Starting phenix.real_space_refine on Mon Oct 26 17:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lp9_23473/10_2026/7lp9_23473_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lp9_23473/10_2026/7lp9_23473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lp9_23473/10_2026/7lp9_23473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lp9_23473/10_2026/7lp9_23473.map" model { file = "/net/cci-nas-00/data/ceres_data/7lp9_23473/10_2026/7lp9_23473_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lp9_23473/10_2026/7lp9_23473_neut.cif" } resolution = 2.63 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 112 5.16 5 Na 2 4.78 5 C 13765 2.51 5 N 3224 2.21 5 O 3838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20977 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 5, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 5, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 5, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 5, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 309 Unusual residues: {' NA': 2, '6OU': 7, 'LBN': 2, 'T7X': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-2': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1, 'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 335 Unusual residues: {'6OU': 7, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'YFP:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1, 'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 369 Unusual residues: {'6OU': 7, 'LBN': 2, 'T7X': 1, 'YFP': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'YFP:plan-3': 2, 'T7X:plan-2': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1, 'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 340 Unusual residues: {'6OU': 7, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-1': 4, 'T7X:plan-2': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1, 'LBN:plan-3': 1, 'YFP:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 39 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA D 204 " occ=0.50 Time building chain proxies: 5.56, per 1000 atoms: 0.27 Number of scatterers: 20977 At special positions: 0 Unit cell: (134.875, 134.875, 121.927, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 112 16.00 P 36 15.00 Na 2 11.00 O 3838 8.00 N 3224 7.00 C 13765 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: 1.96 Conformation dependent library (CDL) restraints added in 834.2 milliseconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 64.3% alpha, 4.3% 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 113 through 123 Processing helix chain 'A' and resid 128 through 140 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.601A pdb=" N LEU A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 4.256A pdb=" N ASN A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.680A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.525A pdb=" N GLU A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.585A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.787A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.559A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.828A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.700A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.995A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.849A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 712 removed outlier: 4.077A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 128 through 140 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.584A pdb=" N LEU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 4.249A pdb=" N ASN B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.687A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.524A pdb=" N GLU B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.586A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.787A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.556A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.830A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.700A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.961A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.849A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 712 removed outlier: 4.076A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 128 through 140 Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.607A pdb=" N LEU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 removed outlier: 4.254A pdb=" N ASN C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.683A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.517A pdb=" N GLU C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.585A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.788A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.572A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.830A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 558 removed outlier: 3.701A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 4.002A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.849A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 712 removed outlier: 4.074A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 128 through 140 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 171 through 183 removed outlier: 3.603A pdb=" N LEU D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 removed outlier: 4.251A pdb=" N ASN D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.678A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.523A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.586A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.786A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 510 through 532 removed outlier: 3.559A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.829A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 558 removed outlier: 3.698A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 4.001A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.848A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 712 removed outlier: 4.078A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.760A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.754A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.757A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.756A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) 1162 hydrogen bonds defined for protein. 3414 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: 3.33 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3164 1.31 - 1.43: 5884 1.43 - 1.56: 11777 1.56 - 1.68: 330 1.68 - 1.81: 232 Bond restraints: 21387 Sorted by residual: bond pdb=" O2 LBN C 902 " pdb=" P1 LBN C 902 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" O2 LBN A 910 " pdb=" P1 LBN A 910 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN D 903 " pdb=" P1 LBN D 903 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O2 LBN B 902 " pdb=" P1 LBN B 902 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O2 LBN D 905 " pdb=" P1 LBN D 905 " ideal model delta sigma weight residual 1.650 1.788 -0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 21382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 28004 3.02 - 6.04: 719 6.04 - 9.06: 38 9.06 - 12.08: 61 12.08 - 15.09: 20 Bond angle restraints: 28842 Sorted by residual: angle pdb=" CG1 VAL C 430 " pdb=" CB VAL C 430 " pdb=" CG2 VAL C 430 " ideal model delta sigma weight residual 110.80 122.35 -11.55 2.20e+00 2.07e-01 2.75e+01 angle pdb=" CG1 VAL B 430 " pdb=" CB VAL B 430 " pdb=" CG2 VAL B 430 " ideal model delta sigma weight residual 110.80 122.34 -11.54 2.20e+00 2.07e-01 2.75e+01 angle pdb=" CG1 VAL D 430 " pdb=" CB VAL D 430 " pdb=" CG2 VAL D 430 " ideal model delta sigma weight residual 110.80 122.32 -11.52 2.20e+00 2.07e-01 2.74e+01 angle pdb=" CG1 VAL A 430 " pdb=" CB VAL A 430 " pdb=" CG2 VAL A 430 " ideal model delta sigma weight residual 110.80 122.29 -11.49 2.20e+00 2.07e-01 2.73e+01 angle pdb=" O1 T7X C 904 " pdb=" P1 T7X C 904 " pdb=" O13 T7X C 904 " ideal model delta sigma weight residual 94.60 109.69 -15.09 3.00e+00 1.11e-01 2.53e+01 ... (remaining 28837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 12204 34.51 - 69.01: 507 69.01 - 103.52: 69 103.52 - 138.03: 39 138.03 - 172.54: 23 Dihedral angle restraints: 12842 sinusoidal: 5398 harmonic: 7444 Sorted by residual: dihedral pdb=" C19 6OU A 903 " pdb=" C20 6OU A 903 " pdb=" C21 6OU A 903 " pdb=" O22 6OU A 903 " ideal model delta sinusoidal sigma weight residual -59.00 113.54 -172.54 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU D 906 " pdb=" C20 6OU D 906 " pdb=" C21 6OU D 906 " pdb=" O22 6OU D 906 " ideal model delta sinusoidal sigma weight residual -59.00 113.49 -172.49 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU B 906 " pdb=" C20 6OU B 906 " pdb=" C21 6OU B 906 " pdb=" O22 6OU B 906 " ideal model delta sinusoidal sigma weight residual -59.00 113.32 -172.32 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 3211 0.965 - 1.931: 8 1.931 - 2.896: 0 2.896 - 3.861: 0 3.861 - 4.827: 4 Chirality restraints: 3223 Sorted by residual: chirality pdb=" C1 T7X B 904 " pdb=" C2 T7X B 904 " pdb=" C6 T7X B 904 " pdb=" O1 T7X B 904 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X C 904 " pdb=" C2 T7X C 904 " pdb=" C6 T7X C 904 " pdb=" O1 T7X C 904 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X A 901 " pdb=" C2 T7X A 901 " pdb=" C6 T7X A 901 " pdb=" O1 T7X A 901 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 ... (remaining 3220 not shown) Planarity restraints: 3516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.010 2.00e-02 2.50e+03 1.15e-02 2.66e+00 pdb=" CG TYR A 653 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " -0.011 2.00e-02 2.50e+03 1.14e-02 2.60e+00 pdb=" CG TYR B 653 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 304 " 0.018 2.00e-02 2.50e+03 1.22e-02 2.59e+00 pdb=" CG PHE D 304 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE D 304 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 304 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 304 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 304 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 304 " 0.008 2.00e-02 2.50e+03 ... (remaining 3513 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 176 2.61 - 3.18: 18435 3.18 - 3.76: 30514 3.76 - 4.33: 43592 4.33 - 4.90: 73762 Nonbonded interactions: 166479 Sorted by model distance: nonbonded pdb=" OD1 ASP C 383 " pdb=" OG SER C 385 " model vdw 2.040 3.040 nonbonded pdb=" OD1 ASP B 383 " pdb=" OG SER B 385 " model vdw 2.040 3.040 nonbonded pdb=" OD1 ASP D 383 " pdb=" OG SER D 385 " model vdw 2.042 3.040 nonbonded pdb=" OD1 ASP A 383 " pdb=" OG SER A 385 " model vdw 2.043 3.040 nonbonded pdb=" NH1 ARG A 355 " pdb=" O LEU A 365 " model vdw 2.099 3.120 ... (remaining 166474 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 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) selection = (chain 'B' and (resid 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) selection = (chain 'C' and (resid 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) selection = (chain 'D' and (resid 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) } 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.330 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.010 0.141 21387 Z= 0.518 Angle : 1.081 15.095 28842 Z= 0.427 Chirality : 0.197 4.827 3223 Planarity : 0.002 0.030 3516 Dihedral : 21.505 172.536 8050 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.57 (0.17), residues: 2520 helix: 2.23 (0.13), residues: 1524 sheet: -1.15 (0.38), residues: 116 loop : -0.79 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 579 TYR 0.026 0.001 TYR A 653 PHE 0.025 0.001 PHE A 304 TRP 0.008 0.001 TRP C 697 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01036 / 0.52 (21387) covalent geometry : angle 1.08072 / 0.43 (28842) hydrogen bonds : bond 0.12565 / 8.52 ( 1162) hydrogen bonds : angle 4.43815 / 3.28 ( 3414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.809 Fit side-chains REVERT: A 562 MET cc_start: 0.8807 (mmm) cc_final: 0.8607 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.5166 time to fit residues: 73.5643 Evaluate side-chains 114 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN A 378 HIS A 700 GLN B 202 GLN B 378 HIS B 700 GLN C 202 GLN C 378 HIS C 700 GLN D 202 GLN D 378 HIS D 700 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065545 restraints weight = 39235.990| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.51 r_work: 0.2723 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21387 Z= 0.157 Angle : 0.530 6.726 28842 Z= 0.271 Chirality : 0.040 0.327 3223 Planarity : 0.003 0.034 3516 Dihedral : 21.275 179.605 3854 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.99 % Allowed : 3.18 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.74 (0.17), residues: 2520 helix: 2.35 (0.13), residues: 1536 sheet: -0.68 (0.45), residues: 84 loop : -0.82 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.011 0.001 TYR D 194 PHE 0.010 0.001 PHE C 429 TRP 0.011 0.001 TRP B 697 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (21387) covalent geometry : angle 0.53011 / 0.27 (28842) hydrogen bonds : bond 0.05359 / 3.61 ( 1162) hydrogen bonds : angle 3.76010 / 2.75 ( 3414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.826 Fit side-chains REVERT: A 214 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7920 (tpt) REVERT: A 304 PHE cc_start: 0.7775 (t80) cc_final: 0.7537 (t80) REVERT: A 562 MET cc_start: 0.8921 (mmm) cc_final: 0.8671 (mmm) REVERT: B 304 PHE cc_start: 0.7789 (t80) cc_final: 0.7538 (t80) REVERT: D 214 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7846 (tpt) outliers start: 20 outliers final: 8 residues processed: 114 average time/residue: 0.5290 time to fit residues: 70.0762 Evaluate side-chains 117 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [234, 41, 127, 36, 3, 240, 206, 48, 59, 247, 213] chunk 234 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 240 optimal weight: 0.4980 chunk 206 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 213 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS B 378 HIS C 378 HIS D 378 HIS D 765 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068080 restraints weight = 39212.423| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.53 r_work: 0.2765 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21387 Z= 0.104 Angle : 0.451 7.965 28842 Z= 0.234 Chirality : 0.037 0.255 3223 Planarity : 0.003 0.037 3516 Dihedral : 19.073 174.956 3854 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.09 % Allowed : 5.57 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.09 (0.17), residues: 2520 helix: 2.65 (0.13), residues: 1536 sheet: -0.48 (0.47), residues: 84 loop : -0.73 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 212 TYR 0.008 0.001 TYR B 194 PHE 0.009 0.001 PHE B 429 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (21387) covalent geometry : angle 0.45072 / 0.23 (28842) hydrogen bonds : bond 0.04301 / 2.90 ( 1162) hydrogen bonds : angle 3.51782 / 2.57 ( 3414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.827 Fit side-chains REVERT: A 562 MET cc_start: 0.8808 (mmm) cc_final: 0.8552 (mmt) REVERT: B 214 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7628 (tpt) REVERT: B 677 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8905 (ttm) REVERT: C 214 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7724 (tpt) REVERT: D 677 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8914 (ttt) outliers start: 22 outliers final: 1 residues processed: 118 average time/residue: 0.5706 time to fit residues: 77.9487 Evaluate side-chains 112 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [157, 9, 177, 180, 150, 233, 138, 22, 50, 90, 53] chunk 157 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.108225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068895 restraints weight = 39557.703| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.58 r_work: 0.2804 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21387 Z= 0.097 Angle : 0.433 9.854 28842 Z= 0.224 Chirality : 0.036 0.218 3223 Planarity : 0.003 0.039 3516 Dihedral : 17.583 177.294 3854 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.29 % Allowed : 6.31 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.27 (0.17), residues: 2520 helix: 2.77 (0.13), residues: 1536 sheet: -0.42 (0.48), residues: 84 loop : -0.61 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.006 0.001 TYR D 309 PHE 0.010 0.001 PHE C 304 TRP 0.010 0.001 TRP A 697 HIS 0.002 0.000 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (21387) covalent geometry : angle 0.43256 / 0.22 (28842) hydrogen bonds : bond 0.04035 / 2.71 ( 1162) hydrogen bonds : angle 3.40097 / 2.49 ( 3414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.894 Fit side-chains REVERT: B 677 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8870 (ttt) REVERT: C 214 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7763 (tpt) REVERT: D 677 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8896 (ttm) outliers start: 26 outliers final: 5 residues processed: 120 average time/residue: 0.5335 time to fit residues: 74.2968 Evaluate side-chains 117 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [142, 237, 63, 32, 122, 228, 110, 187, 138, 239, 149] chunk 142 optimal weight: 0.0470 chunk 237 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.068632 restraints weight = 39307.103| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.58 r_work: 0.2800 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21387 Z= 0.098 Angle : 0.438 11.022 28842 Z= 0.223 Chirality : 0.036 0.231 3223 Planarity : 0.003 0.037 3516 Dihedral : 16.546 179.989 3854 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 7.46 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.32 (0.17), residues: 2520 helix: 2.80 (0.13), residues: 1536 sheet: -0.45 (0.49), residues: 84 loop : -0.56 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 409 TYR 0.006 0.001 TYR C 194 PHE 0.011 0.001 PHE C 304 TRP 0.008 0.001 TRP A 697 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (21387) covalent geometry : angle 0.43765 / 0.22 (28842) hydrogen bonds : bond 0.04071 / 2.74 ( 1162) hydrogen bonds : angle 3.39507 / 2.49 ( 3414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.718 Fit side-chains REVERT: D 260 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7111 (mt0) outliers start: 23 outliers final: 10 residues processed: 127 average time/residue: 0.5162 time to fit residues: 76.6925 Evaluate side-chains 114 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [124, 246, 168, 11, 179, 195, 182, 38, 42, 18, 9] chunk 124 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065927 restraints weight = 39116.444| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.52 r_work: 0.2745 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21387 Z= 0.143 Angle : 0.478 11.456 28842 Z= 0.243 Chirality : 0.038 0.256 3223 Planarity : 0.003 0.037 3516 Dihedral : 16.473 177.584 3854 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.59 % Allowed : 6.96 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.22 (0.17), residues: 2520 helix: 2.68 (0.13), residues: 1540 sheet: -0.50 (0.48), residues: 84 loop : -0.54 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.008 0.001 TYR D 194 PHE 0.010 0.001 PHE C 304 TRP 0.007 0.001 TRP A 697 HIS 0.002 0.000 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (21387) covalent geometry : angle 0.47761 / 0.24 (28842) hydrogen bonds : bond 0.04986 / 3.36 ( 1162) hydrogen bonds : angle 3.50680 / 2.57 ( 3414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.800 Fit side-chains REVERT: A 260 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: A 562 MET cc_start: 0.8939 (mmm) cc_final: 0.8699 (mmp) REVERT: B 260 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7118 (mt0) REVERT: C 260 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7141 (mt0) REVERT: D 260 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7491 (mt0) outliers start: 32 outliers final: 14 residues processed: 121 average time/residue: 0.5446 time to fit residues: 76.9473 Evaluate side-chains 122 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [84, 6, 224, 49, 156, 122, 142, 17, 245, 191, 213] chunk 84 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 245 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066072 restraints weight = 39162.506| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.52 r_work: 0.2744 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21387 Z= 0.135 Angle : 0.470 12.454 28842 Z= 0.239 Chirality : 0.038 0.244 3223 Planarity : 0.003 0.037 3516 Dihedral : 16.044 174.239 3854 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.64 % Allowed : 7.11 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.18 (0.17), residues: 2520 helix: 2.66 (0.13), residues: 1540 sheet: -0.81 (0.41), residues: 116 loop : -0.51 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.008 0.001 TYR D 194 PHE 0.014 0.001 PHE C 304 TRP 0.009 0.001 TRP B 697 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (21387) covalent geometry : angle 0.47044 / 0.24 (28842) hydrogen bonds : bond 0.04801 / 3.24 ( 1162) hydrogen bonds : angle 3.50478 / 2.56 ( 3414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.812 Fit side-chains REVERT: A 260 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7090 (mt0) REVERT: A 562 MET cc_start: 0.8920 (mmm) cc_final: 0.8674 (mmt) REVERT: B 260 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: C 260 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7156 (mt0) REVERT: D 260 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7487 (mt0) outliers start: 33 outliers final: 19 residues processed: 120 average time/residue: 0.5491 time to fit residues: 76.5958 Evaluate side-chains 125 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [168, 73, 202, 83, 221, 78, 174, 138, 103, 5, 171] chunk 168 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 171 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067618 restraints weight = 39058.457| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.55 r_work: 0.2770 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21387 Z= 0.104 Angle : 0.449 9.346 28842 Z= 0.228 Chirality : 0.037 0.224 3223 Planarity : 0.003 0.037 3516 Dihedral : 15.282 171.141 3854 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.04 % Allowed : 7.95 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.29 (0.17), residues: 2520 helix: 2.78 (0.13), residues: 1532 sheet: -0.72 (0.41), residues: 116 loop : -0.52 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 701 TYR 0.007 0.001 TYR D 194 PHE 0.016 0.001 PHE C 304 TRP 0.009 0.001 TRP A 697 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (21387) covalent geometry : angle 0.44925 / 0.23 (28842) hydrogen bonds : bond 0.04284 / 2.88 ( 1162) hydrogen bonds : angle 3.42265 / 2.50 ( 3414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.772 Fit side-chains REVERT: A 260 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7137 (mt0) REVERT: A 562 MET cc_start: 0.8849 (mmm) cc_final: 0.8605 (mmp) REVERT: B 260 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: C 260 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7115 (mt0) REVERT: D 260 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7489 (mt0) outliers start: 21 outliers final: 20 residues processed: 112 average time/residue: 0.5109 time to fit residues: 67.1703 Evaluate side-chains 127 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 758 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [81, 46, 208, 44, 217, 242, 48, 153, 86, 136, 193] chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068090 restraints weight = 39033.070| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.56 r_work: 0.2786 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21387 Z= 0.101 Angle : 0.457 10.723 28842 Z= 0.228 Chirality : 0.037 0.326 3223 Planarity : 0.002 0.035 3516 Dihedral : 14.789 166.818 3854 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.19 % Allowed : 8.15 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.29 (0.17), residues: 2520 helix: 2.77 (0.13), residues: 1532 sheet: -0.70 (0.41), residues: 116 loop : -0.51 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.006 0.001 TYR B 194 PHE 0.015 0.001 PHE C 304 TRP 0.009 0.001 TRP A 697 HIS 0.002 0.000 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (21387) covalent geometry : angle 0.45743 / 0.23 (28842) hydrogen bonds : bond 0.04182 / 2.81 ( 1162) hydrogen bonds : angle 3.44329 / 2.53 ( 3414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.692 Fit side-chains REVERT: A 445 MET cc_start: 0.9083 (tpp) cc_final: 0.8853 (mmm) REVERT: B 445 MET cc_start: 0.9080 (tpp) cc_final: 0.8847 (mmm) REVERT: B 720 PHE cc_start: 0.7649 (m-80) cc_final: 0.7357 (m-80) REVERT: C 445 MET cc_start: 0.9077 (tpp) cc_final: 0.8845 (mmm) REVERT: D 260 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: D 445 MET cc_start: 0.9080 (tpp) cc_final: 0.8851 (mmm) outliers start: 24 outliers final: 17 residues processed: 111 average time/residue: 0.5399 time to fit residues: 69.5917 Evaluate side-chains 121 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [20, 105, 223, 224, 184, 66, 63, 60, 150, 226, 192] chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 226 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.066268 restraints weight = 39251.162| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.53 r_work: 0.2748 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21387 Z= 0.134 Angle : 0.489 10.440 28842 Z= 0.243 Chirality : 0.038 0.318 3223 Planarity : 0.003 0.033 3516 Dihedral : 14.802 162.473 3854 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.99 % Allowed : 8.10 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.20 (0.17), residues: 2520 helix: 2.67 (0.13), residues: 1540 sheet: -0.74 (0.41), residues: 116 loop : -0.51 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.008 0.001 TYR B 194 PHE 0.015 0.001 PHE C 304 TRP 0.008 0.001 TRP B 697 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (21387) covalent geometry : angle 0.48875 / 0.24 (28842) hydrogen bonds : bond 0.04812 / 3.24 ( 1162) hydrogen bonds : angle 3.51587 / 2.58 ( 3414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.704 Fit side-chains REVERT: A 445 MET cc_start: 0.9098 (tpp) cc_final: 0.8894 (mmm) REVERT: A 562 MET cc_start: 0.8914 (mmm) cc_final: 0.8668 (mmp) REVERT: B 445 MET cc_start: 0.9092 (tpp) cc_final: 0.8883 (mmm) REVERT: B 720 PHE cc_start: 0.7750 (m-80) cc_final: 0.7473 (m-80) REVERT: C 445 MET cc_start: 0.9092 (tpp) cc_final: 0.8886 (mmm) REVERT: D 260 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: D 445 MET cc_start: 0.9081 (tpp) cc_final: 0.8872 (mmm) outliers start: 20 outliers final: 18 residues processed: 109 average time/residue: 0.5338 time to fit residues: 68.1450 Evaluate side-chains 122 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [40, 215, 145, 112, 100, 2, 49, 107, 206, 71, 0] chunk 40 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 107 optimal weight: 0.0870 chunk 206 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068537 restraints weight = 39039.017| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.56 r_work: 0.2795 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21387 Z= 0.096 Angle : 0.498 18.010 28842 Z= 0.238 Chirality : 0.037 0.311 3223 Planarity : 0.002 0.033 3516 Dihedral : 14.095 159.104 3854 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.80 % Allowed : 8.55 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.28 (0.17), residues: 2520 helix: 2.75 (0.13), residues: 1532 sheet: -0.65 (0.42), residues: 116 loop : -0.49 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 428 TYR 0.006 0.001 TYR B 309 PHE 0.017 0.001 PHE C 304 TRP 0.009 0.001 TRP A 697 HIS 0.002 0.000 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (21387) covalent geometry : angle 0.49818 / 0.24 (28842) hydrogen bonds : bond 0.04078 / 2.74 ( 1162) hydrogen bonds : angle 3.47141 / 2.56 ( 3414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5664.65 seconds wall clock time: 97 minutes 20.61 seconds (5840.61 seconds total)