Starting phenix.real_space_refine on Sun May 18 11:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8it0_35702/05_2025/8it0_35702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it0_35702/05_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_35702/05_2025/8it0_35702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it0_35702/05_2025/8it0_35702.map" model { file = "/net/cci-nas-00/data/ceres_data/8it0_35702/05_2025/8it0_35702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it0_35702/05_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-5687/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: 9.35, per 1000 atoms: 0.55 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: 4.27 Conformation dependent library (CDL) restraints added in 1.7 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: 4.90 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: 5.00 Time building geometry restraints manager: 4.96 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: 0.03 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: 1.310 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.740 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- 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 : 1.765 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: 0.3274 time to fit residues: 53.3924 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 : 1.704 ------------------------------------------------------------------------------- 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 = 0.045217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038510 restraints weight = 181514.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039098 restraints weight = 120307.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039513 restraints weight = 88863.396| |-----------------------------------------------------------------------------| 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 12.399 24080 Z= 0.405 Chirality : 0.047 0.305 2638 Planarity : 0.006 0.065 2744 Dihedral : 19.649 92.195 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 0.76222 (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 : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6902 (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: 0.8381 (OUTLIER) cc_final: 0.8119 (mmp) REVERT: B 186 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7559 (ptp90) REVERT: B 230 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8440 (p) REVERT: B 264 LEU cc_start: 0.9789 (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: 0.7930 (OUTLIER) cc_final: 0.7637 (p) REVERT: E 96 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8916 (mm) REVERT: F 287 MET cc_start: 0.9008 (tpt) cc_final: 0.8626 (tpt) outliers start: 43 outliers final: 13 residues processed: 101 average time/residue: 0.2959 time to fit residues: 45.6303 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 : 1.693 ------------------------------------------------------------------------------- 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: 3.9990 chunk 178 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 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 18 GLN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN E 90 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.044847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.038067 restraints weight = 178149.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.038643 restraints weight = 118905.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039046 restraints weight = 88268.001| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17516 Z= 0.192 Angle : 0.642 9.117 24080 Z= 0.343 Chirality : 0.044 0.301 2638 Planarity : 0.005 0.048 2744 Dihedral : 19.557 95.596 3194 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.20 % Allowed : 16.95 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.34), residues: 237 loop : -1.82 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.003 0.001 HIS F 340 PHE 0.013 0.001 PHE E 30 TYR 0.024 0.001 TYR A 37 ARG 0.007 0.001 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 526) hydrogen bonds : angle 5.75189 ( 1476) covalent geometry : bond 0.00414 (17516) covalent geometry : angle 0.64205 (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 90 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7621 (pp30) REVERT: B 1 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8136 (mmp) REVERT: B 186 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7832 (ptp90) REVERT: B 230 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8539 (p) REVERT: E 1 MET cc_start: 0.8679 (tpt) cc_final: 0.8286 (tpt) REVERT: E 18 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: E 71 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7535 (p) REVERT: E 96 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8980 (mm) outliers start: 36 outliers final: 14 residues processed: 87 average time/residue: 0.3049 time to fit residues: 41.4493 Evaluate side-chains 69 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 1 MET 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 307 LYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 11 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036672 restraints weight = 180175.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037231 restraints weight = 119351.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037615 restraints weight = 88411.715| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17516 Z= 0.222 Angle : 0.657 9.979 24080 Z= 0.350 Chirality : 0.044 0.303 2638 Planarity : 0.004 0.052 2744 Dihedral : 19.569 96.861 3194 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.68 % Allowed : 17.20 % 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: -1.46 (0.19), residues: 1818 helix: 0.01 (0.20), residues: 632 sheet: -0.94 (0.34), residues: 235 loop : -1.67 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 320 HIS 0.005 0.001 HIS F 340 PHE 0.014 0.001 PHE A 30 TYR 0.013 0.001 TYR A 346 ARG 0.005 0.001 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 526) hydrogen bonds : angle 5.60404 ( 1476) covalent geometry : bond 0.00484 (17516) covalent geometry : angle 0.65730 (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 93 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 49 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6657 (m-80) cc_final: 0.6409 (m-80) REVERT: A 491 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9277 (p) REVERT: B 186 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7939 (ptp90) REVERT: B 230 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8541 (p) REVERT: E 1 MET cc_start: 0.8753 (tpt) cc_final: 0.8525 (tpt) REVERT: E 71 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7773 (p) REVERT: E 96 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9033 (mm) REVERT: E 406 MET cc_start: 0.9328 (pp-130) cc_final: 0.8967 (ppp) REVERT: E 485 LYS cc_start: 0.9688 (mtmm) cc_final: 0.9425 (mtmm) REVERT: F 414 MET cc_start: 0.8738 (ppp) cc_final: 0.8350 (ptp) outliers start: 44 outliers final: 18 residues processed: 87 average time/residue: 0.2814 time to fit residues: 38.4975 Evaluate side-chains 70 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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 491 THR Chi-restraints excluded: chain B residue 20 TRP 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 307 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 404 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 51 optimal weight: 0.2980 chunk 181 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 146 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 3.5584 ------------------------------------------------------------------------------- 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 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 = 0.3090 r_free = 0.3090 target = 0.043731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.037025 restraints weight = 179745.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037606 restraints weight = 118880.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038007 restraints weight = 87621.129| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3475 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= 0.172 Angle : 0.621 8.536 24080 Z= 0.330 Chirality : 0.044 0.280 2638 Planarity : 0.004 0.045 2744 Dihedral : 19.585 97.985 3194 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.01 % Allowed : 18.11 % Favored : 79.88 % 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: -1.36 (0.19), residues: 1818 helix: 0.14 (0.20), residues: 633 sheet: -0.99 (0.34), residues: 230 loop : -1.62 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 20 HIS 0.006 0.001 HIS B 320 PHE 0.014 0.001 PHE B 217 TYR 0.021 0.001 TYR B 293 ARG 0.004 0.000 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 526) hydrogen bonds : angle 5.39010 ( 1476) covalent geometry : bond 0.00377 (17516) covalent geometry : angle 0.62085 (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 85 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8959 (tpp) cc_final: 0.8701 (tpp) REVERT: B 230 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8564 (p) REVERT: E 71 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7774 (p) REVERT: E 96 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9052 (mm) REVERT: E 289 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: E 406 MET cc_start: 0.9364 (pp-130) cc_final: 0.9041 (ppp) REVERT: F 414 MET cc_start: 0.8822 (ppp) cc_final: 0.8351 (ptm) outliers start: 33 outliers final: 15 residues processed: 82 average time/residue: 0.2931 time to fit residues: 38.1264 Evaluate side-chains 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 ILE 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 289 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 181 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.034078 restraints weight = 184874.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.034638 restraints weight = 122875.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035024 restraints weight = 90561.375| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4288 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= 0.286 Angle : 0.703 8.954 24080 Z= 0.376 Chirality : 0.045 0.268 2638 Planarity : 0.005 0.054 2744 Dihedral : 19.789 104.535 3194 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.20 % Allowed : 18.11 % Favored : 79.70 % 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: -1.40 (0.19), residues: 1818 helix: 0.09 (0.20), residues: 639 sheet: -1.04 (0.34), residues: 229 loop : -1.64 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 319 HIS 0.008 0.001 HIS B 320 PHE 0.026 0.002 PHE B 217 TYR 0.028 0.002 TYR B 293 ARG 0.007 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 526) hydrogen bonds : angle 5.66527 ( 1476) covalent geometry : bond 0.00619 (17516) covalent geometry : angle 0.70295 (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 80 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 44 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 THR cc_start: 0.9593 (OUTLIER) cc_final: 0.9290 (p) REVERT: B 92 MET cc_start: 0.8967 (tpp) cc_final: 0.8704 (tpp) REVERT: B 230 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8631 (m) REVERT: E 71 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8219 (p) REVERT: E 406 MET cc_start: 0.9442 (pp-130) cc_final: 0.9109 (ppp) REVERT: F 414 MET cc_start: 0.8847 (ppp) cc_final: 0.8412 (ptm) outliers start: 36 outliers final: 20 residues processed: 76 average time/residue: 0.2849 time to fit residues: 35.6724 Evaluate side-chains 65 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain 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 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 348 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain F residue 103 LEU 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 356 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 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 = 0.3048 r_free = 0.3048 target = 0.041596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034989 restraints weight = 181275.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035545 restraints weight = 118689.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035936 restraints weight = 88417.135| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17516 Z= 0.174 Angle : 0.632 8.017 24080 Z= 0.336 Chirality : 0.044 0.231 2638 Planarity : 0.004 0.045 2744 Dihedral : 19.730 101.702 3194 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.89 % Allowed : 18.23 % Favored : 79.88 % 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: -1.27 (0.20), residues: 1818 helix: 0.23 (0.20), residues: 635 sheet: -0.68 (0.36), residues: 211 loop : -1.65 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 20 HIS 0.005 0.001 HIS B 188 PHE 0.016 0.001 PHE B 217 TYR 0.024 0.001 TYR B 293 ARG 0.005 0.001 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 526) hydrogen bonds : angle 5.44194 ( 1476) covalent geometry : bond 0.00382 (17516) covalent geometry : angle 0.63178 (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 : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6682 (m-80) cc_final: 0.6438 (m-80) REVERT: A 491 THR cc_start: 0.9668 (OUTLIER) cc_final: 0.9380 (p) REVERT: B 92 MET cc_start: 0.8921 (tpp) cc_final: 0.8572 (tpp) REVERT: B 230 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8650 (m) REVERT: E 71 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7986 (p) REVERT: E 406 MET cc_start: 0.9411 (pp-130) cc_final: 0.9194 (ppp) REVERT: F 414 MET cc_start: 0.8883 (ppp) cc_final: 0.8491 (ptm) outliers start: 31 outliers final: 19 residues processed: 73 average time/residue: 0.2984 time to fit residues: 34.8909 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 : 1.687 ------------------------------------------------------------------------------- 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 405 ILE Chi-restraints excluded: chain A residue 491 THR 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 262 GLN Chi-restraints excluded: chain B residue 277 MET 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 103 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 356 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 75 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.041526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034886 restraints weight = 180499.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.035453 restraints weight = 120062.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035846 restraints weight = 88863.048| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17516 Z= 0.174 Angle : 0.623 8.569 24080 Z= 0.332 Chirality : 0.043 0.221 2638 Planarity : 0.004 0.043 2744 Dihedral : 19.712 102.298 3194 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.83 % Allowed : 18.17 % Favored : 80.00 % 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: 0.30 (0.20), residues: 635 sheet: -0.59 (0.36), residues: 209 loop : -1.63 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 86 HIS 0.005 0.001 HIS B 188 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 0.03441 ( 526) hydrogen bonds : angle 5.36406 ( 1476) covalent geometry : bond 0.00384 (17516) covalent geometry : angle 0.62259 (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 74 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6654 (m-80) cc_final: 0.6349 (m-80) REVERT: A 305 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9339 (pp) REVERT: A 491 THR cc_start: 0.9670 (OUTLIER) cc_final: 0.9384 (p) REVERT: B 92 MET cc_start: 0.8930 (tpp) cc_final: 0.8614 (tpp) REVERT: B 230 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8656 (m) REVERT: E 71 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8053 (p) REVERT: E 406 MET cc_start: 0.9436 (pp-130) cc_final: 0.9210 (ppp) REVERT: F 414 MET cc_start: 0.8885 (ppp) cc_final: 0.8627 (ptm) outliers start: 30 outliers final: 21 residues processed: 71 average time/residue: 0.2656 time to fit residues: 30.8896 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 : 1.937 ------------------------------------------------------------------------------- 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 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 262 GLN Chi-restraints excluded: chain B residue 277 MET 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 E residue 462 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 103 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 356 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 133 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 175 optimal weight: 0.0000 chunk 28 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 90 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 127 optimal weight: 0.0170 chunk 168 optimal weight: 0.9980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 341 GLN A 439 ASN E 217 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.043945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037347 restraints weight = 180591.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.037919 restraints weight = 119315.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038311 restraints weight = 88517.835| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17516 Z= 0.117 Angle : 0.603 7.518 24080 Z= 0.318 Chirality : 0.043 0.224 2638 Planarity : 0.004 0.044 2744 Dihedral : 19.530 100.471 3194 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.52 % Allowed : 18.78 % Favored : 79.70 % 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: -1.11 (0.20), residues: 1818 helix: 0.39 (0.20), residues: 631 sheet: -0.92 (0.34), residues: 247 loop : -1.47 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 373 HIS 0.004 0.001 HIS B 188 PHE 0.016 0.001 PHE A 30 TYR 0.020 0.001 TYR B 293 ARG 0.007 0.000 ARG F 240 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 526) hydrogen bonds : angle 5.10358 ( 1476) covalent geometry : bond 0.00257 (17516) covalent geometry : angle 0.60280 (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 78 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6600 (m-80) cc_final: 0.6265 (m-80) REVERT: A 305 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9318 (pp) REVERT: A 491 THR cc_start: 0.9631 (OUTLIER) cc_final: 0.9357 (p) REVERT: B 92 MET cc_start: 0.8868 (tpp) cc_final: 0.8468 (tpp) REVERT: B 230 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8653 (m) REVERT: E 1 MET cc_start: 0.8695 (tpt) cc_final: 0.8399 (tpt) REVERT: E 71 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7907 (p) REVERT: E 406 MET cc_start: 0.9446 (pp-130) cc_final: 0.9217 (ppp) REVERT: F 414 MET cc_start: 0.8816 (ppp) cc_final: 0.8610 (ptm) outliers start: 25 outliers final: 15 residues processed: 77 average time/residue: 0.2624 time to fit residues: 33.0517 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 : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET 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 62 ILE Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 140 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3033 r_free = 0.3033 target = 0.040997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.034399 restraints weight = 183168.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.034969 restraints weight = 121750.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.035361 restraints weight = 89664.878| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17516 Z= 0.228 Angle : 0.639 9.304 24080 Z= 0.340 Chirality : 0.044 0.204 2638 Planarity : 0.004 0.049 2744 Dihedral : 19.652 103.636 3194 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.22 % Allowed : 19.21 % Favored : 79.57 % 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: -1.13 (0.20), residues: 1818 helix: 0.41 (0.20), residues: 634 sheet: -1.02 (0.34), residues: 238 loop : -1.49 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 319 HIS 0.005 0.001 HIS F 340 PHE 0.018 0.001 PHE A 30 TYR 0.022 0.001 TYR B 293 ARG 0.005 0.001 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 526) hydrogen bonds : angle 5.31047 ( 1476) covalent geometry : bond 0.00498 (17516) covalent geometry : angle 0.63899 (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 66 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 1.983 Fit side-chains revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6731 (m-80) cc_final: 0.6368 (m-80) REVERT: A 305 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9291 (pp) REVERT: A 491 THR cc_start: 0.9660 (OUTLIER) cc_final: 0.9384 (p) REVERT: B 92 MET cc_start: 0.8889 (tpp) cc_final: 0.8520 (tpp) REVERT: B 230 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8697 (m) REVERT: E 71 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8205 (p) REVERT: E 229 LEU cc_start: 0.9245 (mt) cc_final: 0.8999 (mt) REVERT: E 406 MET cc_start: 0.9435 (pp-130) cc_final: 0.9198 (ppp) REVERT: F 414 MET cc_start: 0.8836 (ppp) cc_final: 0.8611 (ptm) outliers start: 20 outliers final: 15 residues processed: 64 average time/residue: 0.2875 time to fit residues: 30.3802 Evaluate side-chains 64 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain B residue 75 LEU 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 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 62 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 179 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: ** 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 = 0.3044 r_free = 0.3044 target = 0.041273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034675 restraints weight = 181719.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.035229 restraints weight = 120691.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035623 restraints weight = 89825.413| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4664 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= 0.179 Angle : 0.623 9.772 24080 Z= 0.330 Chirality : 0.043 0.179 2638 Planarity : 0.004 0.049 2744 Dihedral : 19.596 103.111 3194 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.28 % Allowed : 19.21 % Favored : 79.51 % 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: -1.11 (0.20), residues: 1818 helix: 0.44 (0.20), residues: 634 sheet: -0.97 (0.34), residues: 235 loop : -1.50 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 20 HIS 0.005 0.001 HIS B 188 PHE 0.017 0.001 PHE A 30 TYR 0.023 0.001 TYR B 293 ARG 0.004 0.000 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 526) hydrogen bonds : angle 5.26505 ( 1476) covalent geometry : bond 0.00395 (17516) covalent geometry : angle 0.62275 (24080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4636.70 seconds wall clock time: 83 minutes 1.51 seconds (4981.51 seconds total)