Starting phenix.real_space_refine on Sun Jun 15 04:54:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8it0_35702/06_2025/8it0_35702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it0_35702/06_2025/8it0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8it0_35702/06_2025/8it0_35702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it0_35702/06_2025/8it0_35702.map" model { file = "/net/cci-nas-00/data/ceres_data/8it0_35702/06_2025/8it0_35702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it0_35702/06_2025/8it0_35702.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.50, per 1000 atoms: 0.62 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: 4.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.64 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: 5.53 Time building geometry restraints manager: 5.08 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=" 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=" 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 bond pdb=" N ARG B 186 " pdb=" CA ARG B 186 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 8.00e+00 bond pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.82e+00 ... (remaining 17511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 23434 2.49 - 4.99: 503 4.99 - 7.48: 102 7.48 - 9.98: 32 9.98 - 12.47: 9 Bond angle restraints: 24080 Sorted by residual: 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 angle pdb=" C3' DC D 33 " pdb=" O3' DC D 33 " pdb=" P DC D 34 " ideal model delta sigma weight residual 120.20 127.79 -7.59 1.50e+00 4.44e-01 2.56e+01 ... (remaining 24075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 9198 22.18 - 44.37: 957 44.37 - 66.55: 307 66.55 - 88.73: 25 88.73 - 110.92: 1 Dihedral angle restraints: 10488 sinusoidal: 5098 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 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2488 0.108 - 0.217: 140 0.217 - 0.325: 4 0.325 - 0.433: 3 0.433 - 0.541: 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 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.33e+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 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.58e+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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.250 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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= 0.245 Angle : 0.958 12.471 24080 Z= 0.529 Chirality : 0.057 0.541 2638 Planarity : 0.006 0.064 2744 Dihedral : 18.671 110.918 7004 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.065 0.003 TRP A 320 HIS 0.034 0.002 HIS E 67 PHE 0.032 0.002 PHE F 187 TYR 0.037 0.002 TYR B 233 ARG 0.009 0.001 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.18646 ( 526) hydrogen bonds : angle 7.96340 ( 1476) covalent geometry : bond 0.00458 (17516) covalent geometry : angle 0.95788 (24080) *********************** 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 : 1.912 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: 0.3603 time to fit residues: 58.5677 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 : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 430 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038509 restraints weight = 181515.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039097 restraints weight = 120271.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039510 restraints weight = 88817.531| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17516 Z= 0.301 Angle : 0.762 12.400 24080 Z= 0.406 Chirality : 0.047 0.305 2638 Planarity : 0.006 0.065 2744 Dihedral : 19.649 92.194 3194 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.62 % Allowed : 17.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 1818 helix: -0.57 (0.19), residues: 631 sheet: -0.99 (0.33), residues: 243 loop : -1.98 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 320 HIS 0.007 0.001 HIS F 340 PHE 0.036 0.002 PHE E 482 TYR 0.019 0.002 TYR F 416 ARG 0.005 0.001 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 526) hydrogen bonds : angle 6.15837 ( 1476) covalent geometry : bond 0.00650 (17516) covalent geometry : angle 0.76224 (24080) *********************** 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 105 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6901 (m-80) cc_final: 0.6375 (m-80) REVERT: A 305 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9184 (pp) REVERT: B 1 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8122 (mmp) REVERT: B 186 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7560 (ptp90) REVERT: B 230 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 264 LEU cc_start: 0.9790 (OUTLIER) cc_final: 0.9563 (mt) REVERT: B 393 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9329 (mm) REVERT: E 1 MET cc_start: 0.8616 (tpt) cc_final: 0.8237 (tpt) REVERT: E 71 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7634 (p) REVERT: E 96 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8917 (mm) REVERT: F 287 MET cc_start: 0.9006 (tpt) cc_final: 0.8626 (tpt) outliers start: 43 outliers final: 13 residues processed: 101 average time/residue: 0.3629 time to fit residues: 55.8634 Evaluate side-chains 72 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 3.143 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 264 LEU 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 348 GLU Chi-restraints excluded: chain F residue 103 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 109 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.046676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039833 restraints weight = 174319.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.040416 restraints weight = 115670.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.040830 restraints weight = 86152.347| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17516 Z= 0.135 Angle : 0.626 10.098 24080 Z= 0.332 Chirality : 0.044 0.289 2638 Planarity : 0.004 0.046 2744 Dihedral : 19.497 94.396 3194 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.83 % Allowed : 17.13 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1818 helix: -0.19 (0.20), residues: 633 sheet: -0.77 (0.34), residues: 237 loop : -1.84 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 294 HIS 0.004 0.001 HIS B 188 PHE 0.013 0.001 PHE E 30 TYR 0.013 0.001 TYR A 37 ARG 0.007 0.001 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 526) hydrogen bonds : angle 5.67497 ( 1476) covalent geometry : bond 0.00292 (17516) covalent geometry : angle 0.62569 (24080) *********************** 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 87 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8977 (tpp) cc_final: 0.8681 (tpp) REVERT: B 230 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8449 (p) REVERT: E 1 MET cc_start: 0.8569 (tpt) cc_final: 0.7979 (tpt) REVERT: E 71 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7309 (p) REVERT: E 96 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8964 (mm) REVERT: E 485 LYS cc_start: 0.9584 (mtmm) cc_final: 0.9259 (ptpp) REVERT: F 345 MET cc_start: 0.9044 (tmm) cc_final: 0.8839 (tmm) outliers start: 30 outliers final: 10 residues processed: 85 average time/residue: 0.2867 time to fit residues: 38.4912 Evaluate side-chains 62 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 239 ILE 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 348 GLU Chi-restraints excluded: chain E residue 437 VAL 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 11 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 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** F 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.042853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.036246 restraints weight = 182071.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.036801 restraints weight = 119606.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037186 restraints weight = 88526.972| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 17516 Z= 0.292 Angle : 0.718 8.993 24080 Z= 0.382 Chirality : 0.045 0.314 2638 Planarity : 0.005 0.059 2744 Dihedral : 19.624 96.664 3194 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.68 % Allowed : 16.89 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1818 helix: -0.11 (0.20), residues: 631 sheet: -0.85 (0.34), residues: 223 loop : -1.72 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 33 HIS 0.007 0.001 HIS F 340 PHE 0.015 0.002 PHE B 217 TYR 0.019 0.002 TYR A 285 ARG 0.005 0.001 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 526) hydrogen bonds : angle 5.75119 ( 1476) covalent geometry : bond 0.00632 (17516) covalent geometry : angle 0.71799 (24080) *********************** 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 91 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 47 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9494 (OUTLIER) cc_final: 0.9286 (pp20) REVERT: A 285 TYR cc_start: 0.6819 (m-80) cc_final: 0.6574 (m-80) REVERT: A 491 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9290 (p) REVERT: B 1 MET cc_start: 0.8371 (mmm) cc_final: 0.8090 (mmp) REVERT: B 92 MET cc_start: 0.9070 (tpp) cc_final: 0.8798 (tpp) REVERT: B 230 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8472 (m) REVERT: E 1 MET cc_start: 0.8773 (tpt) cc_final: 0.8552 (tpt) REVERT: E 71 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8028 (p) REVERT: E 96 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9016 (mm) REVERT: E 406 MET cc_start: 0.9355 (pp-130) cc_final: 0.9102 (ppp) REVERT: F 336 MET cc_start: 0.8647 (tpp) cc_final: 0.8435 (tpp) REVERT: F 345 MET cc_start: 0.9168 (tmm) cc_final: 0.8931 (tmm) outliers start: 44 outliers final: 17 residues processed: 88 average time/residue: 0.2767 time to fit residues: 38.9377 Evaluate side-chains 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU 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 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 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 302 GLN Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 51 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 341 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.037387 restraints weight = 179553.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037938 restraints weight = 119892.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038322 restraints weight = 89369.201| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17516 Z= 0.175 Angle : 0.632 9.390 24080 Z= 0.335 Chirality : 0.044 0.290 2638 Planarity : 0.004 0.044 2744 Dihedral : 19.609 98.221 3194 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 17.38 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1818 helix: 0.08 (0.20), residues: 632 sheet: -0.75 (0.35), residues: 223 loop : -1.67 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 20 HIS 0.005 0.001 HIS B 320 PHE 0.014 0.001 PHE B 217 TYR 0.016 0.001 TYR B 293 ARG 0.004 0.000 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 526) hydrogen bonds : angle 5.48726 ( 1476) covalent geometry : bond 0.00384 (17516) covalent geometry : angle 0.63198 (24080) *********************** 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 86 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 49 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9288 (pp20) REVERT: A 491 THR cc_start: 0.9599 (OUTLIER) cc_final: 0.9287 (p) REVERT: B 1 MET cc_start: 0.8509 (mmm) cc_final: 0.8245 (mmp) REVERT: B 92 MET cc_start: 0.8927 (tpp) cc_final: 0.8661 (tpp) REVERT: B 230 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8520 (m) REVERT: E 71 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7818 (p) REVERT: E 96 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9039 (mm) REVERT: E 406 MET cc_start: 0.9362 (pp-130) cc_final: 0.9035 (ppp) REVERT: E 485 LYS cc_start: 0.9660 (mtmm) cc_final: 0.9318 (mtmm) REVERT: F 336 MET cc_start: 0.8969 (tpp) cc_final: 0.8639 (tpp) REVERT: F 345 MET cc_start: 0.9212 (tmm) cc_final: 0.8948 (tmm) REVERT: F 414 MET cc_start: 0.8772 (ppp) cc_final: 0.8418 (ptm) outliers start: 37 outliers final: 17 residues processed: 84 average time/residue: 0.2900 time to fit residues: 38.8908 Evaluate side-chains 65 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU 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 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 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 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 181 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** 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 = 0.3071 r_free = 0.3071 target = 0.043442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.036815 restraints weight = 181759.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037366 restraints weight = 121044.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037749 restraints weight = 89927.503| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17516 Z= 0.189 Angle : 0.626 8.530 24080 Z= 0.332 Chirality : 0.043 0.268 2638 Planarity : 0.004 0.046 2744 Dihedral : 19.613 99.518 3194 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.07 % Allowed : 17.80 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1818 helix: 0.20 (0.20), residues: 634 sheet: -0.74 (0.35), residues: 220 loop : -1.63 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 20 HIS 0.005 0.001 HIS B 320 PHE 0.014 0.001 PHE B 217 TYR 0.022 0.001 TYR B 293 ARG 0.005 0.001 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 526) hydrogen bonds : angle 5.40642 ( 1476) covalent geometry : bond 0.00415 (17516) covalent geometry : angle 0.62577 (24080) *********************** 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 79 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6546 (m-80) cc_final: 0.6308 (m-80) REVERT: A 305 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9306 (pp) REVERT: B 1 MET cc_start: 0.8507 (mmm) cc_final: 0.8250 (mmp) REVERT: B 92 MET cc_start: 0.8885 (tpp) cc_final: 0.8590 (tpp) REVERT: B 230 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8566 (m) REVERT: E 71 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7905 (p) REVERT: E 406 MET cc_start: 0.9414 (pp-130) cc_final: 0.9080 (ppp) REVERT: F 336 MET cc_start: 0.9054 (tpp) cc_final: 0.8693 (tpp) REVERT: F 345 MET cc_start: 0.9243 (tmm) cc_final: 0.8955 (tmm) REVERT: F 414 MET cc_start: 0.8822 (ppp) cc_final: 0.8340 (ptm) outliers start: 34 outliers final: 20 residues processed: 77 average time/residue: 0.2923 time to fit residues: 36.6269 Evaluate side-chains 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 A residue 405 ILE 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 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 237 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS 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 152 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 142 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** 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 = 0.3064 r_free = 0.3064 target = 0.043007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036439 restraints weight = 181735.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036981 restraints weight = 121189.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037359 restraints weight = 90364.046| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17516 Z= 0.183 Angle : 0.622 7.832 24080 Z= 0.331 Chirality : 0.044 0.240 2638 Planarity : 0.004 0.045 2744 Dihedral : 19.614 101.635 3194 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.89 % Allowed : 17.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1818 helix: 0.29 (0.20), residues: 635 sheet: -0.70 (0.35), residues: 221 loop : -1.60 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 20 HIS 0.004 0.001 HIS B 320 PHE 0.020 0.001 PHE A 30 TYR 0.018 0.001 TYR B 293 ARG 0.006 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 526) hydrogen bonds : angle 5.34847 ( 1476) covalent geometry : bond 0.00401 (17516) covalent geometry : angle 0.62203 (24080) *********************** 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 75 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8988 (pp20) cc_final: 0.8782 (pp20) REVERT: A 285 TYR cc_start: 0.6619 (m-80) cc_final: 0.6307 (m-80) REVERT: A 305 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9331 (pp) REVERT: A 491 THR cc_start: 0.9640 (OUTLIER) cc_final: 0.9347 (p) REVERT: B 1 MET cc_start: 0.8455 (mmm) cc_final: 0.8232 (mmp) REVERT: B 230 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8650 (m) REVERT: E 71 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8056 (p) REVERT: E 205 GLN cc_start: 0.8736 (pm20) cc_final: 0.8361 (pm20) REVERT: E 406 MET cc_start: 0.9440 (pp-130) cc_final: 0.9216 (ppp) REVERT: E 485 LYS cc_start: 0.9632 (mtmm) cc_final: 0.9426 (mtmm) REVERT: F 336 MET cc_start: 0.9164 (tpp) cc_final: 0.8805 (tpp) REVERT: F 345 MET cc_start: 0.9275 (tmm) cc_final: 0.8973 (tmm) REVERT: F 414 MET cc_start: 0.8874 (ppp) cc_final: 0.8403 (ptm) outliers start: 31 outliers final: 21 residues processed: 72 average time/residue: 0.3167 time to fit residues: 36.9157 Evaluate side-chains 69 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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 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 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 237 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 75 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 170 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 439 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.037693 restraints weight = 178511.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038275 restraints weight = 119134.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038646 restraints weight = 87866.329| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17516 Z= 0.121 Angle : 0.597 8.497 24080 Z= 0.316 Chirality : 0.043 0.213 2638 Planarity : 0.004 0.044 2744 Dihedral : 19.518 99.912 3194 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.46 % Allowed : 18.41 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1818 helix: 0.34 (0.20), residues: 637 sheet: -0.70 (0.34), residues: 242 loop : -1.51 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 373 HIS 0.003 0.001 HIS B 188 PHE 0.012 0.001 PHE B 217 TYR 0.019 0.001 TYR B 293 ARG 0.003 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 526) hydrogen bonds : angle 5.13684 ( 1476) covalent geometry : bond 0.00267 (17516) covalent geometry : angle 0.59714 (24080) *********************** 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 75 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6506 (m-80) cc_final: 0.6301 (m-80) REVERT: A 491 THR cc_start: 0.9632 (OUTLIER) cc_final: 0.9341 (p) REVERT: B 1 MET cc_start: 0.8450 (mmm) cc_final: 0.8243 (mmp) REVERT: B 230 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8650 (m) REVERT: B 287 MET cc_start: 0.8727 (ptp) cc_final: 0.8156 (ptp) REVERT: E 71 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7870 (p) REVERT: E 406 MET cc_start: 0.9451 (pp-130) cc_final: 0.9213 (ppp) REVERT: F 336 MET cc_start: 0.9155 (tpp) cc_final: 0.8793 (tpp) REVERT: F 345 MET cc_start: 0.9278 (tmm) cc_final: 0.8981 (tmm) REVERT: F 414 MET cc_start: 0.8879 (ppp) cc_final: 0.8535 (ptm) outliers start: 24 outliers final: 16 residues processed: 74 average time/residue: 0.3171 time to fit residues: 38.0509 Evaluate side-chains 67 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 GLN 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 237 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS 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 133 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 175 optimal weight: 0.0270 chunk 28 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 3.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 439 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.042387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035771 restraints weight = 184119.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.036340 restraints weight = 121443.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036733 restraints weight = 89455.894| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17516 Z= 0.177 Angle : 0.608 9.041 24080 Z= 0.323 Chirality : 0.043 0.220 2638 Planarity : 0.004 0.046 2744 Dihedral : 19.550 101.868 3194 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.34 % Allowed : 18.60 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1818 helix: 0.41 (0.20), residues: 635 sheet: -0.74 (0.34), residues: 237 loop : -1.46 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.004 0.001 HIS F 340 PHE 0.016 0.001 PHE A 30 TYR 0.018 0.001 TYR B 293 ARG 0.004 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 526) hydrogen bonds : angle 5.19880 ( 1476) covalent geometry : bond 0.00390 (17516) covalent geometry : angle 0.60845 (24080) *********************** 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 69 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6611 (m-80) cc_final: 0.6401 (m-80) REVERT: A 305 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9322 (pp) REVERT: A 491 THR cc_start: 0.9651 (OUTLIER) cc_final: 0.9360 (p) REVERT: B 1 MET cc_start: 0.8366 (mmm) cc_final: 0.8147 (mmp) REVERT: B 230 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8690 (m) REVERT: E 71 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8076 (p) REVERT: E 406 MET cc_start: 0.9439 (pp-130) cc_final: 0.9211 (ppp) REVERT: F 336 MET cc_start: 0.9160 (tpp) cc_final: 0.8787 (tpp) REVERT: F 345 MET cc_start: 0.9291 (tmm) cc_final: 0.8978 (tmm) REVERT: F 414 MET cc_start: 0.8855 (ppp) cc_final: 0.8528 (ptm) outliers start: 22 outliers final: 16 residues processed: 69 average time/residue: 0.2786 time to fit residues: 31.5072 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 : 1.744 ------------------------------------------------------------------------------- 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 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 230 THR Chi-restraints excluded: chain B residue 232 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 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 341 ILE 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 140 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 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** ** F 435 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 = 0.3015 r_free = 0.3015 target = 0.040371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.033814 restraints weight = 184542.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.034339 restraints weight = 121680.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034701 restraints weight = 91341.778| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17516 Z= 0.295 Angle : 0.705 12.050 24080 Z= 0.375 Chirality : 0.045 0.234 2638 Planarity : 0.005 0.066 2744 Dihedral : 19.729 103.830 3194 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.52 % Allowed : 18.41 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1818 helix: 0.28 (0.20), residues: 639 sheet: -0.73 (0.35), residues: 214 loop : -1.59 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 319 HIS 0.009 0.002 HIS A 16 PHE 0.017 0.002 PHE A 503 TYR 0.023 0.002 TYR B 293 ARG 0.007 0.001 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 526) hydrogen bonds : angle 5.51222 ( 1476) covalent geometry : bond 0.00638 (17516) covalent geometry : angle 0.70544 (24080) ********************** 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 68 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6670 (m-80) cc_final: 0.6433 (m-80) REVERT: A 305 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9347 (pp) REVERT: A 491 THR cc_start: 0.9660 (OUTLIER) cc_final: 0.9383 (p) REVERT: B 1 MET cc_start: 0.8224 (mmm) cc_final: 0.7958 (mmp) REVERT: B 230 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8741 (m) REVERT: E 71 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8362 (p) REVERT: E 406 MET cc_start: 0.9449 (pp-130) cc_final: 0.9199 (ppp) REVERT: E 485 LYS cc_start: 0.9760 (mtmm) cc_final: 0.9538 (mtmm) REVERT: F 336 MET cc_start: 0.9169 (tpp) cc_final: 0.8803 (tpp) REVERT: F 345 MET cc_start: 0.9264 (tmm) cc_final: 0.8957 (tmm) REVERT: F 414 MET cc_start: 0.8877 (ppp) cc_final: 0.8477 (ptm) outliers start: 25 outliers final: 17 residues processed: 66 average time/residue: 0.2848 time to fit residues: 30.6370 Evaluate side-chains 63 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 118 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 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 341 ILE 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 115 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 439 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.042364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035790 restraints weight = 181678.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036365 restraints weight = 119695.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036756 restraints weight = 88157.309| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17516 Z= 0.136 Angle : 0.616 9.375 24080 Z= 0.326 Chirality : 0.043 0.196 2638 Planarity : 0.004 0.045 2744 Dihedral : 19.564 101.388 3194 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.16 % Allowed : 18.72 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1818 helix: 0.47 (0.20), residues: 623 sheet: -0.72 (0.35), residues: 232 loop : -1.50 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 373 HIS 0.004 0.001 HIS B 188 PHE 0.016 0.001 PHE A 30 TYR 0.023 0.001 TYR B 293 ARG 0.013 0.001 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 526) hydrogen bonds : angle 5.23115 ( 1476) covalent geometry : bond 0.00302 (17516) covalent geometry : angle 0.61610 (24080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5144.26 seconds wall clock time: 94 minutes 6.21 seconds (5646.21 seconds total)