Starting phenix.real_space_refine on Fri Jul 3 19:26:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxj_18729/07_2026/8qxj_18729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxj_18729/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxj_18729/07_2026/8qxj_18729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxj_18729/07_2026/8qxj_18729.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxj_18729/07_2026/8qxj_18729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxj_18729/07_2026/8qxj_18729.cif" } 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-dev-6108/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, 95 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 3, 'DZ4': 2, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 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: 5.15, 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: 1.49 Conformation dependent library (CDL) restraints added in 1.2 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: 0.52 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: 2.96 Time building geometry restraints manager: 1.92 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 3.000 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 3.000 ... (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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.150 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- 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 : 0.579 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: 0.6959 time to fit residues: 204.2994 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 : 0.380 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.149000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109775 restraints weight = 46279.465| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.33 r_work: 0.3383 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1967 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 : 0.608 8.950 21903 Z= 0.307 Chirality : 0.047 0.180 2327 Planarity : 0.005 0.051 2787 Dihedral : 19.180 178.973 2437 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.47 % Favored : 97.26 % Rotamer: Outliers : 1.28 % Allowed : 9.33 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1907 helix: 1.50 (0.19), residues: 885 sheet: 1.02 (0.44), residues: 140 loop : -0.87 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 566 TYR 0.034 0.002 TYR D 315 PHE 0.018 0.002 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 0.00272 / 0.13 (16120) covalent geometry : angle 0.60751 / 0.31 (21903) hydrogen bonds : bond 0.04872 / 3.35 ( 725) hydrogen bonds : angle 4.15462 / 3.05 ( 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: 19 poor density : 157 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7905 (mtm) cc_final: 0.7555 (mtp) REVERT: A 346 GLU cc_start: 0.6898 (tp30) cc_final: 0.6367 (tt0) REVERT: A 474 GLU cc_start: 0.7621 (pm20) cc_final: 0.7320 (mp0) REVERT: A 494 LYS cc_start: 0.7378 (ttmm) cc_final: 0.6439 (ttpp) REVERT: A 528 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7349 (ptt90) REVERT: A 544 LYS cc_start: 0.7734 (mttp) cc_final: 0.7439 (mttm) REVERT: B 239 MET cc_start: 0.7903 (mtm) cc_final: 0.7557 (mtp) REVERT: B 330 ASP cc_start: 0.8006 (t0) cc_final: 0.7804 (t70) REVERT: B 344 ASP cc_start: 0.8109 (p0) cc_final: 0.7893 (p0) REVERT: B 348 ARG cc_start: 0.7404 (mtm-85) cc_final: 0.6803 (mtt180) REVERT: B 494 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7462 (ttpt) REVERT: B 497 ASP cc_start: 0.6338 (m-30) cc_final: 0.6033 (m-30) REVERT: B 528 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7611 (ptt90) REVERT: C 185 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6699 (mtmm) REVERT: C 239 MET cc_start: 0.7962 (mtm) cc_final: 0.7599 (mtp) REVERT: C 556 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7413 (mttt) REVERT: C 566 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6301 (tpp-160) REVERT: D 239 MET cc_start: 0.7948 (mtm) cc_final: 0.7642 (mtp) REVERT: D 408 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6836 (mtp85) REVERT: D 528 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7522 (ptt90) outliers start: 19 outliers final: 7 residues processed: 171 average time/residue: 0.6434 time to fit residues: 119.6492 Evaluate side-chains 149 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 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: 4.9990 chunk 156 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.139762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100521 restraints weight = 49159.760| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.37 r_work: 0.3222 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16120 Z= 0.220 Angle : 0.688 7.343 21903 Z= 0.353 Chirality : 0.051 0.199 2327 Planarity : 0.005 0.043 2787 Dihedral : 19.075 173.049 2437 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 1.71 % Allowed : 9.88 % Favored : 88.41 % 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: 0.25 (0.19), residues: 1907 helix: 1.19 (0.18), residues: 893 sheet: 1.19 (0.46), residues: 132 loop : -1.09 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.035 0.002 TYR C 315 PHE 0.016 0.003 PHE C 427 TRP 0.011 0.002 TRP B 572 HIS 0.009 0.002 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (16120) covalent geometry : angle 0.68809 / 0.35 (21903) hydrogen bonds : bond 0.07212 / 4.98 ( 725) hydrogen bonds : angle 4.24641 / 3.11 ( 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 184 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7889 (mtm) cc_final: 0.7533 (mtp) REVERT: A 346 GLU cc_start: 0.6772 (tp30) cc_final: 0.6087 (tt0) REVERT: A 439 LYS cc_start: 0.7117 (ttpp) cc_final: 0.6799 (ttmm) REVERT: A 459 GLU cc_start: 0.8400 (tt0) cc_final: 0.7836 (tp30) REVERT: A 494 LYS cc_start: 0.7657 (ttmm) cc_final: 0.6624 (ttpp) REVERT: A 497 ASP cc_start: 0.6456 (m-30) cc_final: 0.6221 (m-30) REVERT: A 528 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7131 (ptt90) REVERT: A 544 LYS cc_start: 0.7883 (mttp) cc_final: 0.7498 (mttm) REVERT: B 239 MET cc_start: 0.7946 (mtm) cc_final: 0.7575 (mtp) REVERT: B 348 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.6621 (mtt180) REVERT: B 494 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7543 (ttpt) REVERT: B 497 ASP cc_start: 0.6374 (m-30) cc_final: 0.6124 (m-30) REVERT: C 239 MET cc_start: 0.7899 (mtm) cc_final: 0.7561 (mtp) REVERT: C 535 ASN cc_start: 0.7869 (m-40) cc_final: 0.7509 (p0) REVERT: D 239 MET cc_start: 0.7878 (mtm) cc_final: 0.7501 (mtp) REVERT: D 348 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6140 (mtp85) REVERT: D 408 ARG cc_start: 0.7232 (mtt180) cc_final: 0.6909 (mtp85) REVERT: D 528 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7401 (ttp-170) outliers start: 26 outliers final: 5 residues processed: 172 average time/residue: 0.7196 time to fit residues: 134.3821 Evaluate side-chains 155 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 328 ASN C 328 ASN D 186 GLN D 328 ASN D 535 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101426 restraints weight = 42901.338| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.20 r_work: 0.3247 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16120 Z= 0.191 Angle : 0.637 7.219 21903 Z= 0.326 Chirality : 0.049 0.195 2327 Planarity : 0.005 0.043 2787 Dihedral : 18.799 172.642 2437 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.53 % Favored : 97.21 % Rotamer: Outliers : 1.65 % Allowed : 11.04 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1907 helix: 1.26 (0.18), residues: 893 sheet: 1.20 (0.47), residues: 132 loop : -1.00 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 408 TYR 0.035 0.002 TYR A 315 PHE 0.013 0.002 PHE B 165 TRP 0.010 0.001 TRP A 572 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (16120) covalent geometry : angle 0.63735 / 0.33 (21903) hydrogen bonds : bond 0.06278 / 4.34 ( 725) hydrogen bonds : angle 4.08979 / 2.99 ( 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 181 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7826 (mtm) cc_final: 0.7420 (mtp) REVERT: A 346 GLU cc_start: 0.7067 (tp30) cc_final: 0.6210 (tt0) REVERT: A 439 LYS cc_start: 0.7130 (ttpp) cc_final: 0.6825 (tttm) REVERT: A 466 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7606 (pt) REVERT: A 494 LYS cc_start: 0.7732 (ttmm) cc_final: 0.6693 (ttpp) REVERT: A 497 ASP cc_start: 0.6446 (m-30) cc_final: 0.6223 (m-30) REVERT: A 528 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7194 (ptt-90) REVERT: A 544 LYS cc_start: 0.7900 (mttp) cc_final: 0.7553 (mttm) REVERT: B 239 MET cc_start: 0.7874 (mtm) cc_final: 0.7420 (mtp) REVERT: B 326 GLN cc_start: 0.7625 (tp40) cc_final: 0.7308 (tp40) REVERT: B 348 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.6591 (mtt180) REVERT: B 494 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7455 (ttpt) REVERT: B 497 ASP cc_start: 0.6350 (m-30) cc_final: 0.6112 (m-30) REVERT: B 528 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7211 (ptt90) REVERT: C 185 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6734 (mtmm) REVERT: C 239 MET cc_start: 0.7848 (mtm) cc_final: 0.7448 (mtp) REVERT: C 372 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7242 (mtm180) REVERT: C 459 GLU cc_start: 0.8565 (tt0) cc_final: 0.8268 (tt0) REVERT: C 497 ASP cc_start: 0.6432 (m-30) cc_final: 0.6224 (m-30) REVERT: C 535 ASN cc_start: 0.7721 (m-40) cc_final: 0.7384 (p0) REVERT: D 239 MET cc_start: 0.7864 (mtm) cc_final: 0.7500 (mtp) REVERT: D 348 ARG cc_start: 0.6848 (mtp180) cc_final: 0.6214 (mtp85) REVERT: D 408 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6956 (mtp85) REVERT: D 528 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7275 (ttp-170) outliers start: 25 outliers final: 9 residues processed: 170 average time/residue: 0.8157 time to fit residues: 150.2676 Evaluate side-chains 161 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 B residue 293 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 494 LYS 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 509 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN A 536 GLN B 246 ASN C 328 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 = 0.3738 r_free = 0.3738 target = 0.142743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104262 restraints weight = 40114.428| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.09 r_work: 0.3281 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16120 Z= 0.136 Angle : 0.572 6.922 21903 Z= 0.292 Chirality : 0.047 0.197 2327 Planarity : 0.005 0.042 2787 Dihedral : 18.315 174.553 2437 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.47 % Favored : 97.26 % Rotamer: Outliers : 1.65 % Allowed : 11.10 % 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: 0.63 (0.19), residues: 1907 helix: 1.47 (0.18), residues: 893 sheet: 1.24 (0.47), residues: 132 loop : -0.82 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.032 0.002 TYR C 315 PHE 0.013 0.002 PHE C 165 TRP 0.009 0.001 TRP B 572 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16120) covalent geometry : angle 0.57166 / 0.29 (21903) hydrogen bonds : bond 0.05205 / 3.60 ( 725) hydrogen bonds : angle 3.92204 / 2.87 ( 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: 24 poor density : 145 time to evaluate : 0.602 Fit side-chains REVERT: A 239 MET cc_start: 0.7761 (mtm) cc_final: 0.7350 (mtp) REVERT: A 348 ARG cc_start: 0.6830 (ptm160) cc_final: 0.6505 (ptp-170) REVERT: A 439 LYS cc_start: 0.7063 (ttpp) cc_final: 0.6764 (tttm) REVERT: A 466 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7594 (pt) REVERT: A 494 LYS cc_start: 0.7645 (ttmm) cc_final: 0.6620 (ttpp) REVERT: A 497 ASP cc_start: 0.6395 (m-30) cc_final: 0.6154 (m-30) REVERT: A 528 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7109 (ptt-90) REVERT: A 544 LYS cc_start: 0.7927 (mttp) cc_final: 0.7560 (mttm) REVERT: B 239 MET cc_start: 0.7847 (mtm) cc_final: 0.7461 (mtp) REVERT: B 326 GLN cc_start: 0.7662 (tp40) cc_final: 0.7349 (tp40) REVERT: B 348 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6559 (mtt180) REVERT: B 494 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7489 (ttpt) REVERT: B 497 ASP cc_start: 0.6328 (m-30) cc_final: 0.6091 (m-30) REVERT: B 528 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7109 (ptt-90) REVERT: C 185 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6366 (mtmm) REVERT: C 239 MET cc_start: 0.7797 (mtm) cc_final: 0.7373 (mtp) REVERT: C 326 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6598 (mp-120) REVERT: C 348 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6192 (mtt180) REVERT: C 459 GLU cc_start: 0.8447 (tt0) cc_final: 0.8183 (tt0) REVERT: C 494 LYS cc_start: 0.7585 (ttpt) cc_final: 0.7378 (tmtt) REVERT: C 497 ASP cc_start: 0.6541 (m-30) cc_final: 0.6334 (m-30) REVERT: C 535 ASN cc_start: 0.7685 (m-40) cc_final: 0.7411 (p0) REVERT: C 566 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6348 (tpp-160) REVERT: D 239 MET cc_start: 0.7819 (mtm) cc_final: 0.7424 (mtp) REVERT: D 326 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6536 (mp-120) REVERT: D 348 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6161 (mtp85) REVERT: D 408 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6908 (mtp85) REVERT: D 497 ASP cc_start: 0.6608 (m-30) cc_final: 0.6339 (m-30) REVERT: D 528 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7129 (ttp-170) REVERT: D 531 ARG cc_start: 0.7843 (mmt180) cc_final: 0.7617 (mmm160) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 0.7739 time to fit residues: 131.8955 Evaluate side-chains 160 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain B residue 293 ASN 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 309 ASP Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 397 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 181 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.102483 restraints weight = 44812.434| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.23 r_work: 0.3255 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16120 Z= 0.161 Angle : 0.599 8.648 21903 Z= 0.305 Chirality : 0.048 0.188 2327 Planarity : 0.005 0.043 2787 Dihedral : 18.302 174.751 2437 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.53 % Favored : 97.21 % Rotamer: Outliers : 1.59 % Allowed : 11.59 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1907 helix: 1.42 (0.18), residues: 893 sheet: 1.17 (0.46), residues: 132 loop : -0.81 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.032 0.002 TYR A 315 PHE 0.012 0.002 PHE C 165 TRP 0.009 0.001 TRP B 572 HIS 0.007 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (16120) covalent geometry : angle 0.59908 / 0.30 (21903) hydrogen bonds : bond 0.05856 / 4.06 ( 725) hydrogen bonds : angle 3.98065 / 2.91 ( 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 170 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7796 (mtm) cc_final: 0.7381 (mtp) REVERT: A 342 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 346 GLU cc_start: 0.6983 (tp30) cc_final: 0.6083 (tt0) REVERT: A 439 LYS cc_start: 0.7098 (ttpp) cc_final: 0.6807 (tttm) REVERT: A 497 ASP cc_start: 0.6406 (m-30) cc_final: 0.6197 (m-30) REVERT: A 528 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7260 (ttp-170) REVERT: A 544 LYS cc_start: 0.7918 (mttp) cc_final: 0.7588 (mttm) REVERT: B 239 MET cc_start: 0.7876 (mtm) cc_final: 0.7455 (mtp) REVERT: B 326 GLN cc_start: 0.7638 (tp40) cc_final: 0.7266 (tp40) REVERT: B 348 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6547 (mtt180) REVERT: B 528 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7332 (ttp-170) REVERT: C 185 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6737 (ttmt) REVERT: C 239 MET cc_start: 0.7833 (mtm) cc_final: 0.7387 (mtp) REVERT: C 348 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6256 (mtt180) REVERT: C 459 GLU cc_start: 0.8504 (tt0) cc_final: 0.8233 (tt0) REVERT: C 535 ASN cc_start: 0.7746 (m-40) cc_final: 0.7462 (p0) REVERT: C 566 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6347 (tpp-160) REVERT: D 239 MET cc_start: 0.7847 (mtm) cc_final: 0.7465 (mtp) REVERT: D 326 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6534 (mp-120) REVERT: D 348 ARG cc_start: 0.7027 (mtp180) cc_final: 0.6222 (mtp85) REVERT: D 408 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6851 (mtp85) REVERT: D 528 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7091 (ttp-170) REVERT: D 531 ARG cc_start: 0.7884 (mmt180) cc_final: 0.7648 (mmm160) outliers start: 23 outliers final: 14 residues processed: 156 average time/residue: 0.7812 time to fit residues: 132.1371 Evaluate side-chains 160 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 B residue 115 MET Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 397 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 154 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 186 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.144924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106769 restraints weight = 38453.412| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.06 r_work: 0.3312 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16120 Z= 0.108 Angle : 0.528 6.287 21903 Z= 0.269 Chirality : 0.045 0.171 2327 Planarity : 0.004 0.040 2787 Dihedral : 17.838 179.264 2437 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.53 % Favored : 97.26 % Rotamer: Outliers : 1.34 % Allowed : 12.14 % Favored : 86.52 % 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: 0.91 (0.19), residues: 1907 helix: 1.66 (0.18), residues: 893 sheet: 1.32 (0.46), residues: 120 loop : -0.59 (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 0.014 0.001 PHE A 165 TRP 0.006 0.001 TRP B 572 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16120) covalent geometry : angle 0.52806 / 0.27 (21903) hydrogen bonds : bond 0.04362 / 3.02 ( 725) hydrogen bonds : angle 3.78094 / 2.76 ( 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 166 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.633 Fit side-chains REVERT: A 239 MET cc_start: 0.7632 (mtm) cc_final: 0.7250 (mtp) REVERT: A 342 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 348 ARG cc_start: 0.6782 (ptm160) cc_final: 0.6443 (ptp-170) REVERT: A 439 LYS cc_start: 0.7007 (ttpp) cc_final: 0.6748 (tttm) REVERT: A 466 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7664 (pt) REVERT: A 497 ASP cc_start: 0.6348 (m-30) cc_final: 0.6129 (m-30) REVERT: A 528 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7421 (ttp80) REVERT: A 544 LYS cc_start: 0.7884 (mttp) cc_final: 0.7540 (mttm) REVERT: B 239 MET cc_start: 0.7772 (mtm) cc_final: 0.7388 (mtp) REVERT: B 326 GLN cc_start: 0.7589 (tp40) cc_final: 0.7258 (tp40) REVERT: B 342 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 348 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6537 (mtt180) REVERT: B 494 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7215 (tmtt) REVERT: B 497 ASP cc_start: 0.6276 (m-30) cc_final: 0.6017 (m-30) REVERT: B 528 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7310 (ttp80) REVERT: C 239 MET cc_start: 0.7681 (mtm) cc_final: 0.7299 (mtp) REVERT: C 344 ASP cc_start: 0.8299 (p0) cc_final: 0.7779 (p0) REVERT: C 348 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6211 (mtt180) REVERT: C 372 ARG cc_start: 0.7325 (mtt180) cc_final: 0.7083 (mtm180) REVERT: C 459 GLU cc_start: 0.8349 (tt0) cc_final: 0.8143 (tt0) REVERT: C 494 LYS cc_start: 0.7542 (ttpt) cc_final: 0.7130 (tmtt) REVERT: C 497 ASP cc_start: 0.6403 (m-30) cc_final: 0.6136 (m-30) REVERT: C 531 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7862 (mmm160) REVERT: C 535 ASN cc_start: 0.7669 (m-40) cc_final: 0.7423 (p0) REVERT: C 566 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6238 (tpp-160) REVERT: D 239 MET cc_start: 0.7690 (mtm) cc_final: 0.7236 (mtp) REVERT: D 326 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6512 (mp-120) REVERT: D 348 ARG cc_start: 0.6975 (mtp180) cc_final: 0.6201 (mtp85) REVERT: D 408 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6878 (mtp85) REVERT: D 497 ASP cc_start: 0.6531 (m-30) cc_final: 0.6273 (m-30) REVERT: D 528 ARG cc_start: 0.7427 (ttp80) cc_final: 0.6981 (ttp-170) REVERT: D 531 ARG cc_start: 0.7836 (mmt180) cc_final: 0.7607 (mmm160) outliers start: 19 outliers final: 10 residues processed: 156 average time/residue: 0.7957 time to fit residues: 134.6392 Evaluate side-chains 157 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 B residue 184 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 509 MET 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 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: 0.9990 chunk 185 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 326 GLN B 328 ASN D 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101989 restraints weight = 47079.238| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.30 r_work: 0.3244 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.004 0.036 16120 Z= 0.180 Angle : 0.615 8.186 21903 Z= 0.313 Chirality : 0.048 0.250 2327 Planarity : 0.005 0.042 2787 Dihedral : 18.156 176.721 2437 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.53 % Favored : 97.21 % Rotamer: Outliers : 1.40 % Allowed : 12.32 % Favored : 86.27 % 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: 0.68 (0.19), residues: 1907 helix: 1.48 (0.18), residues: 893 sheet: 1.10 (0.46), residues: 132 loop : -0.73 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.032 0.002 TYR A 315 PHE 0.012 0.002 PHE A 427 TRP 0.010 0.001 TRP C 572 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (16120) covalent geometry : angle 0.61509 / 0.31 (21903) hydrogen bonds : bond 0.06127 / 4.24 ( 725) hydrogen bonds : angle 3.96688 / 2.90 ( 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 161 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7820 (mtm) cc_final: 0.7459 (mtp) REVERT: A 342 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 346 GLU cc_start: 0.7099 (tp30) cc_final: 0.6233 (tt0) REVERT: A 439 LYS cc_start: 0.7107 (ttpp) cc_final: 0.6837 (tttm) REVERT: A 466 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7662 (pt) REVERT: A 497 ASP cc_start: 0.6430 (m-30) cc_final: 0.6218 (m-30) REVERT: A 528 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7204 (ttp-170) REVERT: A 544 LYS cc_start: 0.7947 (mttp) cc_final: 0.7596 (mttm) REVERT: B 239 MET cc_start: 0.7877 (mtm) cc_final: 0.7512 (mtp) REVERT: B 326 GLN cc_start: 0.7623 (tp40) cc_final: 0.7230 (tp40) REVERT: B 348 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.6630 (mtt180) REVERT: B 494 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7287 (tmtt) REVERT: B 497 ASP cc_start: 0.6230 (m-30) cc_final: 0.5961 (m-30) REVERT: B 528 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7301 (ttp-170) REVERT: C 239 MET cc_start: 0.7845 (mtm) cc_final: 0.7406 (mtp) REVERT: C 344 ASP cc_start: 0.8412 (p0) cc_final: 0.8090 (p0) REVERT: C 348 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6336 (mtt180) REVERT: C 459 GLU cc_start: 0.8536 (tt0) cc_final: 0.8281 (tt0) REVERT: C 535 ASN cc_start: 0.7760 (m-40) cc_final: 0.7486 (p0) REVERT: C 566 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6346 (ttm170) REVERT: D 239 MET cc_start: 0.7860 (mtm) cc_final: 0.7460 (mtp) REVERT: D 326 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6515 (mp-120) REVERT: D 348 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6297 (mtp85) REVERT: D 408 ARG cc_start: 0.7305 (mtt180) cc_final: 0.6928 (mtp85) REVERT: D 528 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7043 (ttp-170) REVERT: D 531 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7649 (mmm160) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 0.7947 time to fit residues: 130.9394 Evaluate side-chains 158 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 368 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 509 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 134 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.142076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103350 restraints weight = 44296.696| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.23 r_work: 0.3268 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16120 Z= 0.147 Angle : 0.579 8.021 21903 Z= 0.295 Chirality : 0.047 0.231 2327 Planarity : 0.004 0.042 2787 Dihedral : 17.974 177.471 2437 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.42 % Favored : 97.37 % Rotamer: Outliers : 1.40 % Allowed : 12.51 % 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: 0.78 (0.19), residues: 1907 helix: 1.55 (0.18), residues: 893 sheet: 1.60 (0.47), residues: 112 loop : -0.68 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.031 0.002 TYR A 315 PHE 0.012 0.002 PHE B 165 TRP 0.008 0.001 TRP B 572 HIS 0.006 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (16120) covalent geometry : angle 0.57868 / 0.30 (21903) hydrogen bonds : bond 0.05415 / 3.76 ( 725) hydrogen bonds : angle 3.90049 / 2.85 ( 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 161 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.651 Fit side-chains REVERT: A 239 MET cc_start: 0.7765 (mtm) cc_final: 0.7393 (mtp) REVERT: A 342 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 348 ARG cc_start: 0.6912 (ptm160) cc_final: 0.6535 (ptp-170) REVERT: A 439 LYS cc_start: 0.7077 (ttpp) cc_final: 0.6817 (tttm) REVERT: A 466 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7728 (pt) REVERT: A 497 ASP cc_start: 0.6389 (m-30) cc_final: 0.6173 (m-30) REVERT: A 528 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7208 (ttp-170) REVERT: A 544 LYS cc_start: 0.7969 (mttp) cc_final: 0.7633 (mttm) REVERT: B 239 MET cc_start: 0.7854 (mtm) cc_final: 0.7426 (mtp) REVERT: B 326 GLN cc_start: 0.7601 (tp40) cc_final: 0.7237 (tp40) REVERT: B 342 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 348 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.6598 (mtt180) REVERT: B 494 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7256 (tmtt) REVERT: B 497 ASP cc_start: 0.6239 (m-30) cc_final: 0.5947 (m-30) REVERT: B 528 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7272 (ttp-170) REVERT: C 239 MET cc_start: 0.7793 (mtm) cc_final: 0.7419 (mtp) REVERT: C 344 ASP cc_start: 0.8424 (p0) cc_final: 0.8175 (p0) REVERT: C 348 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6265 (mtt180) REVERT: C 459 GLU cc_start: 0.8438 (tt0) cc_final: 0.8179 (tt0) REVERT: C 494 LYS cc_start: 0.7235 (tmtt) cc_final: 0.6959 (tmtt) REVERT: C 497 ASP cc_start: 0.6426 (m-30) cc_final: 0.6146 (m-30) REVERT: C 535 ASN cc_start: 0.7750 (m-40) cc_final: 0.7483 (p0) REVERT: C 566 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6268 (tpp-160) REVERT: D 239 MET cc_start: 0.7804 (mtm) cc_final: 0.7405 (mtp) REVERT: D 326 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6526 (mp-120) REVERT: D 348 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6281 (mtp85) REVERT: D 408 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6666 (mtp85) REVERT: D 497 ASP cc_start: 0.6586 (m-30) cc_final: 0.6332 (m-30) REVERT: D 528 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7009 (ttp-170) REVERT: D 531 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7688 (mmm160) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 0.7649 time to fit residues: 124.7019 Evaluate side-chains 157 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 B residue 115 MET Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 509 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 328 ASN D 321 HIS D 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107668 restraints weight = 47215.886| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.36 r_work: 0.3321 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16120 Z= 0.101 Angle : 0.515 10.950 21903 Z= 0.262 Chirality : 0.044 0.280 2327 Planarity : 0.004 0.041 2787 Dihedral : 17.482 177.674 2437 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 1.22 % Allowed : 12.69 % 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: 1.10 (0.19), residues: 1907 helix: 1.77 (0.18), residues: 893 sheet: 1.37 (0.46), residues: 120 loop : -0.42 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.026 0.001 TYR A 315 PHE 0.014 0.001 PHE C 165 TRP 0.006 0.001 TRP B 285 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (16120) covalent geometry : angle 0.51535 / 0.26 (21903) hydrogen bonds : bond 0.03946 / 2.74 ( 725) hydrogen bonds : angle 3.71378 / 2.71 ( 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 163 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.7612 (mtm) cc_final: 0.7215 (mtp) REVERT: A 342 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 346 GLU cc_start: 0.6961 (tp30) cc_final: 0.6123 (tt0) REVERT: A 439 LYS cc_start: 0.6996 (ttpp) cc_final: 0.6788 (tttm) REVERT: A 466 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7659 (pt) REVERT: A 497 ASP cc_start: 0.6308 (m-30) cc_final: 0.6081 (m-30) REVERT: A 528 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7145 (ttp-170) REVERT: A 544 LYS cc_start: 0.7907 (mttp) cc_final: 0.7565 (mttm) REVERT: B 239 MET cc_start: 0.7714 (mtm) cc_final: 0.7295 (mtp) REVERT: B 326 GLN cc_start: 0.7580 (tp40) cc_final: 0.7298 (tp40) REVERT: B 342 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 348 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.6613 (mtt180) REVERT: B 494 LYS cc_start: 0.7596 (ttpt) cc_final: 0.7271 (tmtt) REVERT: B 497 ASP cc_start: 0.6289 (m-30) cc_final: 0.6014 (m-30) REVERT: B 528 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7265 (ttp-170) REVERT: B 577 ASN cc_start: 0.7030 (m110) cc_final: 0.6779 (m110) REVERT: C 239 MET cc_start: 0.7626 (mtm) cc_final: 0.7230 (mtp) REVERT: C 344 ASP cc_start: 0.8407 (p0) cc_final: 0.8047 (p0) REVERT: C 348 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6337 (mtt180) REVERT: C 494 LYS cc_start: 0.7076 (tmtt) cc_final: 0.6811 (tmtt) REVERT: C 497 ASP cc_start: 0.6381 (m-30) cc_final: 0.6139 (m-30) REVERT: C 531 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7887 (mmm160) REVERT: C 535 ASN cc_start: 0.7772 (m-40) cc_final: 0.7526 (p0) REVERT: C 566 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.6158 (tpp-160) REVERT: D 239 MET cc_start: 0.7662 (mtm) cc_final: 0.7211 (mtp) REVERT: D 326 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6462 (mp-120) REVERT: D 348 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6295 (mtp85) REVERT: D 408 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6634 (mtp85) REVERT: D 497 ASP cc_start: 0.6515 (m-30) cc_final: 0.6253 (m-30) REVERT: D 528 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7047 (ttp-170) REVERT: D 531 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7648 (mmm160) outliers start: 17 outliers final: 9 residues processed: 155 average time/residue: 0.7989 time to fit residues: 134.4237 Evaluate side-chains 151 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 466 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 509 MET 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 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: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN C 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108512 restraints weight = 34330.206| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.92 r_work: 0.3345 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 16120 Z= 0.104 Angle : 0.523 13.021 21903 Z= 0.267 Chirality : 0.045 0.268 2327 Planarity : 0.004 0.040 2787 Dihedral : 17.366 179.620 2437 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 1.34 % Allowed : 12.51 % 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: 1.14 (0.20), residues: 1907 helix: 1.75 (0.18), residues: 901 sheet: 1.42 (0.46), residues: 120 loop : -0.35 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.027 0.001 TYR C 315 PHE 0.014 0.001 PHE B 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 0.00225 / 0.10 (16120) covalent geometry : angle 0.52291 / 0.27 (21903) hydrogen bonds : bond 0.04079 / 2.83 ( 725) hydrogen bonds : angle 3.68860 / 2.69 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5094.92 seconds wall clock time: 87 minutes 31.16 seconds (5251.16 seconds total)