cc_start: 0.7308 (mtt180) cc_final: 0.6928 (mtp85) REVERT: D 528 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7049 (ttp-170) REVERT: D 531 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7663 (mmm160) outliers start: 21 outliers final: 8 residues processed: 157 average time/residue: 0.7773 time to fit residues: 132.5264 Evaluate side-chains 157 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 326 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN C 328 ASN D 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105578 restraints weight = 44168.470| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.23 r_work: 0.3292 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16120 Z= 0.118 Angle : 0.543 8.001 21903 Z= 0.277 Chirality : 0.046 0.232 2327 Planarity : 0.004 0.042 2787 Dihedral : 17.701 178.568 2437 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.32 % Favored : 97.47 % Rotamer: Outliers : 1.04 % Allowed : 12.81 % Favored : 86.15 % 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: 0.99 (0.19), residues: 1907 helix: 1.68 (0.18), residues: 893 sheet: 1.28 (0.46), residues: 120 loop : -0.48 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.028 0.001 TYR C 315 PHE 0.013 0.001 PHE B 165 TRP 0.007 0.001 TRP B 572 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (16120) covalent geometry : angle 0.54302 / 0.28 (21903) hydrogen bonds : bond 0.04573 / 3.17 ( 725) hydrogen bonds : angle 3.77330 / 2.75 ( 1947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7680 (mtm) cc_final: 0.7279 (mtp) REVERT: A 342 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 346 GLU cc_start: 0.6972 (tp30) cc_final: 0.6110 (tt0) REVERT: A 408 ARG cc_start: 0.7270 (mtt-85) cc_final: 0.6808 (mtp85) REVERT: A 439 LYS cc_start: 0.7053 (ttpp) cc_final: 0.6818 (tttm) REVERT: A 466 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7712 (pt) REVERT: A 497 ASP cc_start: 0.6353 (m-30) cc_final: 0.6132 (m-30) REVERT: A 528 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7173 (ttp-170) REVERT: A 544 LYS cc_start: 0.7921 (mttp) cc_final: 0.7597 (mttm) REVERT: B 239 MET cc_start: 0.7819 (mtm) cc_final: 0.7405 (mtp) REVERT: B 326 GLN cc_start: 0.7560 (tp40) cc_final: 0.7228 (tp40) REVERT: B 342 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 348 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.6629 (mtt180) REVERT: B 528 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7149 (ptt-90) REVERT: C 239 MET cc_start: 0.7690 (mtm) cc_final: 0.7297 (mtp) REVERT: C 344 ASP cc_start: 0.8443 (p0) cc_final: 0.7985 (p0) REVERT: C 348 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6326 (mtt180) REVERT: C 408 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7040 (mtp85) REVERT: C 494 LYS cc_start: 0.6964 (pptt) cc_final: 0.6718 (pptt) REVERT: C 535 ASN cc_start: 0.7768 (m-40) cc_final: 0.7532 (p0) REVERT: C 566 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6217 (tpp-160) REVERT: D 239 MET cc_start: 0.7745 (mtm) cc_final: 0.7310 (mtp) REVERT: D 326 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6532 (mp-120) REVERT: D 348 ARG cc_start: 0.7050 (mtp180) cc_final: 0.6281 (mtp85) REVERT: D 408 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6746 (mtp85) REVERT: D 497 ASP cc_start: 0.6625 (m-30) cc_final: 0.6396 (m-30) REVERT: D 528 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7132 (ttp-170) REVERT: D 531 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7658 (mmm160) outliers start: 14 outliers final: 9 residues processed: 156 average time/residue: 0.7671 time to fit residues: 130.0910 Evaluate side-chains 156 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 328 ASN C 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105035 restraints weight = 47683.662| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.35 r_work: 0.3285 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16120 Z= 0.120 Angle : 0.552 11.651 21903 Z= 0.281 Chirality : 0.046 0.271 2327 Planarity : 0.004 0.042 2787 Dihedral : 17.571 179.634 2437 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.53 % Favored : 97.26 % Rotamer: Outliers : 1.28 % Allowed : 12.75 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1907 helix: 1.72 (0.18), residues: 893 sheet: 1.65 (0.47), residues: 112 loop : -0.46 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.029 0.001 TYR A 315 PHE 0.014 0.001 PHE B 165 TRP 0.007 0.001 TRP C 572 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16120) covalent geometry : angle 0.55208 / 0.28 (21903) hydrogen bonds : bond 0.04721 / 3.28 ( 725) hydrogen bonds : angle 3.77217 / 2.75 ( 1947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7647 (mtm) cc_final: 0.7250 (mtp) REVERT: A 342 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 346 GLU cc_start: 0.6965 (tp30) cc_final: 0.6139 (tt0) REVERT: A 439 LYS cc_start: 0.7031 (ttpp) cc_final: 0.6817 (tttm) REVERT: A 466 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7662 (pt) REVERT: A 497 ASP cc_start: 0.6365 (m-30) cc_final: 0.6137 (m-30) REVERT: A 528 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7150 (ttp-170) REVERT: A 544 LYS cc_start: 0.7921 (mttp) cc_final: 0.7596 (mttm) REVERT: B 239 MET cc_start: 0.7749 (mtm) cc_final: 0.7348 (mtp) REVERT: B 326 GLN cc_start: 0.7547 (tp40) cc_final: 0.7213 (tp40) REVERT: B 342 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 348 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.6647 (mtt180) REVERT: B 528 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7306 (ttp-170) REVERT: C 239 MET cc_start: 0.7677 (mtm) cc_final: 0.7285 (mtp) REVERT: C 344 ASP cc_start: 0.8420 (p0) cc_final: 0.8070 (p0) REVERT: C 348 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6311 (mtt180) REVERT: C 408 ARG cc_start: 0.7406 (mtt180) cc_final: 0.7050 (mtp85) REVERT: C 535 ASN cc_start: 0.7768 (m-40) cc_final: 0.7538 (p0) REVERT: C 566 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6255 (tpp-160) REVERT: D 239 MET cc_start: 0.7788 (mtm) cc_final: 0.7355 (mtp) REVERT: D 326 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6509 (mp-120) REVERT: D 348 ARG cc_start: 0.7060 (mtp180) cc_final: 0.6289 (mtp85) REVERT: D 408 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6705 (mtp85) REVERT: D 497 ASP cc_start: 0.6625 (m-30) cc_final: 0.6395 (m-30) REVERT: D 528 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7062 (ttp-170) outliers start: 18 outliers final: 11 residues processed: 159 average time/residue: 0.7672 time to fit residues: 132.8274 Evaluate side-chains 160 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105601 restraints weight = 34569.211| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.90 r_work: 0.3299 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 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: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16120 Z= 0.131 Angle : 0.562 11.806 21903 Z= 0.287 Chirality : 0.046 0.262 2327 Planarity : 0.004 0.042 2787 Dihedral : 17.568 178.552 2437 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.42 % Favored : 97.37 % Rotamer: Outliers : 1.10 % Allowed : 12.81 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1907 helix: 1.68 (0.18), residues: 893 sheet: 1.62 (0.47), residues: 112 loop : -0.47 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 408 TYR 0.030 0.001 TYR A 315 PHE 0.012 0.002 PHE C 165 TRP 0.008 0.001 TRP B 572 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16120) covalent geometry : angle 0.56188 / 0.29 (21903) hydrogen bonds : bond 0.04980 / 3.46 ( 725) hydrogen bonds : angle 3.80206 / 2.77 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.37 seconds wall clock time: 88 minutes 17.09 seconds (5297.09 seconds total)