Starting phenix.real_space_refine on Fri Jul 3 23:42:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it0_35702/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it0_35702/07_2026/8it0_35702.map" } 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-dev-6108/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: {'RNA': 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: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Time building chain proxies: 2.85, per 1000 atoms: 0.17 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: 1.52 Conformation dependent library (CDL) restraints added in 610.4 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: 1.78 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: 2.67 Time building geometry restraints manager: 2.00 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: 23411 2.49 - 4.99: 527 4.99 - 7.48: 101 7.48 - 9.98: 32 9.98 - 12.47: 9 Bond angle restraints: 24080 Sorted by residual: 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 angle pdb=" CA GLU F 212 " pdb=" CB GLU F 212 " pdb=" CG GLU F 212 " ideal model delta sigma weight residual 114.10 124.51 -10.41 2.00e+00 2.50e-01 2.71e+01 ... (remaining 24075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 9121 22.18 - 44.37: 930 44.37 - 66.55: 251 66.55 - 88.73: 25 88.73 - 110.92: 1 Dihedral angle restraints: 10328 sinusoidal: 4938 harmonic: 5390 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ILE B 208 " pdb=" C ILE B 208 " pdb=" N ARG B 209 " pdb=" CA ARG B 209 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS F 211 " pdb=" C LYS F 211 " pdb=" N GLU F 212 " pdb=" CA GLU F 212 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 10325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2494 0.110 - 0.221: 135 0.221 - 0.331: 3 0.331 - 0.441: 3 0.441 - 0.552: 3 Chirality restraints: 2638 Sorted by residual: chirality pdb=" P DA D 36 " pdb=" OP1 DA D 36 " pdb=" OP2 DA D 36 " pdb=" O5' DA D 36 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" P DC D 34 " pdb=" OP1 DC D 34 " pdb=" OP2 DC D 34 " pdb=" O5' DC D 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.84e+00 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 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.66e+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: 1.690 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- 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= 0.297 Angle : 0.971 12.471 24080 Z= 0.568 Chirality : 0.058 0.552 2638 Planarity : 0.006 0.064 2744 Dihedral : 17.963 110.918 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 0.00483 / 0.30 (17516) covalent geometry : angle 0.97135 / 0.57 (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 : 0.632 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: 0.1374 time to fit residues: 22.3984 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 : 0.493 ------------------------------------------------------------------------------- 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: 10.0000 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 ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3253 r_free = 0.3253 target = 0.050195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.043254 restraints weight = 173808.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.043887 restraints weight = 115437.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044338 restraints weight = 84738.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044664 restraints weight = 67551.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.044885 restraints weight = 57045.126| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17516 Z= 0.148 Angle : 0.685 12.259 24080 Z= 0.365 Chirality : 0.045 0.186 2638 Planarity : 0.005 0.054 2744 Dihedral : 18.051 100.975 3034 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.07 % Allowed : 17.26 % 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: -2.14 (0.18), residues: 1818 helix: -0.59 (0.19), residues: 642 sheet: -0.74 (0.33), residues: 240 loop : -2.25 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 209 TYR 0.021 0.001 TYR E 56 PHE 0.014 0.001 PHE B 273 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 0.00305 / 0.15 (17516) covalent geometry : angle 0.68473 / 0.37 (24080) hydrogen bonds : bond 0.04484 / 2.84 ( 526) hydrogen bonds : angle 6.19033 / 4.37 ( 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 101 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.9288 (ptt) cc_final: 0.9056 (ptt) REVERT: B 92 MET cc_start: 0.8986 (tpp) cc_final: 0.8752 (tpp) REVERT: B 393 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9326 (mm) REVERT: E 1 MET cc_start: 0.8325 (tpt) cc_final: 0.7750 (tpt) REVERT: E 71 THR cc_start: 0.7235 (OUTLIER) cc_final: 0.7019 (p) REVERT: E 96 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8831 (mm) REVERT: F 75 LEU cc_start: 0.9550 (tt) cc_final: 0.9345 (tt) REVERT: F 287 MET cc_start: 0.8851 (tpt) cc_final: 0.8586 (tpp) outliers start: 34 outliers final: 10 residues processed: 98 average time/residue: 0.1244 time to fit residues: 19.2117 Evaluate side-chains 68 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 103 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038886 restraints weight = 182865.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.039483 restraints weight = 119207.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039892 restraints weight = 88268.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.040194 restraints weight = 71172.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040362 restraints weight = 60442.439| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17516 Z= 0.237 Angle : 0.704 8.219 24080 Z= 0.376 Chirality : 0.045 0.234 2638 Planarity : 0.005 0.050 2744 Dihedral : 18.035 92.460 3034 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.44 % Allowed : 17.07 % Favored : 80.49 % 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: -1.71 (0.19), residues: 1818 helix: -0.24 (0.20), residues: 633 sheet: -0.74 (0.34), residues: 235 loop : -1.89 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 186 TYR 0.028 0.002 TYR A 37 PHE 0.018 0.002 PHE E 30 TRP 0.015 0.001 TRP F 33 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (17516) covalent geometry : angle 0.70436 / 0.38 (24080) hydrogen bonds : bond 0.04133 / 2.64 ( 526) hydrogen bonds : angle 5.79806 / 4.08 ( 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 99 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 18 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7590 (pp30) REVERT: A 285 TYR cc_start: 0.6863 (m-80) cc_final: 0.6409 (m-80) REVERT: A 305 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9226 (pp) REVERT: A 435 MET cc_start: 0.8840 (tpp) cc_final: 0.8141 (tmm) REVERT: B 1 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8085 (mmp) REVERT: B 230 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8395 (p) REVERT: E 1 MET cc_start: 0.8560 (tpt) cc_final: 0.8203 (tpt) REVERT: E 71 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (p) REVERT: E 96 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8985 (mm) outliers start: 40 outliers final: 13 residues processed: 92 average time/residue: 0.1121 time to fit residues: 16.2507 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 : 0.562 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 LEU 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 230 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037929 restraints weight = 183414.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.038537 restraints weight = 119970.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.038943 restraints weight = 87959.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039239 restraints weight = 70877.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039439 restraints weight = 60172.487| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17516 Z= 0.224 Angle : 0.668 9.781 24080 Z= 0.357 Chirality : 0.045 0.263 2638 Planarity : 0.004 0.045 2744 Dihedral : 18.069 94.268 3034 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.13 % Allowed : 17.01 % Favored : 80.85 % 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: -1.54 (0.19), residues: 1818 helix: -0.07 (0.20), residues: 634 sheet: -0.82 (0.34), residues: 235 loop : -1.76 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 362 TYR 0.013 0.001 TYR A 346 PHE 0.022 0.001 PHE A 30 TRP 0.016 0.001 TRP F 33 HIS 0.003 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (17516) covalent geometry : angle 0.66818 / 0.36 (24080) hydrogen bonds : bond 0.03717 / 2.41 ( 526) hydrogen bonds : angle 5.64161 / 3.98 ( 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 85 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9297 (pp) REVERT: B 1 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8077 (mmp) REVERT: B 92 MET cc_start: 0.9100 (tpp) cc_final: 0.8777 (tpp) REVERT: B 230 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8564 (p) REVERT: E 1 MET cc_start: 0.8635 (tpt) cc_final: 0.8232 (tpt) REVERT: E 71 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7681 (p) REVERT: E 96 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9004 (mm) REVERT: F 336 MET cc_start: 0.8693 (tpp) cc_final: 0.8369 (tpp) outliers start: 35 outliers final: 12 residues processed: 79 average time/residue: 0.1056 time to fit residues: 13.6489 Evaluate side-chains 63 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 A residue 305 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 118 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 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: 20.0000 chunk 45 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.037028 restraints weight = 182221.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037571 restraints weight = 121736.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037954 restraints weight = 90320.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.038220 restraints weight = 73306.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038414 restraints weight = 62957.922| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17516 Z= 0.253 Angle : 0.679 9.547 24080 Z= 0.364 Chirality : 0.046 0.295 2638 Planarity : 0.005 0.046 2744 Dihedral : 18.169 96.313 3034 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.83 % Allowed : 17.07 % Favored : 81.10 % 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: -1.45 (0.19), residues: 1818 helix: 0.09 (0.20), residues: 624 sheet: -0.96 (0.34), residues: 236 loop : -1.70 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 243 TYR 0.034 0.002 TYR A 285 PHE 0.015 0.001 PHE B 217 TRP 0.012 0.001 TRP F 33 HIS 0.009 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.25 (17516) covalent geometry : angle 0.67909 / 0.36 (24080) hydrogen bonds : bond 0.03800 / 2.47 ( 526) hydrogen bonds : angle 5.63596 / 3.96 ( 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 78 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9297 (pp) REVERT: A 491 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9291 (p) REVERT: B 92 MET cc_start: 0.8963 (tpp) cc_final: 0.8708 (tpp) REVERT: B 230 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8582 (p) REVERT: E 1 MET cc_start: 0.8715 (tpt) cc_final: 0.8505 (tpt) REVERT: E 71 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7810 (p) REVERT: E 96 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9042 (mm) REVERT: E 205 GLN cc_start: 0.8810 (pm20) cc_final: 0.8465 (pm20) REVERT: E 406 MET cc_start: 0.9342 (pp-130) cc_final: 0.9001 (ppp) REVERT: F 336 MET cc_start: 0.8944 (tpp) cc_final: 0.8541 (tpp) outliers start: 30 outliers final: 15 residues processed: 73 average time/residue: 0.1223 time to fit residues: 14.1946 Evaluate side-chains 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 121 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 69 optimal weight: 0.2980 chunk 85 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** 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 = 0.3093 r_free = 0.3093 target = 0.044289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.037646 restraints weight = 179181.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.038225 restraints weight = 119860.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038593 restraints weight = 88675.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038866 restraints weight = 71998.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.039066 restraints weight = 61925.404| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17516 Z= 0.154 Angle : 0.619 9.140 24080 Z= 0.331 Chirality : 0.044 0.298 2638 Planarity : 0.004 0.044 2744 Dihedral : 18.122 97.064 3034 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.26 % Allowed : 17.07 % 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: -1.31 (0.20), residues: 1818 helix: 0.20 (0.20), residues: 628 sheet: -0.91 (0.34), residues: 235 loop : -1.62 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 243 TYR 0.018 0.001 TYR B 293 PHE 0.014 0.001 PHE B 217 TRP 0.011 0.001 TRP F 20 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (17516) covalent geometry : angle 0.61906 / 0.33 (24080) hydrogen bonds : bond 0.03388 / 2.20 ( 526) hydrogen bonds : angle 5.42258 / 3.80 ( 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 87 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9304 (pp) REVERT: A 491 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9288 (p) REVERT: B 92 MET cc_start: 0.8897 (tpp) cc_final: 0.8589 (tpp) REVERT: B 230 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8582 (p) REVERT: E 71 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7767 (p) REVERT: E 96 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9032 (mm) REVERT: E 406 MET cc_start: 0.9379 (pp-130) cc_final: 0.9015 (ppp) REVERT: F 336 MET cc_start: 0.9018 (tpp) cc_final: 0.8604 (tpp) REVERT: F 414 MET cc_start: 0.9091 (ptp) cc_final: 0.8834 (ppp) outliers start: 37 outliers final: 17 residues processed: 83 average time/residue: 0.1046 time to fit residues: 13.9179 Evaluate side-chains 68 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR 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 305 LEU 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 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: 20.0000 chunk 171 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 60 optimal weight: 0.0170 chunk 147 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 296 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 = 0.3081 r_free = 0.3081 target = 0.043755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.037162 restraints weight = 179586.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037731 restraints weight = 119900.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.038107 restraints weight = 88737.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038382 restraints weight = 72249.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038523 restraints weight = 62120.933| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17516 Z= 0.176 Angle : 0.625 8.002 24080 Z= 0.334 Chirality : 0.044 0.282 2638 Planarity : 0.004 0.046 2744 Dihedral : 18.129 99.752 3034 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.83 % Allowed : 17.62 % 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: -1.23 (0.20), residues: 1818 helix: 0.25 (0.20), residues: 627 sheet: -0.84 (0.34), residues: 235 loop : -1.56 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 243 TYR 0.016 0.001 TYR B 293 PHE 0.014 0.001 PHE B 217 TRP 0.010 0.001 TRP A 320 HIS 0.004 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (17516) covalent geometry : angle 0.62519 / 0.33 (24080) hydrogen bonds : bond 0.03418 / 2.22 ( 526) hydrogen bonds : angle 5.37141 / 3.76 ( 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 78 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9338 (pp) REVERT: A 491 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9313 (p) REVERT: B 92 MET cc_start: 0.9018 (tpp) cc_final: 0.8668 (tpp) REVERT: B 230 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8584 (m) REVERT: E 71 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7802 (p) REVERT: E 96 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9063 (mm) REVERT: E 205 GLN cc_start: 0.8811 (pm20) cc_final: 0.8481 (pm20) REVERT: E 406 MET cc_start: 0.9407 (pp-130) cc_final: 0.9078 (ppp) REVERT: F 336 MET cc_start: 0.9047 (tpp) cc_final: 0.8618 (tpp) REVERT: F 414 MET cc_start: 0.9120 (ptp) cc_final: 0.8870 (ppp) outliers start: 30 outliers final: 17 residues processed: 74 average time/residue: 0.1147 time to fit residues: 13.8972 Evaluate side-chains 68 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR 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 305 LEU 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 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 E residue 462 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 296 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 = 0.3044 r_free = 0.3044 target = 0.042302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035791 restraints weight = 186394.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.036343 restraints weight = 122898.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036718 restraints weight = 91190.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.036979 restraints weight = 73833.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037193 restraints weight = 63533.082| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17516 Z= 0.228 Angle : 0.660 8.705 24080 Z= 0.353 Chirality : 0.045 0.227 2638 Planarity : 0.004 0.045 2744 Dihedral : 18.257 102.842 3034 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.01 % Allowed : 17.80 % Favored : 80.18 % 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: -1.26 (0.20), residues: 1818 helix: 0.20 (0.20), residues: 635 sheet: -0.91 (0.35), residues: 231 loop : -1.55 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 243 TYR 0.024 0.002 TYR B 293 PHE 0.020 0.002 PHE B 217 TRP 0.010 0.001 TRP F 33 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (17516) covalent geometry : angle 0.65974 / 0.35 (24080) hydrogen bonds : bond 0.03677 / 2.39 ( 526) hydrogen bonds : angle 5.46749 / 3.82 ( 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: 33 poor density : 46 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9339 (pp) REVERT: A 491 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9366 (p) REVERT: B 230 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8655 (m) REVERT: E 71 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (p) REVERT: E 406 MET cc_start: 0.9429 (pp-130) cc_final: 0.9065 (ppp) REVERT: F 336 MET cc_start: 0.9060 (tpp) cc_final: 0.8617 (tpp) REVERT: F 414 MET cc_start: 0.9167 (ptp) cc_final: 0.8870 (ppp) outliers start: 33 outliers final: 20 residues processed: 76 average time/residue: 0.0979 time to fit residues: 12.2728 Evaluate side-chains 68 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR 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 305 LEU 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 232 THR Chi-restraints excluded: chain B residue 277 MET 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 E residue 462 LEU Chi-restraints excluded: chain F residue 341 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: 1.9990 chunk 182 optimal weight: 30.0000 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 116 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 157 optimal weight: 0.0670 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 296 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 = 0.3086 r_free = 0.3086 target = 0.043620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.037075 restraints weight = 181480.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037627 restraints weight = 120061.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.038016 restraints weight = 88906.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038242 restraints weight = 71808.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038486 restraints weight = 62432.558| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17516 Z= 0.128 Angle : 0.621 9.540 24080 Z= 0.330 Chirality : 0.044 0.183 2638 Planarity : 0.004 0.048 2744 Dihedral : 18.211 101.217 3034 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.28 % Allowed : 18.41 % Favored : 80.30 % 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: -1.14 (0.20), residues: 1818 helix: 0.28 (0.20), residues: 634 sheet: -0.79 (0.35), residues: 233 loop : -1.48 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 243 TYR 0.023 0.001 TYR B 293 PHE 0.017 0.001 PHE F 273 TRP 0.013 0.001 TRP B 373 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (17516) covalent geometry : angle 0.62065 / 0.33 (24080) hydrogen bonds : bond 0.03266 / 2.10 ( 526) hydrogen bonds : angle 5.27528 / 3.68 ( 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 73 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9340 (pp) REVERT: B 92 MET cc_start: 0.8939 (tpp) cc_final: 0.8595 (tpp) REVERT: B 230 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8665 (m) REVERT: E 71 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7800 (p) REVERT: E 205 GLN cc_start: 0.8783 (pm20) cc_final: 0.8407 (pm20) REVERT: E 406 MET cc_start: 0.9424 (pp-130) cc_final: 0.9037 (ppp) REVERT: F 336 MET cc_start: 0.9049 (tpp) cc_final: 0.8594 (tpp) REVERT: F 414 MET cc_start: 0.9158 (ptp) cc_final: 0.8828 (ppp) outliers start: 21 outliers final: 15 residues processed: 70 average time/residue: 0.1075 time to fit residues: 12.1968 Evaluate side-chains 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 MET 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 437 VAL Chi-restraints excluded: chain E residue 462 LEU 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: 0.6980 chunk 41 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS ** E 296 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 = 0.3091 r_free = 0.3091 target = 0.043859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037283 restraints weight = 180043.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.037850 restraints weight = 119550.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.038233 restraints weight = 88433.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038519 restraints weight = 71613.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.038716 restraints weight = 61146.381| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17516 Z= 0.137 Angle : 0.605 9.428 24080 Z= 0.322 Chirality : 0.043 0.160 2638 Planarity : 0.004 0.046 2744 Dihedral : 18.145 101.593 3034 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.10 % Allowed : 18.66 % Favored : 80.24 % 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: -1.13 (0.20), residues: 1818 helix: 0.35 (0.20), residues: 638 sheet: -0.98 (0.33), residues: 250 loop : -1.46 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 243 TYR 0.019 0.001 TYR E 285 PHE 0.012 0.001 PHE B 217 TRP 0.013 0.001 TRP B 373 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (17516) covalent geometry : angle 0.60520 / 0.32 (24080) hydrogen bonds : bond 0.03183 / 2.05 ( 526) hydrogen bonds : angle 5.16884 / 3.61 ( 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 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9317 (pp) REVERT: A 491 THR cc_start: 0.9639 (OUTLIER) cc_final: 0.9364 (p) REVERT: B 230 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8576 (m) REVERT: E 71 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (p) REVERT: E 406 MET cc_start: 0.9411 (pp-130) cc_final: 0.9035 (ppp) REVERT: F 336 MET cc_start: 0.9098 (tpp) cc_final: 0.8638 (tpp) REVERT: F 414 MET cc_start: 0.9123 (ptp) cc_final: 0.8846 (ppp) outliers start: 18 outliers final: 12 residues processed: 65 average time/residue: 0.1053 time to fit residues: 11.2543 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 : 0.605 ------------------------------------------------------------------------------- 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 305 LEU 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 230 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 MET 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 437 VAL Chi-restraints excluded: chain E residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 175 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 439 ASN E 209 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** 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 = 0.3111 r_free = 0.3111 target = 0.044480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037866 restraints weight = 179099.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.038437 restraints weight = 119466.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038828 restraints weight = 88736.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.039115 restraints weight = 71825.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.039259 restraints weight = 61307.634| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17516 Z= 0.118 Angle : 0.606 9.542 24080 Z= 0.320 Chirality : 0.043 0.156 2638 Planarity : 0.004 0.047 2744 Dihedral : 18.088 101.102 3034 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.04 % Allowed : 18.78 % Favored : 80.18 % 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: -1.07 (0.20), residues: 1818 helix: 0.39 (0.20), residues: 633 sheet: -0.87 (0.34), residues: 243 loop : -1.45 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.020 0.001 TYR B 293 PHE 0.011 0.001 PHE B 217 TRP 0.014 0.001 TRP B 373 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (17516) covalent geometry : angle 0.60574 / 0.32 (24080) hydrogen bonds : bond 0.03080 / 1.97 ( 526) hydrogen bonds : angle 5.08118 / 3.54 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.66 seconds wall clock time: 41 minutes 57.96 seconds (2517.96 seconds total)