Starting phenix.real_space_refine on Thu Aug 6 19:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.map" model { file = "/net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it0_35702/08_2026/8it0_35702.cif" } resolution = 3.5 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= 0.001 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 46 5.16 5 C 10602 2.51 5 N 2836 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16922 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNAv2': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNAv2': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Time building chain proxies: 3.07, per 1000 atoms: 0.18 Number of scatterers: 16922 At special positions: 0 Unit cell: (173.68, 107.12, 142.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 90 15.00 O 3348 8.00 N 2836 7.00 C 10602 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: 1.46 Conformation dependent library (CDL) restraints added in 571.8 milliseconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 38.7% alpha, 11.4% beta 2 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.547A pdb=" N ARG A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.615A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.521A pdb=" N TYR A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.751A pdb=" N THR A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.560A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.564A pdb=" N TRP A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.749A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 removed outlier: 3.753A pdb=" N ARG B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 21 " --> pdb=" O PHE B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 46 through 56 removed outlier: 4.184A pdb=" N ARG B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.919A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.854A pdb=" N VAL B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 114' Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.742A pdb=" N GLN B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.584A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.554A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 238 " --> pdb=" O GLY B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 258 through 280 Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.871A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.829A pdb=" N TRP B 373 " --> pdb=" O TRP B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.784A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.062A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 removed outlier: 3.535A pdb=" N PHE E 30 " --> pdb=" O GLY E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 105 removed outlier: 4.222A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.512A pdb=" N ASP E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 205 through 214 removed outlier: 3.845A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.828A pdb=" N THR E 218 " --> pdb=" O LEU E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 263 removed outlier: 3.740A pdb=" N LEU E 252 " --> pdb=" O ILE E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 326 removed outlier: 3.614A pdb=" N GLY E 326 " --> pdb=" O PRO E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 351 Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.652A pdb=" N GLU E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 377 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.777A pdb=" N ALA E 483 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS E 485 " --> pdb=" O ARG E 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.577A pdb=" N LEU F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.302A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 removed outlier: 3.608A pdb=" N ALA F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.527A pdb=" N THR F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 231' Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.608A pdb=" N GLU F 237 " --> pdb=" O ASN F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.736A pdb=" N ILE F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 280 Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.721A pdb=" N ASP F 303 " --> pdb=" O LEU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 366 removed outlier: 3.910A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS F 366 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'F' and resid 421 through 438 removed outlier: 4.293A pdb=" N GLU F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 438 " --> pdb=" O ASN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.911A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.687A pdb=" N LYS A 94 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 45 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.606A pdb=" N PHE A 304 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 280 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 447 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A 443 " --> pdb=" O THR A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 3.535A pdb=" N GLY A 318 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 removed outlier: 3.602A pdb=" N ASP B 172 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.968A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.134A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE B 95 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE B 60 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 62 " --> pdb=" O LEU B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 328 removed outlier: 3.527A pdb=" N LEU B 402 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'E' and resid 92 through 94 removed outlier: 3.774A pdb=" N VAL E 92 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 301 through 302 removed outlier: 6.424A pdb=" N VAL E 357 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL E 386 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 359 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 388 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 361 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 444 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 420 " --> pdb=" O ILE E 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 397 through 398 Processing sheet with id=AB6, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.792A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.286A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS F 4 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS F 59 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 318 through 328 removed outlier: 3.526A pdb=" N MET F 336 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 404 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE F 403 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 186 through 189 Processing sheet with id=AC1, first strand: chain 'F' and resid 283 through 284 522 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3470 1.33 - 1.45: 4465 1.45 - 1.57: 9334 1.57 - 1.69: 177 1.69 - 1.81: 70 Bond restraints: 17516 Sorted by residual: bond pdb=" C3' DC D 43 " pdb=" C2' DC D 43 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" N ILE B 308 " pdb=" CA ILE B 308 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.28e-02 6.10e+03 9.76e+00 bond pdb=" C3' DC H 40 " pdb=" C2' DC H 40 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.49e+00 bond pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta sigma weight residual 1.462 1.491 -0.029 9.50e-03 1.11e+04 9.46e+00 bond pdb=" N GLU B 13 " pdb=" CA GLU B 13 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.20e+00 ... (remaining 17511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 23169 2.49 - 4.99: 742 4.99 - 7.48: 127 7.48 - 9.98: 33 9.98 - 12.47: 9 Bond angle restraints: 24080 Sorted by residual: angle pdb=" C3' DC D 33 " pdb=" O3' DC D 33 " pdb=" P DC D 34 " ideal model delta sigma weight residual 119.70 127.79 -8.09 1.20e+00 6.94e-01 4.54e+01 angle pdb=" O4' DC D 34 " pdb=" C4' DC D 34 " pdb=" C3' DC D 34 " ideal model delta sigma weight residual 106.00 102.35 3.65 6.00e-01 2.78e+00 3.71e+01 angle pdb=" C GLN B 314 " pdb=" N LYS B 315 " pdb=" CA LYS B 315 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.28e+01 angle pdb=" N ILE E 52 " pdb=" CA ILE E 52 " pdb=" C ILE E 52 " ideal model delta sigma weight residual 110.72 105.22 5.50 1.01e+00 9.80e-01 2.97e+01 angle pdb=" CA ARG B 209 " pdb=" CB ARG B 209 " pdb=" CG ARG B 209 " ideal model delta sigma weight residual 114.10 124.98 -10.88 2.00e+00 2.50e-01 2.96e+01 ... (remaining 24075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 8876 22.18 - 44.37: 1003 44.37 - 66.55: 381 66.55 - 88.73: 67 88.73 - 110.92: 1 Dihedral angle restraints: 10328 sinusoidal: 4938 harmonic: 5390 Sorted by residual: dihedral pdb=" C4' G G 2 " pdb=" C3' G G 2 " pdb=" C2' G G 2 " pdb=" C1' G G 2 " ideal model delta sinusoidal sigma weight residual 36.34 -47.12 83.46 1 3.10e+00 1.04e-01 8.85e+02 dihedral pdb=" C4' A G 10 " pdb=" C3' A G 10 " pdb=" C2' A G 10 " pdb=" C1' A G 10 " ideal model delta sinusoidal sigma weight residual 36.35 -44.38 80.73 1 3.10e+00 1.04e-01 8.38e+02 dihedral pdb=" C4' G C 8 " pdb=" C3' G C 8 " pdb=" C2' G C 8 " pdb=" C1' G C 8 " ideal model delta sinusoidal sigma weight residual 36.35 -42.76 79.11 1 3.10e+00 1.04e-01 8.10e+02 ... (remaining 10325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2476 0.143 - 0.285: 119 0.285 - 0.428: 38 0.428 - 0.570: 2 0.570 - 0.713: 3 Chirality restraints: 2638 Sorted by residual: chirality pdb=" P A G 10 " pdb=" OP1 A G 10 " pdb=" OP2 A G 10 " pdb=" O5' A G 10 " both_signs ideal model delta sigma weight residual True 2.17 -2.89 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" P G C 12 " pdb=" OP1 G C 12 " pdb=" OP2 G C 12 " pdb=" O5' G C 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.83 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P G G 2 " pdb=" OP1 G G 2 " pdb=" OP2 G G 2 " pdb=" O5' G G 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.81 -0.63 2.00e-01 2.50e+01 9.98e+00 ... (remaining 2635 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 320 " 0.021 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP A 320 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 320 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 320 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 320 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 320 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 320 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 320 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 384 " -0.017 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU F 384 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU F 384 " -0.025 2.00e-02 2.50e+03 pdb=" N SER F 385 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 67 " -0.018 2.00e-02 2.50e+03 2.61e-02 1.02e+01 pdb=" CG HIS E 67 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS E 67 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS E 67 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS E 67 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 67 " 0.002 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1932 2.75 - 3.29: 16125 3.29 - 3.83: 28468 3.83 - 4.36: 32298 4.36 - 4.90: 53319 Nonbonded interactions: 132142 Sorted by model distance: nonbonded pdb=" O PHE A 373 " pdb=" OG1 THR A 377 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 233 " pdb=" OG SER B 238 " model vdw 2.221 3.040 nonbonded pdb=" O2 DT D 26 " pdb=" N2 G C 20 " model vdw 2.228 2.496 nonbonded pdb=" OG1 THR A 387 " pdb=" OE1 GLU A 444 " model vdw 2.236 3.040 nonbonded pdb=" O TYR A 321 " pdb=" OD1 ASN A 322 " model vdw 2.267 3.040 ... (remaining 132137 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.550 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 : 0.005 0.066 17516 Z= 0.302 Angle : 1.060 12.471 24080 Z= 0.593 Chirality : 0.083 0.713 2638 Planarity : 0.006 0.064 2744 Dihedral : 20.632 110.918 6844 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.12 % Allowed : 18.90 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.18), residues: 1818 helix: -1.16 (0.18), residues: 614 sheet: -0.92 (0.34), residues: 225 loop : -2.38 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 407 TYR 0.037 0.002 TYR B 233 PHE 0.032 0.002 PHE F 187 TRP 0.065 0.003 TRP A 320 HIS 0.034 0.002 HIS E 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.30 (17516) covalent geometry : angle 1.05978 / 0.59 (24080) hydrogen bonds : bond 0.18646 / 11.91 ( 526) hydrogen bonds : angle 7.96340 / 5.64 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.6939 (tpt) cc_final: 0.6707 (tpt) REVERT: F 414 MET cc_start: 0.5948 (ptt) cc_final: 0.4422 (ptt) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.1316 time to fit residues: 21.7305 Evaluate side-chains 59 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 1.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 341 GLN B 262 GLN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN F 357 GLN F 434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.050365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043380 restraints weight = 172747.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.044042 restraints weight = 113927.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044493 restraints weight = 83139.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044813 restraints weight = 66289.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045036 restraints weight = 55987.468| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17516 Z= 0.244 Angle : 1.450 30.369 24080 Z= 0.615 Chirality : 0.148 1.708 2638 Planarity : 0.005 0.057 2744 Dihedral : 20.720 151.113 3034 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.83 % Allowed : 17.32 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.18), residues: 1818 helix: -0.56 (0.19), residues: 629 sheet: -0.77 (0.33), residues: 242 loop : -2.25 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 209 TYR 0.015 0.001 TYR E 56 PHE 0.028 0.001 PHE E 482 TRP 0.017 0.001 TRP B 192 HIS 0.005 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (17516) covalent geometry : angle 1.45027 / 0.62 (24080) hydrogen bonds : bond 0.05017 / 3.09 ( 526) hydrogen bonds : angle 6.23359 / 4.41 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.9271 (ptt) cc_final: 0.9032 (ptt) REVERT: B 92 MET cc_start: 0.8957 (tpp) cc_final: 0.8722 (tpp) REVERT: B 393 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9326 (mm) REVERT: E 1 MET cc_start: 0.8317 (tpt) cc_final: 0.7747 (tpt) REVERT: E 71 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.7022 (p) REVERT: E 96 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8820 (mm) REVERT: F 75 LEU cc_start: 0.9550 (tt) cc_final: 0.9346 (tt) REVERT: F 287 MET cc_start: 0.8869 (tpt) cc_final: 0.8567 (tpt) REVERT: F 336 MET cc_start: 0.8665 (tpp) cc_final: 0.8447 (tpp) outliers start: 30 outliers final: 9 residues processed: 95 average time/residue: 0.1119 time to fit residues: 16.8943 Evaluate side-chains 67 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 356 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 176 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 181 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 322 ASN ** E 302 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 = 0.3210 r_free = 0.3210 target = 0.048086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041207 restraints weight = 178526.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041831 restraints weight = 117071.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042261 restraints weight = 86003.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.042547 restraints weight = 68725.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.042758 restraints weight = 58536.643| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17516 Z= 0.206 Angle : 1.020 20.122 24080 Z= 0.459 Chirality : 0.091 1.419 2638 Planarity : 0.005 0.051 2744 Dihedral : 20.327 171.372 3034 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.38 % Allowed : 16.95 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 1818 helix: -0.25 (0.20), residues: 631 sheet: -0.67 (0.34), residues: 237 loop : -1.96 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 186 TYR 0.017 0.001 TYR A 285 PHE 0.009 0.001 PHE A 419 TRP 0.012 0.001 TRP B 192 HIS 0.004 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (17516) covalent geometry : angle 1.01963 / 0.46 (24080) hydrogen bonds : bond 0.04003 / 2.50 ( 526) hydrogen bonds : angle 5.72635 / 4.03 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6827 (m-80) cc_final: 0.6289 (m-80) REVERT: A 435 MET cc_start: 0.8813 (tpp) cc_final: 0.8062 (tmm) REVERT: B 1 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8005 (mmp) REVERT: B 230 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8329 (p) REVERT: B 393 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9363 (mm) REVERT: E 1 MET cc_start: 0.8432 (tpt) cc_final: 0.7888 (tpt) REVERT: E 71 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7175 (p) REVERT: E 96 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8902 (mm) REVERT: F 287 MET cc_start: 0.8910 (tpt) cc_final: 0.8491 (tpt) REVERT: F 336 MET cc_start: 0.8695 (tpp) cc_final: 0.7208 (tpp) outliers start: 39 outliers final: 14 residues processed: 93 average time/residue: 0.1186 time to fit residues: 17.2538 Evaluate side-chains 71 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 181 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 147 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN E 90 ASN ** E 302 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 = 0.3174 r_free = 0.3174 target = 0.046714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039833 restraints weight = 177130.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.040439 restraints weight = 117576.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.040866 restraints weight = 86595.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.041159 restraints weight = 69416.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041358 restraints weight = 59069.151| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17516 Z= 0.193 Angle : 0.874 17.454 24080 Z= 0.408 Chirality : 0.073 1.044 2638 Planarity : 0.004 0.053 2744 Dihedral : 20.270 177.899 3034 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.01 % Allowed : 17.38 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.47 (0.19), residues: 1818 helix: -0.02 (0.20), residues: 633 sheet: -0.64 (0.35), residues: 232 loop : -1.75 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 362 TYR 0.011 0.001 TYR A 346 PHE 0.012 0.001 PHE B 217 TRP 0.013 0.001 TRP F 33 HIS 0.003 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (17516) covalent geometry : angle 0.87397 / 0.41 (24080) hydrogen bonds : bond 0.03580 / 2.28 ( 526) hydrogen bonds : angle 5.45780 / 3.83 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8816 (tpp) cc_final: 0.8130 (tmm) REVERT: B 1 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8006 (mmp) REVERT: B 92 MET cc_start: 0.9019 (tpp) cc_final: 0.8726 (tpp) REVERT: B 230 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8427 (p) REVERT: B 393 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9360 (mm) REVERT: E 1 MET cc_start: 0.8533 (tpt) cc_final: 0.8200 (tpt) REVERT: E 71 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7456 (p) REVERT: E 96 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8980 (mm) REVERT: E 485 LYS cc_start: 0.9569 (ptpp) cc_final: 0.9358 (pttm) REVERT: F 287 MET cc_start: 0.9001 (tpt) cc_final: 0.8459 (tpt) REVERT: F 336 MET cc_start: 0.8495 (tpp) cc_final: 0.8112 (tpp) REVERT: F 345 MET cc_start: 0.9038 (tmm) cc_final: 0.8709 (tmm) outliers start: 33 outliers final: 14 residues processed: 83 average time/residue: 0.1119 time to fit residues: 14.8963 Evaluate side-chains 69 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038096 restraints weight = 182793.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038660 restraints weight = 122011.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039042 restraints weight = 90064.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039217 restraints weight = 72929.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039480 restraints weight = 64642.803| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 17516 Z= 0.281 Angle : 0.870 17.459 24080 Z= 0.421 Chirality : 0.069 1.025 2638 Planarity : 0.005 0.053 2744 Dihedral : 20.244 179.734 3034 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.20 % Allowed : 16.65 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.44 (0.19), residues: 1818 helix: 0.03 (0.20), residues: 632 sheet: -0.86 (0.34), residues: 240 loop : -1.70 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 243 TYR 0.023 0.002 TYR A 285 PHE 0.014 0.002 PHE B 217 TRP 0.017 0.002 TRP F 33 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 (17516) covalent geometry : angle 0.86994 / 0.42 (24080) hydrogen bonds : bond 0.03808 / 2.48 ( 526) hydrogen bonds : angle 5.56172 / 3.90 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9473 (OUTLIER) cc_final: 0.9256 (pp20) REVERT: A 435 MET cc_start: 0.8784 (tpp) cc_final: 0.8377 (tmm) REVERT: A 491 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9294 (p) REVERT: B 92 MET cc_start: 0.9029 (tpp) cc_final: 0.8773 (tpp) REVERT: B 230 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 393 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9390 (mm) REVERT: E 1 MET cc_start: 0.8638 (tpt) cc_final: 0.8412 (tpt) REVERT: E 71 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7871 (p) REVERT: E 96 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9042 (mm) REVERT: E 205 GLN cc_start: 0.8804 (pm20) cc_final: 0.8484 (pm20) REVERT: E 485 LYS cc_start: 0.9555 (ptpp) cc_final: 0.9301 (ptpp) REVERT: F 287 MET cc_start: 0.9130 (tpt) cc_final: 0.8550 (tpt) REVERT: F 336 MET cc_start: 0.8724 (tpp) cc_final: 0.8450 (tpp) REVERT: F 345 MET cc_start: 0.9081 (tmm) cc_final: 0.8847 (tmm) REVERT: F 414 MET cc_start: 0.8677 (ppp) cc_final: 0.8257 (ptp) outliers start: 36 outliers final: 18 residues processed: 77 average time/residue: 0.1297 time to fit residues: 16.0541 Evaluate side-chains 70 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 121 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 0.0170 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 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 = 0.3129 r_free = 0.3129 target = 0.045488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.038696 restraints weight = 180472.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039259 restraints weight = 120258.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039671 restraints weight = 89413.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.039960 restraints weight = 71987.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.040171 restraints weight = 61401.362| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17516 Z= 0.174 Angle : 0.790 16.345 24080 Z= 0.378 Chirality : 0.067 0.963 2638 Planarity : 0.004 0.043 2744 Dihedral : 20.131 178.834 3034 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.65 % Allowed : 17.68 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.33 (0.20), residues: 1818 helix: 0.12 (0.20), residues: 634 sheet: -0.83 (0.34), residues: 241 loop : -1.62 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.015 0.001 TYR B 293 PHE 0.013 0.001 PHE B 217 TRP 0.010 0.001 TRP F 20 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (17516) covalent geometry : angle 0.79047 / 0.38 (24080) hydrogen bonds : bond 0.03457 / 2.21 ( 526) hydrogen bonds : angle 5.38547 / 3.77 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 18 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: A 435 MET cc_start: 0.8796 (tpp) cc_final: 0.8413 (tmm) REVERT: A 491 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9287 (p) REVERT: B 92 MET cc_start: 0.8942 (tpp) cc_final: 0.8721 (tpp) REVERT: B 230 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8560 (p) REVERT: E 1 MET cc_start: 0.8661 (tpt) cc_final: 0.8459 (tpt) REVERT: E 71 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7616 (p) REVERT: E 96 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9046 (mm) REVERT: E 205 GLN cc_start: 0.8748 (pm20) cc_final: 0.8428 (pm20) REVERT: E 485 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9225 (ptpp) REVERT: F 287 MET cc_start: 0.8989 (tpt) cc_final: 0.8493 (tpt) REVERT: F 336 MET cc_start: 0.9005 (tpp) cc_final: 0.8493 (tpp) REVERT: F 345 MET cc_start: 0.9113 (tmm) cc_final: 0.8848 (tmm) REVERT: F 414 MET cc_start: 0.8721 (ppp) cc_final: 0.8335 (ptp) outliers start: 27 outliers final: 14 residues processed: 71 average time/residue: 0.1251 time to fit residues: 14.3191 Evaluate side-chains 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 38 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 0.0040 chunk 60 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 overall best weight: 3.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.038649 restraints weight = 177019.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039228 restraints weight = 118936.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039609 restraints weight = 88129.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039890 restraints weight = 71521.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040067 restraints weight = 61317.683| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17516 Z= 0.171 Angle : 0.773 15.674 24080 Z= 0.372 Chirality : 0.065 0.898 2638 Planarity : 0.004 0.044 2744 Dihedral : 20.076 179.323 3034 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.65 % Allowed : 17.80 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.30 (0.20), residues: 1818 helix: 0.21 (0.20), residues: 630 sheet: -0.90 (0.34), residues: 239 loop : -1.61 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.014 0.001 TYR B 293 PHE 0.013 0.001 PHE B 217 TRP 0.009 0.001 TRP B 20 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (17516) covalent geometry : angle 0.77306 / 0.37 (24080) hydrogen bonds : bond 0.03410 / 2.17 ( 526) hydrogen bonds : angle 5.29161 / 3.70 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8779 (tpp) cc_final: 0.8432 (tmm) REVERT: A 491 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9306 (p) REVERT: B 92 MET cc_start: 0.8932 (tpp) cc_final: 0.8597 (tpp) REVERT: B 230 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8557 (p) REVERT: E 71 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7718 (p) REVERT: E 96 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9049 (mm) REVERT: E 205 GLN cc_start: 0.8765 (pm20) cc_final: 0.8437 (pm20) REVERT: E 485 LYS cc_start: 0.9476 (ptpp) cc_final: 0.9203 (ptpp) REVERT: F 287 MET cc_start: 0.8854 (tpt) cc_final: 0.8470 (tpt) REVERT: F 336 MET cc_start: 0.9019 (tpp) cc_final: 0.8487 (tpp) REVERT: F 345 MET cc_start: 0.9129 (tmm) cc_final: 0.8844 (tmm) REVERT: F 414 MET cc_start: 0.8760 (ppp) cc_final: 0.8417 (ptp) outliers start: 27 outliers final: 17 residues processed: 72 average time/residue: 0.1159 time to fit residues: 13.7387 Evaluate side-chains 68 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 45 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.042343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035617 restraints weight = 184028.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.036195 restraints weight = 121095.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036588 restraints weight = 88691.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.036866 restraints weight = 71373.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.037027 restraints weight = 60909.011| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17516 Z= 0.255 Angle : 0.825 15.056 24080 Z= 0.405 Chirality : 0.065 0.847 2638 Planarity : 0.005 0.052 2744 Dihedral : 20.206 178.598 3034 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.95 % Allowed : 17.50 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.35 (0.19), residues: 1818 helix: 0.14 (0.20), residues: 633 sheet: -0.95 (0.35), residues: 230 loop : -1.61 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 243 TYR 0.024 0.002 TYR A 6 PHE 0.019 0.002 PHE B 217 TRP 0.013 0.002 TRP F 33 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (17516) covalent geometry : angle 0.82500 / 0.40 (24080) hydrogen bonds : bond 0.03803 / 2.46 ( 526) hydrogen bonds : angle 5.47537 / 3.83 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8805 (tpp) cc_final: 0.8303 (tmm) REVERT: A 491 THR cc_start: 0.9608 (OUTLIER) cc_final: 0.9322 (p) REVERT: B 230 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8640 (m) REVERT: E 71 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8064 (p) REVERT: E 96 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9113 (mm) REVERT: E 406 MET cc_start: 0.9325 (pp-130) cc_final: 0.8956 (ppp) REVERT: F 336 MET cc_start: 0.9089 (tpp) cc_final: 0.8564 (tpp) REVERT: F 345 MET cc_start: 0.9196 (tmm) cc_final: 0.8901 (tmm) REVERT: F 414 MET cc_start: 0.8758 (ppp) cc_final: 0.8401 (ptp) outliers start: 32 outliers final: 19 residues processed: 74 average time/residue: 0.1179 time to fit residues: 14.1854 Evaluate side-chains 65 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 165 optimal weight: 0.0050 chunk 182 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.0060 chunk 36 optimal weight: 0.0970 chunk 157 optimal weight: 3.9990 chunk 14 optimal weight: 0.0670 chunk 64 optimal weight: 7.9990 overall best weight: 0.1746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 302 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 = 0.3151 r_free = 0.3151 target = 0.045722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038913 restraints weight = 175216.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039496 restraints weight = 117857.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039900 restraints weight = 87540.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.040081 restraints weight = 70654.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040358 restraints weight = 62591.603| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17516 Z= 0.141 Angle : 0.766 13.869 24080 Z= 0.372 Chirality : 0.064 0.879 2638 Planarity : 0.004 0.043 2744 Dihedral : 20.046 176.512 3034 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.28 % Allowed : 18.17 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.18 (0.20), residues: 1818 helix: 0.25 (0.20), residues: 634 sheet: -0.71 (0.35), residues: 231 loop : -1.53 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 186 TYR 0.018 0.001 TYR B 293 PHE 0.014 0.001 PHE B 217 TRP 0.017 0.001 TRP B 373 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (17516) covalent geometry : angle 0.76630 / 0.37 (24080) hydrogen bonds : bond 0.03392 / 2.09 ( 526) hydrogen bonds : angle 5.20089 / 3.63 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.502 Fit side-chains REVERT: A 8 GLU cc_start: 0.8948 (pp20) cc_final: 0.8675 (pp20) REVERT: B 230 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8585 (m) REVERT: B 287 MET cc_start: 0.8892 (ptp) cc_final: 0.8387 (ptp) REVERT: E 71 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7674 (p) REVERT: E 205 GLN cc_start: 0.8693 (pm20) cc_final: 0.8318 (pm20) REVERT: E 406 MET cc_start: 0.9281 (pp-130) cc_final: 0.8903 (ppp) REVERT: F 287 MET cc_start: 0.8745 (tpt) cc_final: 0.8505 (tpt) REVERT: F 336 MET cc_start: 0.9098 (tpp) cc_final: 0.8592 (tpp) REVERT: F 345 MET cc_start: 0.9184 (tmm) cc_final: 0.8895 (tmm) REVERT: F 414 MET cc_start: 0.8747 (ppp) cc_final: 0.8496 (ptp) outliers start: 21 outliers final: 12 residues processed: 73 average time/residue: 0.1124 time to fit residues: 13.0791 Evaluate side-chains 65 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 19 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 302 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 = 0.3116 r_free = 0.3116 target = 0.043672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036889 restraints weight = 179801.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.037472 restraints weight = 121009.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037870 restraints weight = 89125.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038161 restraints weight = 71648.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038362 restraints weight = 60936.159| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17516 Z= 0.182 Angle : 0.762 13.609 24080 Z= 0.369 Chirality : 0.062 0.760 2638 Planarity : 0.004 0.048 2744 Dihedral : 20.079 176.885 3034 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.98 % Allowed : 18.60 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.15 (0.20), residues: 1818 helix: 0.32 (0.20), residues: 633 sheet: -0.76 (0.34), residues: 235 loop : -1.54 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 362 TYR 0.019 0.001 TYR E 285 PHE 0.014 0.001 PHE B 217 TRP 0.010 0.001 TRP A 254 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (17516) covalent geometry : angle 0.76194 / 0.37 (24080) hydrogen bonds : bond 0.03395 / 2.16 ( 526) hydrogen bonds : angle 5.21887 / 3.64 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.622 Fit side-chains REVERT: A 18 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7660 (pp30) REVERT: A 491 THR cc_start: 0.9646 (OUTLIER) cc_final: 0.9368 (p) REVERT: B 230 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8636 (m) REVERT: E 71 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7790 (p) REVERT: E 96 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9070 (mm) REVERT: E 406 MET cc_start: 0.9286 (pp-130) cc_final: 0.8926 (ppp) REVERT: F 287 MET cc_start: 0.8807 (tpt) cc_final: 0.8467 (tpt) REVERT: F 336 MET cc_start: 0.9090 (tpp) cc_final: 0.8577 (tpp) REVERT: F 345 MET cc_start: 0.9217 (tmm) cc_final: 0.8921 (tmm) REVERT: F 414 MET cc_start: 0.8754 (ppp) cc_final: 0.8502 (ptp) outliers start: 16 outliers final: 11 residues processed: 62 average time/residue: 0.1218 time to fit residues: 12.3941 Evaluate side-chains 62 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 76 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 302 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 = 0.3118 r_free = 0.3118 target = 0.043955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.037168 restraints weight = 180387.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037755 restraints weight = 120333.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038166 restraints weight = 88754.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038424 restraints weight = 70811.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038644 restraints weight = 60829.051| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 17516 Z= 0.226 Angle : 0.928 58.812 24080 Z= 0.487 Chirality : 0.063 0.757 2638 Planarity : 0.004 0.048 2744 Dihedral : 20.081 176.936 3034 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.85 % Allowed : 18.60 % Favored : 80.55 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.25 % 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: -1.15 (0.20), residues: 1818 helix: 0.33 (0.20), residues: 633 sheet: -0.77 (0.34), residues: 235 loop : -1.54 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 243 TYR 0.023 0.001 TYR E 328 PHE 0.012 0.001 PHE B 217 TRP 0.010 0.001 TRP A 254 HIS 0.004 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (17516) covalent geometry : angle 0.92833 / 0.49 (24080) hydrogen bonds : bond 0.03386 / 2.15 ( 526) hydrogen bonds : angle 5.21816 / 3.64 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.85 seconds wall clock time: 44 minutes 46.88 seconds (2686.88 seconds total)