Starting phenix.real_space_refine on Thu Mar 5 01:21:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvy_27021/03_2026/8cvy_27021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvy_27021/03_2026/8cvy_27021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cvy_27021/03_2026/8cvy_27021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvy_27021/03_2026/8cvy_27021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cvy_27021/03_2026/8cvy_27021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvy_27021/03_2026/8cvy_27021.map" } resolution = 3.6 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= 0.092 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11490 2.51 5 N 3092 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17930 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4862 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 277 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 4867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4867 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4851 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2503 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 296} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 4.06, per 1000 atoms: 0.23 Number of scatterers: 17930 At special positions: 0 Unit cell: (119.76, 126.16, 136.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3260 8.00 N 3092 7.00 C 11490 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: 1.51 Conformation dependent library (CDL) restraints added in 882.4 milliseconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 12 sheets defined 56.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.846A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.525A pdb=" N LYS A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.885A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.732A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 292 through 312 removed outlier: 3.617A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.939A pdb=" N LEU A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.887A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.612A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.532A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.535A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 removed outlier: 3.504A pdb=" N ARG C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 136 Processing helix chain 'C' and resid 145 through 169 removed outlier: 3.992A pdb=" N LEU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.631A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.725A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 292 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.617A pdb=" N LEU C 420 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 559 through 577 Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.531A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 597 removed outlier: 3.887A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 616 removed outlier: 4.404A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 616 " --> pdb=" O ALA C 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 328 Processing helix chain 'G' and resid 337 through 348 removed outlier: 3.761A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.851A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.528A pdb=" N LYS D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.400A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 146 through 169 Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.963A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.724A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 376 through 411 removed outlier: 3.548A pdb=" N GLN D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.474A pdb=" N LEU D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.829A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 616 removed outlier: 4.425A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 616 " --> pdb=" O ALA D 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 328 removed outlier: 3.535A pdb=" N LYS H 322 " --> pdb=" O SER H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 removed outlier: 3.719A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.838A pdb=" N LEU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.886A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.724A pdb=" N LEU A 116 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 255 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.511A pdb=" N VAL A 362 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 476 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 364 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.623A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.381A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE C 255 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.507A pdb=" N VAL C 362 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 476 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA C 364 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 372 through 375 removed outlier: 4.977A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.050A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 255 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'D' and resid 473 through 478 removed outlier: 6.323A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE D 476 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA D 364 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS D 478 " --> pdb=" O ALA D 364 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N PHE D 366 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.710A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.502A pdb=" N VAL B 362 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 476 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA B 364 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 328 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.620A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2631 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: 3.27 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3472 1.33 - 1.45: 5745 1.45 - 1.58: 9050 1.58 - 1.71: 0 1.71 - 1.84: 131 Bond restraints: 18398 Sorted by residual: bond pdb=" CE1 HIS B 311 " pdb=" NE2 HIS B 311 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" C PHE B 440 " pdb=" N PRO B 441 " ideal model delta sigma weight residual 1.331 1.366 -0.034 8.70e-03 1.32e+04 1.55e+01 bond pdb=" CE1 HIS C 501 " pdb=" NE2 HIS C 501 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.51e+01 bond pdb=" C PHE D 440 " pdb=" N PRO D 441 " ideal model delta sigma weight residual 1.331 1.364 -0.033 8.70e-03 1.32e+04 1.45e+01 bond pdb=" CE1 HIS B 446 " pdb=" NE2 HIS B 446 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.43e+01 ... (remaining 18393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 23384 2.82 - 5.64: 1489 5.64 - 8.46: 53 8.46 - 11.28: 6 11.28 - 14.10: 3 Bond angle restraints: 24935 Sorted by residual: angle pdb=" C THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta sigma weight residual 109.24 123.32 -14.08 1.75e+00 3.27e-01 6.47e+01 angle pdb=" C THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta sigma weight residual 109.29 123.39 -14.10 1.82e+00 3.02e-01 6.00e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 107.20 6.60 1.00e+00 1.00e+00 4.35e+01 angle pdb=" C PHE A 617 " pdb=" CA PHE A 617 " pdb=" CB PHE A 617 " ideal model delta sigma weight residual 111.20 115.41 -4.21 7.10e-01 1.98e+00 3.52e+01 angle pdb=" C PHE D 617 " pdb=" CA PHE D 617 " pdb=" CB PHE D 617 " ideal model delta sigma weight residual 111.20 115.35 -4.15 7.10e-01 1.98e+00 3.41e+01 ... (remaining 24930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 9312 14.70 - 29.41: 997 29.41 - 44.11: 363 44.11 - 58.81: 119 58.81 - 73.52: 23 Dihedral angle restraints: 10814 sinusoidal: 4321 harmonic: 6493 Sorted by residual: dihedral pdb=" C THR D 49 " pdb=" N THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta harmonic sigma weight residual -122.00 -141.54 19.54 0 2.50e+00 1.60e-01 6.11e+01 dihedral pdb=" C THR A 49 " pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta harmonic sigma weight residual -122.00 -141.26 19.26 0 2.50e+00 1.60e-01 5.94e+01 dihedral pdb=" C ASP A 424 " pdb=" N ASP A 424 " pdb=" CA ASP A 424 " pdb=" CB ASP A 424 " ideal model delta harmonic sigma weight residual -122.60 -135.78 13.18 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 10811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2141 0.141 - 0.282: 474 0.282 - 0.423: 50 0.423 - 0.564: 2 0.564 - 0.705: 2 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CA THR D 49 " pdb=" N THR D 49 " pdb=" C THR D 49 " pdb=" CB THR D 49 " both_signs ideal model delta sigma weight residual False 2.53 1.82 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ASP B 424 " pdb=" N ASP B 424 " pdb=" C ASP B 424 " pdb=" CB ASP B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 2666 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.040 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP A 143 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 44 " 0.042 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR C 44 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 44 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 44 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 44 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 44 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 44 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 400 " 0.029 2.00e-02 2.50e+03 2.37e-02 9.80e+00 pdb=" CG PHE A 400 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 400 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 400 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 400 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 400 " -0.003 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1149 2.75 - 3.29: 18768 3.29 - 3.83: 31457 3.83 - 4.36: 38684 4.36 - 4.90: 63087 Nonbonded interactions: 153145 Sorted by model distance: nonbonded pdb=" OH TYR A 242 " pdb=" O LEU A 269 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR D 242 " pdb=" O LEU D 269 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR C 242 " pdb=" O LEU C 269 " model vdw 2.216 3.040 nonbonded pdb=" O THR A 45 " pdb=" OG1 THR A 49 " model vdw 2.419 3.040 nonbonded pdb=" O THR D 45 " pdb=" OG1 THR D 49 " model vdw 2.428 3.040 ... (remaining 153140 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 22 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 415 or (resid 4 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 417 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) or r \ esid 423 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 through 626)) selection = (chain 'C' and (resid 22 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 47 through 421 or (resid 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 520 or (resid 521 and (name N or name CA or name C or \ name O or name CB )) or resid 522 through 626)) selection = (chain 'D' and (resid 22 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 626)) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 316 through 348) selection = (chain 'H' and resid 316 through 348) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.008 0.055 18398 Z= 0.552 Angle : 1.472 14.100 24935 Z= 1.028 Chirality : 0.115 0.705 2669 Planarity : 0.007 0.030 3222 Dihedral : 15.011 73.516 6634 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 6.05 % Allowed : 11.37 % Favored : 82.58 % Cbeta Deviations : 0.77 % 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: 0.51 (0.16), residues: 2212 helix: 1.38 (0.14), residues: 1132 sheet: -0.76 (0.32), residues: 281 loop : -0.67 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 582 TYR 0.042 0.006 TYR C 44 PHE 0.053 0.007 PHE A 400 TRP 0.051 0.007 TRP A 143 HIS 0.032 0.005 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00790 (18398) covalent geometry : angle 1.47175 (24935) hydrogen bonds : bond 0.19433 ( 890) hydrogen bonds : angle 6.83983 ( 2631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 652 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8663 (m-30) cc_final: 0.8235 (t70) REVERT: A 227 PHE cc_start: 0.5242 (m-80) cc_final: 0.4741 (m-80) REVERT: A 321 ASP cc_start: 0.8103 (p0) cc_final: 0.7650 (m-30) REVERT: A 375 PHE cc_start: 0.7945 (m-80) cc_final: 0.7728 (m-80) REVERT: A 424 ASP cc_start: 0.8423 (p0) cc_final: 0.8086 (p0) REVERT: A 480 GLU cc_start: 0.8533 (tt0) cc_final: 0.8216 (mm-30) REVERT: A 606 MET cc_start: 0.6653 (mtm) cc_final: 0.6265 (mtp) REVERT: E 317 SER cc_start: 0.7752 (OUTLIER) cc_final: 0.7520 (p) REVERT: C 127 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6550 (tp30) REVERT: C 296 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8107 (mt) REVERT: C 316 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 403 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7399 (mttm) REVERT: C 409 LEU cc_start: 0.8588 (mt) cc_final: 0.8105 (mt) REVERT: C 425 PHE cc_start: 0.8399 (t80) cc_final: 0.8194 (t80) REVERT: C 509 TYR cc_start: 0.7858 (t80) cc_final: 0.7650 (t80) REVERT: C 552 ILE cc_start: 0.8661 (mm) cc_final: 0.8344 (mm) REVERT: C 554 ASP cc_start: 0.7732 (t0) cc_final: 0.7359 (t0) REVERT: C 579 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7513 (tpp-160) REVERT: C 597 ASP cc_start: 0.8773 (t0) cc_final: 0.8221 (t0) REVERT: G 333 MET cc_start: 0.8728 (mmm) cc_final: 0.7876 (mtm) REVERT: G 346 ASP cc_start: 0.8352 (m-30) cc_final: 0.7742 (m-30) REVERT: D 162 LEU cc_start: 0.8693 (pp) cc_final: 0.7879 (mt) REVERT: D 273 LYS cc_start: 0.8253 (mttt) cc_final: 0.8033 (tptp) REVERT: D 483 SER cc_start: 0.8699 (m) cc_final: 0.8446 (p) REVERT: D 597 ASP cc_start: 0.8439 (t0) cc_final: 0.8024 (t0) REVERT: H 316 VAL cc_start: 0.6247 (OUTLIER) cc_final: 0.5831 (m) REVERT: H 317 SER cc_start: 0.6043 (OUTLIER) cc_final: 0.5182 (p) REVERT: B 299 GLN cc_start: 0.7782 (mt0) cc_final: 0.7333 (tm-30) REVERT: B 319 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7493 (m-40) REVERT: B 360 GLN cc_start: 0.3343 (mt0) cc_final: 0.3140 (mm-40) REVERT: B 379 THR cc_start: 0.7962 (m) cc_final: 0.7618 (p) REVERT: B 391 ASP cc_start: 0.8382 (m-30) cc_final: 0.8019 (t0) REVERT: B 414 PRO cc_start: 0.8592 (Cg_endo) cc_final: 0.8031 (Cg_exo) REVERT: B 428 MET cc_start: 0.8283 (mtm) cc_final: 0.8031 (mtt) REVERT: B 443 VAL cc_start: 0.8054 (m) cc_final: 0.7780 (t) REVERT: B 471 ASP cc_start: 0.7130 (m-30) cc_final: 0.6498 (p0) REVERT: B 486 SER cc_start: 0.8580 (m) cc_final: 0.8320 (p) REVERT: B 524 ILE cc_start: 0.5224 (mm) cc_final: 0.4673 (tp) REVERT: B 568 THR cc_start: 0.3951 (p) cc_final: 0.3550 (p) REVERT: B 572 TYR cc_start: 0.6230 (t80) cc_final: 0.5554 (t80) REVERT: B 584 ILE cc_start: 0.5429 (mt) cc_final: 0.5162 (mt) REVERT: B 594 ASP cc_start: 0.6832 (m-30) cc_final: 0.6564 (m-30) outliers start: 115 outliers final: 23 residues processed: 723 average time/residue: 0.1690 time to fit residues: 174.6082 Evaluate side-chains 403 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 373 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 253 HIS A 260 GLN A 283 ASN A 417 ASN A 530 ASN A 581 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN A 620 HIS C 38 ASN C 71 GLN C 95 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 253 HIS C 260 GLN C 283 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN C 388 GLN C 530 ASN C 577 GLN C 585 GLN C 587 ASN D 95 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN D 581 GLN D 587 ASN B 297 HIS B 315 HIS B 374 ASN B 530 ASN B 576 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.205992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169762 restraints weight = 23500.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173280 restraints weight = 18306.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175540 restraints weight = 12534.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175803 restraints weight = 9386.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.176502 restraints weight = 9185.079| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18398 Z= 0.175 Angle : 0.634 9.159 24935 Z= 0.342 Chirality : 0.045 0.250 2669 Planarity : 0.004 0.036 3222 Dihedral : 6.517 59.677 2508 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.89 % Allowed : 16.26 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2212 helix: 2.05 (0.14), residues: 1139 sheet: -1.03 (0.32), residues: 278 loop : -0.69 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 461 TYR 0.028 0.002 TYR A 493 PHE 0.030 0.002 PHE B 334 TRP 0.011 0.001 TRP A 34 HIS 0.013 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00394 (18398) covalent geometry : angle 0.63407 (24935) hydrogen bonds : bond 0.05293 ( 890) hydrogen bonds : angle 5.10809 ( 2631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 389 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7424 (mtm180) cc_final: 0.6865 (mtm-85) REVERT: A 228 ASN cc_start: 0.8132 (t0) cc_final: 0.7924 (t0) REVERT: C 94 MET cc_start: 0.7604 (mmm) cc_final: 0.6933 (mmm) REVERT: C 127 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.5266 (tp30) REVERT: C 212 TYR cc_start: 0.7794 (m-80) cc_final: 0.7519 (m-80) REVERT: C 245 GLU cc_start: 0.8494 (tp30) cc_final: 0.7552 (tp30) REVERT: C 284 VAL cc_start: 0.8500 (m) cc_final: 0.8086 (m) REVERT: C 293 PHE cc_start: 0.6012 (OUTLIER) cc_final: 0.4951 (t80) REVERT: C 296 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8122 (mt) REVERT: C 316 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 350 ASN cc_start: 0.7649 (t0) cc_final: 0.7121 (t0) REVERT: C 425 PHE cc_start: 0.8220 (t80) cc_final: 0.7947 (t80) REVERT: C 428 MET cc_start: 0.7821 (mtm) cc_final: 0.7607 (mtm) REVERT: C 597 ASP cc_start: 0.8029 (t0) cc_final: 0.7799 (t0) REVERT: D 285 LYS cc_start: 0.8189 (mptt) cc_final: 0.7862 (mmtp) REVERT: D 355 VAL cc_start: 0.8355 (p) cc_final: 0.8119 (m) REVERT: D 473 VAL cc_start: 0.8884 (t) cc_final: 0.8354 (p) REVERT: D 597 ASP cc_start: 0.8014 (t0) cc_final: 0.7639 (t0) REVERT: B 295 ASN cc_start: 0.5411 (t0) cc_final: 0.5091 (t0) REVERT: B 301 LYS cc_start: 0.8274 (ptmt) cc_final: 0.7695 (ptmt) REVERT: B 316 LEU cc_start: 0.8004 (mp) cc_final: 0.7760 (mt) REVERT: B 378 GLU cc_start: 0.6588 (tp30) cc_final: 0.6385 (tm-30) REVERT: B 404 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.7917 (pp) REVERT: B 568 THR cc_start: 0.5651 (p) cc_final: 0.5129 (p) outliers start: 74 outliers final: 42 residues processed: 437 average time/residue: 0.1534 time to fit residues: 99.4027 Evaluate side-chains 349 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 211 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 315 HIS ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 585 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 283 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 360 GLN B 305 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.207081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171766 restraints weight = 23153.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174737 restraints weight = 17690.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.176490 restraints weight = 13813.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176753 restraints weight = 10153.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.177449 restraints weight = 9820.846| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 18398 Z= 0.196 Angle : 0.606 8.450 24935 Z= 0.323 Chirality : 0.044 0.180 2669 Planarity : 0.004 0.046 3222 Dihedral : 5.881 59.612 2479 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.32 % Allowed : 17.05 % Favored : 78.63 % 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: 0.74 (0.17), residues: 2212 helix: 1.81 (0.15), residues: 1141 sheet: -1.37 (0.29), residues: 308 loop : -0.67 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 236 TYR 0.019 0.002 TYR B 313 PHE 0.029 0.002 PHE B 334 TRP 0.010 0.001 TRP C 134 HIS 0.015 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00458 (18398) covalent geometry : angle 0.60638 (24935) hydrogen bonds : bond 0.04591 ( 890) hydrogen bonds : angle 4.89597 ( 2631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 332 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7353 (mtm180) cc_final: 0.7028 (mtm-85) REVERT: A 106 TRP cc_start: 0.8137 (t60) cc_final: 0.7742 (t60) REVERT: A 108 ILE cc_start: 0.8176 (pp) cc_final: 0.7974 (pp) REVERT: A 400 PHE cc_start: 0.8238 (t80) cc_final: 0.7733 (t80) REVERT: A 449 LEU cc_start: 0.8712 (mm) cc_final: 0.8324 (mt) REVERT: A 480 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7748 (tp30) REVERT: C 127 GLU cc_start: 0.5522 (OUTLIER) cc_final: 0.5265 (tp30) REVERT: C 153 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7673 (mm) REVERT: C 227 PHE cc_start: 0.6307 (m-80) cc_final: 0.6077 (m-80) REVERT: C 293 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.4890 (t80) REVERT: C 425 PHE cc_start: 0.8237 (t80) cc_final: 0.7982 (t80) REVERT: C 553 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7642 (mt) REVERT: D 156 PHE cc_start: 0.8202 (m-80) cc_final: 0.7999 (m-80) REVERT: D 355 VAL cc_start: 0.8309 (p) cc_final: 0.8035 (t) REVERT: D 597 ASP cc_start: 0.7942 (t0) cc_final: 0.7575 (t0) REVERT: D 614 SER cc_start: 0.8079 (m) cc_final: 0.7812 (t) REVERT: B 419 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6571 (mpp) REVERT: B 495 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7700 (mp0) REVERT: B 568 THR cc_start: 0.5744 (p) cc_final: 0.5267 (p) outliers start: 82 outliers final: 59 residues processed: 383 average time/residue: 0.1502 time to fit residues: 85.8794 Evaluate side-chains 363 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS C 446 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 HIS D 446 HIS B 383 GLN B 566 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.207848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.173059 restraints weight = 23076.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.176652 restraints weight = 17797.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178114 restraints weight = 12831.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.179065 restraints weight = 9741.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179955 restraints weight = 9302.865| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18398 Z= 0.150 Angle : 0.559 9.975 24935 Z= 0.294 Chirality : 0.041 0.196 2669 Planarity : 0.004 0.045 3222 Dihedral : 5.687 59.830 2477 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.05 % Allowed : 18.63 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2212 helix: 1.83 (0.15), residues: 1142 sheet: -1.48 (0.29), residues: 311 loop : -0.64 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 236 TYR 0.029 0.002 TYR B 493 PHE 0.028 0.002 PHE A 156 TRP 0.007 0.001 TRP E 325 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00342 (18398) covalent geometry : angle 0.55899 (24935) hydrogen bonds : bond 0.04038 ( 890) hydrogen bonds : angle 4.67559 ( 2631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 338 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.7212 (t0) cc_final: 0.6999 (m-30) REVERT: A 305 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: A 425 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 480 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7668 (tp30) REVERT: C 127 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.5119 (tp30) REVERT: C 132 GLU cc_start: 0.7533 (tp30) cc_final: 0.7272 (tm-30) REVERT: C 153 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7686 (mm) REVERT: C 293 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.4790 (t80) REVERT: C 296 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 419 MET cc_start: 0.7746 (mmm) cc_final: 0.7533 (mmp) REVERT: D 195 ARG cc_start: 0.8268 (tpp80) cc_final: 0.8018 (tpp80) REVERT: D 355 VAL cc_start: 0.8326 (p) cc_final: 0.8059 (t) REVERT: D 597 ASP cc_start: 0.7882 (t0) cc_final: 0.7592 (t0) REVERT: D 614 SER cc_start: 0.8133 (m) cc_final: 0.7880 (t) REVERT: B 316 LEU cc_start: 0.8071 (mt) cc_final: 0.7752 (mp) REVERT: B 404 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8575 (tt) REVERT: B 419 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6586 (mpp) REVERT: B 495 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7623 (mp0) REVERT: B 568 THR cc_start: 0.5786 (p) cc_final: 0.5299 (p) REVERT: B 583 ILE cc_start: 0.7580 (mm) cc_final: 0.7337 (tp) outliers start: 77 outliers final: 54 residues processed: 388 average time/residue: 0.1466 time to fit residues: 84.6885 Evaluate side-chains 365 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 122 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 620 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN B 585 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.209076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173282 restraints weight = 22961.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177264 restraints weight = 16927.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179399 restraints weight = 11392.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179739 restraints weight = 8931.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180075 restraints weight = 8559.761| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18398 Z= 0.124 Angle : 0.544 9.722 24935 Z= 0.284 Chirality : 0.041 0.276 2669 Planarity : 0.003 0.048 3222 Dihedral : 5.471 59.063 2475 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.79 % Allowed : 19.11 % Favored : 77.11 % 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: 0.83 (0.18), residues: 2212 helix: 1.88 (0.15), residues: 1144 sheet: -1.45 (0.29), residues: 306 loop : -0.56 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 558 TYR 0.017 0.001 TYR C 68 PHE 0.032 0.002 PHE D 227 TRP 0.013 0.001 TRP C 182 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00284 (18398) covalent geometry : angle 0.54372 (24935) hydrogen bonds : bond 0.03772 ( 890) hydrogen bonds : angle 4.54406 ( 2631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 334 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.7231 (t0) cc_final: 0.7025 (m-30) REVERT: A 425 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 480 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7693 (tp30) REVERT: A 581 GLN cc_start: 0.7365 (tp40) cc_final: 0.7136 (tp-100) REVERT: C 94 MET cc_start: 0.8102 (mmm) cc_final: 0.7708 (mtp) REVERT: C 127 GLU cc_start: 0.5255 (OUTLIER) cc_final: 0.4972 (tp30) REVERT: C 153 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7731 (mm) REVERT: C 293 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.4793 (t80) REVERT: C 296 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7897 (mt) REVERT: C 594 ASP cc_start: 0.7602 (t0) cc_final: 0.7251 (t0) REVERT: C 597 ASP cc_start: 0.7464 (t0) cc_final: 0.7100 (m-30) REVERT: D 195 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7975 (tpp80) REVERT: D 355 VAL cc_start: 0.8217 (p) cc_final: 0.7912 (t) REVERT: D 597 ASP cc_start: 0.7845 (t0) cc_final: 0.7572 (t0) REVERT: D 614 SER cc_start: 0.8094 (m) cc_final: 0.7855 (t) REVERT: B 316 LEU cc_start: 0.8145 (mt) cc_final: 0.7842 (mp) REVERT: B 415 ASP cc_start: 0.7062 (t0) cc_final: 0.6737 (t0) REVERT: B 419 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6230 (mpp) REVERT: B 568 THR cc_start: 0.5697 (p) cc_final: 0.5218 (p) REVERT: B 583 ILE cc_start: 0.7695 (mm) cc_final: 0.7367 (tt) outliers start: 72 outliers final: 48 residues processed: 377 average time/residue: 0.1462 time to fit residues: 82.9639 Evaluate side-chains 355 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.206049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170359 restraints weight = 22964.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173548 restraints weight = 16862.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175293 restraints weight = 12657.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175931 restraints weight = 9458.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176287 restraints weight = 8842.136| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18398 Z= 0.156 Angle : 0.557 9.086 24935 Z= 0.290 Chirality : 0.041 0.188 2669 Planarity : 0.004 0.078 3222 Dihedral : 5.352 59.818 2472 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.16 % Allowed : 19.58 % Favored : 76.26 % 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: 0.81 (0.18), residues: 2212 helix: 1.87 (0.15), residues: 1139 sheet: -1.51 (0.29), residues: 321 loop : -0.52 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 555 TYR 0.019 0.002 TYR C 68 PHE 0.029 0.002 PHE E 338 TRP 0.013 0.001 TRP C 182 HIS 0.005 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00368 (18398) covalent geometry : angle 0.55653 (24935) hydrogen bonds : bond 0.03747 ( 890) hydrogen bonds : angle 4.51014 ( 2631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 319 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5688 (mmt) cc_final: 0.5334 (mmt) REVERT: A 425 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6969 (t80) REVERT: A 480 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7713 (tp30) REVERT: A 581 GLN cc_start: 0.7451 (tp40) cc_final: 0.7228 (tp-100) REVERT: C 94 MET cc_start: 0.8194 (mmm) cc_final: 0.7837 (mtp) REVERT: C 127 GLU cc_start: 0.5333 (OUTLIER) cc_final: 0.5017 (tp30) REVERT: C 153 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7725 (mm) REVERT: C 245 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: C 293 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.4918 (t80) REVERT: C 296 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7862 (mt) REVERT: C 419 MET cc_start: 0.7979 (mmm) cc_final: 0.7730 (mmp) REVERT: C 597 ASP cc_start: 0.7496 (t0) cc_final: 0.7139 (m-30) REVERT: D 195 ARG cc_start: 0.8204 (tpp80) cc_final: 0.7954 (tpp80) REVERT: D 355 VAL cc_start: 0.8239 (p) cc_final: 0.7935 (t) REVERT: D 597 ASP cc_start: 0.7882 (t0) cc_final: 0.7607 (t0) REVERT: D 614 SER cc_start: 0.8246 (m) cc_final: 0.8036 (t) REVERT: B 316 LEU cc_start: 0.8137 (mt) cc_final: 0.7839 (mp) REVERT: B 415 ASP cc_start: 0.7058 (t0) cc_final: 0.6850 (t0) REVERT: B 419 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.5891 (mpp) REVERT: B 527 ILE cc_start: 0.3678 (OUTLIER) cc_final: 0.3361 (mt) REVERT: B 568 THR cc_start: 0.5778 (p) cc_final: 0.5313 (p) REVERT: B 583 ILE cc_start: 0.7655 (mm) cc_final: 0.7390 (tt) outliers start: 79 outliers final: 53 residues processed: 369 average time/residue: 0.1395 time to fit residues: 77.7070 Evaluate side-chains 353 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain B residue 527 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 109 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 209 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.203782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168179 restraints weight = 23035.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171282 restraints weight = 17428.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172963 restraints weight = 13364.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173407 restraints weight = 9761.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174127 restraints weight = 9446.769| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18398 Z= 0.173 Angle : 0.582 13.066 24935 Z= 0.303 Chirality : 0.043 0.399 2669 Planarity : 0.004 0.051 3222 Dihedral : 5.271 58.315 2470 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.05 % Allowed : 19.37 % Favored : 76.58 % 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: 0.67 (0.18), residues: 2212 helix: 1.76 (0.15), residues: 1153 sheet: -1.70 (0.29), residues: 324 loop : -0.55 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 211 TYR 0.021 0.002 TYR A 493 PHE 0.030 0.002 PHE B 307 TRP 0.015 0.001 TRP C 182 HIS 0.005 0.001 HIS D 446 Details of bonding type rmsd covalent geometry : bond 0.00409 (18398) covalent geometry : angle 0.58150 (24935) hydrogen bonds : bond 0.03763 ( 890) hydrogen bonds : angle 4.55707 ( 2631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 299 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5711 (mmt) cc_final: 0.5202 (mmt) REVERT: A 106 TRP cc_start: 0.8158 (t60) cc_final: 0.7910 (t60) REVERT: A 425 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 480 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7710 (tp30) REVERT: A 581 GLN cc_start: 0.7523 (tp40) cc_final: 0.7303 (tp-100) REVERT: C 94 MET cc_start: 0.8297 (mmm) cc_final: 0.7921 (mtp) REVERT: C 127 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.5003 (tp30) REVERT: C 153 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7734 (mm) REVERT: C 245 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: C 293 PHE cc_start: 0.6010 (OUTLIER) cc_final: 0.5075 (t80) REVERT: C 296 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7871 (mt) REVERT: C 419 MET cc_start: 0.8061 (mmm) cc_final: 0.7790 (mmp) REVERT: D 147 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8037 (mm-30) REVERT: D 195 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7922 (tpp80) REVERT: D 355 VAL cc_start: 0.8247 (p) cc_final: 0.7961 (t) REVERT: D 405 TYR cc_start: 0.8185 (t80) cc_final: 0.7979 (t80) REVERT: D 597 ASP cc_start: 0.7931 (t0) cc_final: 0.7651 (t0) REVERT: B 316 LEU cc_start: 0.8155 (mt) cc_final: 0.7858 (mp) REVERT: B 366 PHE cc_start: 0.7324 (m-80) cc_final: 0.6806 (m-10) REVERT: B 415 ASP cc_start: 0.7023 (t0) cc_final: 0.6799 (t0) REVERT: B 419 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6177 (mpp) REVERT: B 568 THR cc_start: 0.5881 (p) cc_final: 0.5423 (p) REVERT: B 583 ILE cc_start: 0.7573 (mm) cc_final: 0.7303 (tt) outliers start: 77 outliers final: 60 residues processed: 351 average time/residue: 0.1403 time to fit residues: 74.9525 Evaluate side-chains 347 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 280 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168763 restraints weight = 22914.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172200 restraints weight = 17292.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174129 restraints weight = 12404.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.174563 restraints weight = 9353.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175239 restraints weight = 9142.136| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18398 Z= 0.138 Angle : 0.558 10.291 24935 Z= 0.291 Chirality : 0.042 0.367 2669 Planarity : 0.004 0.052 3222 Dihedral : 5.225 58.199 2470 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.26 % Allowed : 20.79 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2212 helix: 1.83 (0.15), residues: 1153 sheet: -1.73 (0.29), residues: 324 loop : -0.53 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 303 TYR 0.021 0.001 TYR C 68 PHE 0.023 0.002 PHE E 338 TRP 0.013 0.001 TRP C 182 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00323 (18398) covalent geometry : angle 0.55751 (24935) hydrogen bonds : bond 0.03583 ( 890) hydrogen bonds : angle 4.51392 ( 2631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5751 (mmt) cc_final: 0.5248 (mmt) REVERT: A 425 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 480 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7668 (tp30) REVERT: C 94 MET cc_start: 0.8312 (mmm) cc_final: 0.7989 (mtp) REVERT: C 127 GLU cc_start: 0.5153 (OUTLIER) cc_final: 0.4850 (tp30) REVERT: C 153 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7720 (mm) REVERT: C 245 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7424 (tp30) REVERT: C 419 MET cc_start: 0.8056 (mmm) cc_final: 0.7834 (mmp) REVERT: D 147 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8058 (mm-30) REVERT: D 195 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7874 (tpp80) REVERT: D 355 VAL cc_start: 0.8251 (p) cc_final: 0.7979 (t) REVERT: D 597 ASP cc_start: 0.7934 (t0) cc_final: 0.7679 (t0) REVERT: B 316 LEU cc_start: 0.8212 (mt) cc_final: 0.7927 (mp) REVERT: B 419 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6278 (mpp) REVERT: B 568 THR cc_start: 0.5898 (p) cc_final: 0.5458 (p) outliers start: 62 outliers final: 48 residues processed: 330 average time/residue: 0.1435 time to fit residues: 71.5204 Evaluate side-chains 324 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 577 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 42 optimal weight: 0.0030 chunk 197 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN B 566 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.200591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165192 restraints weight = 22989.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167738 restraints weight = 17653.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.169475 restraints weight = 13803.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169846 restraints weight = 10188.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170418 restraints weight = 9920.078| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18398 Z= 0.199 Angle : 0.610 10.572 24935 Z= 0.316 Chirality : 0.043 0.254 2669 Planarity : 0.004 0.054 3222 Dihedral : 5.274 56.930 2470 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.74 % Allowed : 20.63 % Favored : 75.63 % 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: 0.53 (0.18), residues: 2212 helix: 1.67 (0.15), residues: 1153 sheet: -1.99 (0.29), residues: 312 loop : -0.59 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 303 TYR 0.024 0.002 TYR C 68 PHE 0.024 0.002 PHE E 338 TRP 0.024 0.001 TRP A 134 HIS 0.006 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00475 (18398) covalent geometry : angle 0.61023 (24935) hydrogen bonds : bond 0.03799 ( 890) hydrogen bonds : angle 4.60746 ( 2631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5829 (mmt) cc_final: 0.5316 (mmt) REVERT: A 425 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.7023 (t80) REVERT: C 94 MET cc_start: 0.8387 (mmm) cc_final: 0.8112 (mtp) REVERT: C 127 GLU cc_start: 0.5336 (OUTLIER) cc_final: 0.4995 (tp30) REVERT: C 245 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: C 293 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5274 (t80) REVERT: C 419 MET cc_start: 0.8143 (mmm) cc_final: 0.7853 (mmp) REVERT: D 195 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7870 (tpp80) REVERT: D 277 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8729 (m) REVERT: D 355 VAL cc_start: 0.8324 (p) cc_final: 0.8066 (t) REVERT: D 524 ILE cc_start: 0.9173 (mm) cc_final: 0.8868 (mm) REVERT: D 531 LEU cc_start: 0.9366 (mt) cc_final: 0.9126 (mt) REVERT: D 597 ASP cc_start: 0.8053 (t0) cc_final: 0.7778 (t0) REVERT: B 415 ASP cc_start: 0.6878 (t0) cc_final: 0.6411 (t0) REVERT: B 419 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6417 (mpp) REVERT: B 538 MET cc_start: 0.6444 (tpt) cc_final: 0.6221 (tpt) REVERT: B 568 THR cc_start: 0.5995 (p) cc_final: 0.5569 (p) outliers start: 71 outliers final: 59 residues processed: 334 average time/residue: 0.1351 time to fit residues: 68.8139 Evaluate side-chains 331 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 577 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 28 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.203827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168781 restraints weight = 22906.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171204 restraints weight = 17731.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173288 restraints weight = 13692.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173665 restraints weight = 10403.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175041 restraints weight = 9836.878| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18398 Z= 0.138 Angle : 0.567 10.263 24935 Z= 0.297 Chirality : 0.041 0.292 2669 Planarity : 0.004 0.054 3222 Dihedral : 5.254 57.065 2470 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.11 % Allowed : 21.84 % Favored : 75.05 % 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 (0.18), residues: 2212 helix: 1.73 (0.15), residues: 1156 sheet: -1.90 (0.29), residues: 309 loop : -0.63 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 211 TYR 0.025 0.001 TYR C 68 PHE 0.023 0.002 PHE E 338 TRP 0.029 0.001 TRP B 512 HIS 0.006 0.001 HIS C 620 Details of bonding type rmsd covalent geometry : bond 0.00324 (18398) covalent geometry : angle 0.56691 (24935) hydrogen bonds : bond 0.03554 ( 890) hydrogen bonds : angle 4.52994 ( 2631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5813 (mmt) cc_final: 0.5241 (mmt) REVERT: A 425 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.7050 (t80) REVERT: A 489 LEU cc_start: 0.6614 (mp) cc_final: 0.6348 (tp) REVERT: C 127 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4728 (tp30) REVERT: C 153 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7708 (mm) REVERT: C 245 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: C 293 PHE cc_start: 0.5810 (OUTLIER) cc_final: 0.5001 (t80) REVERT: C 590 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7400 (mt-10) REVERT: D 195 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7823 (tpp80) REVERT: D 277 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8672 (m) REVERT: D 290 MET cc_start: 0.3971 (pmm) cc_final: 0.2695 (ptp) REVERT: D 524 ILE cc_start: 0.9154 (mm) cc_final: 0.8808 (mm) REVERT: D 597 ASP cc_start: 0.8016 (t0) cc_final: 0.7742 (t0) REVERT: B 415 ASP cc_start: 0.6921 (t0) cc_final: 0.6517 (t0) REVERT: B 419 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6461 (mpp) REVERT: B 568 THR cc_start: 0.5971 (p) cc_final: 0.5556 (p) outliers start: 59 outliers final: 45 residues processed: 321 average time/residue: 0.1454 time to fit residues: 70.4179 Evaluate side-chains 320 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 509 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 74 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.203670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168670 restraints weight = 23090.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.171330 restraints weight = 18039.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.173529 restraints weight = 13546.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.173973 restraints weight = 10288.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175166 restraints weight = 9361.869| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18398 Z= 0.131 Angle : 0.574 15.201 24935 Z= 0.296 Chirality : 0.041 0.369 2669 Planarity : 0.004 0.054 3222 Dihedral : 4.995 56.945 2467 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 22.53 % Favored : 74.63 % 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: 0.65 (0.18), residues: 2212 helix: 1.78 (0.15), residues: 1156 sheet: -1.88 (0.29), residues: 309 loop : -0.58 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 211 TYR 0.023 0.001 TYR C 68 PHE 0.024 0.002 PHE E 338 TRP 0.025 0.001 TRP A 134 HIS 0.007 0.001 HIS C 620 Details of bonding type rmsd covalent geometry : bond 0.00304 (18398) covalent geometry : angle 0.57423 (24935) hydrogen bonds : bond 0.03497 ( 890) hydrogen bonds : angle 4.48545 ( 2631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.82 seconds wall clock time: 53 minutes 34.12 seconds (3214.12 seconds total)