Starting phenix.real_space_refine on Thu Aug 6 15:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2026/8hg1_34731.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2139 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 8953 2.51 5 N 2354 2.21 5 O 2737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8207 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 967} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.77, per 1000 atoms: 0.20 Number of scatterers: 14155 At special positions: 0 Unit cell: (93.5, 119.85, 146.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 39 15.00 Mg 1 11.99 O 2737 8.00 N 2354 7.00 C 8953 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: 0.90 Conformation dependent library (CDL) restraints added in 449.9 milliseconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 21 sheets defined 40.7% alpha, 21.3% beta 14 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.529A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.738A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 474 " --> pdb=" O TRP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.618A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.809A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 643 Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.840A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 764 through 782 Processing helix chain 'A' and resid 837 through 857 removed outlier: 3.901A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.027A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 983 removed outlier: 4.490A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 983 " --> pdb=" O ILE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 16 through 21 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 22 through 32 removed outlier: 4.131A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.698A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 152 removed outlier: 5.555A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 108 through 121 removed outlier: 4.165A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.571A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.510A pdb=" N LYS C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.813A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 341 removed outlier: 3.705A pdb=" N ASP C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.641A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.993A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.587A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.884A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 17 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 135 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.992A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.434A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.188A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 200 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 305 removed outlier: 3.549A pdb=" N ASN A 315 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.582A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 750 removed outlier: 6.764A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB3, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.907A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB7, first strand: chain 'C' and resid 69 through 71 removed outlier: 3.609A pdb=" N ILE C 71 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 166 through 169 removed outlier: 7.539A pdb=" N TYR C 75 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 201 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 77 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR C 199 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 79 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE C 197 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 81 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 197 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.539A pdb=" N VAL C 96 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE C 126 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 142 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 140 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 130 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N MET C 138 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 217 through 219 removed outlier: 3.579A pdb=" N LYS C 267 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C 273 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 238 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 217 through 219 removed outlier: 3.579A pdb=" N LYS C 267 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C 273 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.909A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2249 1.32 - 1.44: 4117 1.44 - 1.56: 7986 1.56 - 1.69: 76 1.69 - 1.81: 108 Bond restraints: 14536 Sorted by residual: bond pdb=" C PRO A 594 " pdb=" O PRO A 594 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C PRO A 593 " pdb=" O PRO A 593 " ideal model delta sigma weight residual 1.240 1.204 0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" C3' DT P 15 " pdb=" C2' DT P 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 bond pdb=" C3' DA T 7 " pdb=" C2' DA T 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.59e+00 bond pdb=" C3' DC P 18 " pdb=" C2' DC P 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.57e+00 ... (remaining 14531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 19767 4.40 - 8.80: 34 8.80 - 13.20: 2 13.20 - 17.60: 0 17.60 - 22.00: 1 Bond angle restraints: 19804 Sorted by residual: angle pdb=" PA TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " ideal model delta sigma weight residual 120.50 142.50 -22.00 3.00e+00 1.11e-01 5.38e+01 angle pdb=" N PRO A 593 " pdb=" CA PRO A 593 " pdb=" C PRO A 593 " ideal model delta sigma weight residual 110.70 119.47 -8.77 1.22e+00 6.72e-01 5.17e+01 angle pdb=" C PRO A 593 " pdb=" CA PRO A 593 " pdb=" CB PRO A 593 " ideal model delta sigma weight residual 110.92 104.60 6.32 1.22e+00 6.72e-01 2.68e+01 angle pdb=" CA PRO A 593 " pdb=" C PRO A 593 " pdb=" N PRO A 594 " ideal model delta sigma weight residual 117.93 123.76 -5.83 1.20e+00 6.94e-01 2.36e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 19799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 8459 35.03 - 70.06: 222 70.06 - 105.09: 10 105.09 - 140.12: 2 140.12 - 175.16: 2 Dihedral angle restraints: 8695 sinusoidal: 3822 harmonic: 4873 Sorted by residual: dihedral pdb=" O3B TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " pdb=" PA TTP A1102 " ideal model delta sinusoidal sigma weight residual -180.00 -4.84 -175.16 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP A1102 " pdb=" C1' TTP A1102 " pdb=" N1 TTP A1102 " pdb=" O4' TTP A1102 " ideal model delta sinusoidal sigma weight residual 301.68 150.46 151.22 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' TTP A1102 " pdb=" O5' TTP A1102 " pdb=" PA TTP A1102 " pdb=" O3A TTP A1102 " ideal model delta sinusoidal sigma weight residual 179.97 48.42 131.55 1 2.00e+01 2.50e-03 3.99e+01 ... (remaining 8692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1553 0.041 - 0.082: 457 0.082 - 0.123: 165 0.123 - 0.164: 10 0.164 - 0.205: 6 Chirality restraints: 2191 Sorted by residual: chirality pdb=" CA LYS A 661 " pdb=" N LYS A 661 " pdb=" C LYS A 661 " pdb=" CB LYS A 661 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU A 341 " pdb=" CB LEU A 341 " pdb=" CD1 LEU A 341 " pdb=" CD2 LEU A 341 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PRO C 107 " pdb=" N PRO C 107 " pdb=" C PRO C 107 " pdb=" CB PRO C 107 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 2188 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 50 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C VAL C 50 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL C 50 " 0.025 2.00e-02 2.50e+03 pdb=" N THR C 51 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 209 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 737 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 738 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " -0.030 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 202 2.66 - 3.22: 12611 3.22 - 3.78: 20566 3.78 - 4.34: 28730 4.34 - 4.90: 47479 Nonbonded interactions: 109588 Sorted by model distance: nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A1101 " model vdw 2.100 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A1101 " model vdw 2.101 2.170 nonbonded pdb=" OG SER B 97 " pdb=" O VAL B 102 " model vdw 2.154 3.040 nonbonded pdb="MG MG A1101 " pdb=" O1B TTP A1102 " model vdw 2.170 2.170 nonbonded pdb=" OD1 ASP A 549 " pdb="MG MG A1101 " model vdw 2.199 2.170 ... (remaining 109583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 : 0.004 0.050 14536 Z= 0.248 Angle : 0.687 21.996 19804 Z= 0.422 Chirality : 0.044 0.205 2191 Planarity : 0.004 0.054 2388 Dihedral : 15.318 175.155 5553 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.02 % Favored : 94.68 % Rotamer: Outliers : 0.13 % Allowed : 0.00 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1634 helix: 1.49 (0.22), residues: 578 sheet: 0.50 (0.28), residues: 376 loop : -1.32 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 776 TYR 0.019 0.001 TYR C 276 PHE 0.017 0.001 PHE C 22 TRP 0.011 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.25 (14536) covalent geometry : angle 0.68740 / 0.42 (19804) hydrogen bonds : bond 0.19327 / 13.20 ( 606) hydrogen bonds : angle 6.23824 / 4.26 ( 1707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6943 (mm-30) REVERT: A 223 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7381 (ttt-90) REVERT: A 361 LEU cc_start: 0.8885 (tp) cc_final: 0.8651 (tt) REVERT: A 400 ASP cc_start: 0.7104 (t70) cc_final: 0.6824 (t0) REVERT: A 655 SER cc_start: 0.7757 (m) cc_final: 0.7544 (m) REVERT: A 709 ASN cc_start: 0.7737 (m-40) cc_final: 0.7518 (m-40) REVERT: A 986 LYS cc_start: 0.7718 (mppt) cc_final: 0.7454 (mppt) REVERT: B 210 ILE cc_start: 0.8950 (mm) cc_final: 0.8749 (mt) REVERT: C 36 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6245 (mt-10) REVERT: C 185 GLU cc_start: 0.7353 (tt0) cc_final: 0.7144 (tt0) REVERT: C 347 LYS cc_start: 0.8349 (tptp) cc_final: 0.8082 (tptp) REVERT: C 355 ASP cc_start: 0.7141 (m-30) cc_final: 0.6830 (m-30) REVERT: C 393 ASN cc_start: 0.7493 (m110) cc_final: 0.7052 (m110) REVERT: C 396 ASN cc_start: 0.7854 (m-40) cc_final: 0.7653 (m-40) outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 0.4934 time to fit residues: 202.4180 Evaluate side-chains 332 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 204 ASN A 336 GLN A 426 ASN A 801 GLN B 59 ASN C 386 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118070 restraints weight = 20532.036| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.03 r_work: 0.3453 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14536 Z= 0.139 Angle : 0.613 10.547 19804 Z= 0.331 Chirality : 0.044 0.180 2191 Planarity : 0.005 0.080 2388 Dihedral : 14.826 178.363 2232 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.22 % Favored : 95.47 % Rotamer: Outliers : 2.05 % Allowed : 9.17 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1634 helix: 1.50 (0.22), residues: 590 sheet: 0.63 (0.27), residues: 383 loop : -1.20 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.020 0.001 TYR C 158 PHE 0.020 0.001 PHE A 838 TRP 0.010 0.001 TRP A 470 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (14536) covalent geometry : angle 0.61322 / 0.33 (19804) hydrogen bonds : bond 0.05368 / 3.60 ( 606) hydrogen bonds : angle 4.88703 / 3.33 ( 1707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 357 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8065 (p0) cc_final: 0.7847 (p0) REVERT: A 93 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 361 LEU cc_start: 0.8885 (tp) cc_final: 0.8676 (tt) REVERT: A 362 ASN cc_start: 0.8909 (t0) cc_final: 0.8546 (t0) REVERT: A 367 GLU cc_start: 0.8067 (pp20) cc_final: 0.7666 (pp20) REVERT: A 373 ASP cc_start: 0.7791 (t0) cc_final: 0.7495 (t0) REVERT: A 587 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7848 (tt) REVERT: A 709 ASN cc_start: 0.8127 (m-40) cc_final: 0.7908 (m-40) REVERT: A 809 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8032 (mmt) REVERT: A 825 ASN cc_start: 0.8718 (m110) cc_final: 0.8496 (m-40) REVERT: A 986 LYS cc_start: 0.7848 (mppt) cc_final: 0.7505 (mppt) REVERT: B 94 SER cc_start: 0.8043 (t) cc_final: 0.7767 (p) REVERT: C 36 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6730 (mt-10) REVERT: C 72 ASP cc_start: 0.5571 (t0) cc_final: 0.4988 (t70) REVERT: C 185 GLU cc_start: 0.7583 (tt0) cc_final: 0.7220 (tt0) REVERT: C 228 ILE cc_start: 0.7991 (tp) cc_final: 0.7788 (pp) REVERT: C 355 ASP cc_start: 0.8029 (m-30) cc_final: 0.7685 (m-30) REVERT: C 393 ASN cc_start: 0.8079 (m110) cc_final: 0.7663 (m110) REVERT: C 396 ASN cc_start: 0.8290 (m-40) cc_final: 0.8001 (m-40) outliers start: 31 outliers final: 11 residues processed: 365 average time/residue: 0.5733 time to fit residues: 229.0454 Evaluate side-chains 343 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 330 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 107 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 225 GLN B 59 ASN C 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115750 restraints weight = 20578.349| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.05 r_work: 0.3418 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14536 Z= 0.216 Angle : 0.617 9.891 19804 Z= 0.332 Chirality : 0.045 0.197 2191 Planarity : 0.005 0.085 2388 Dihedral : 14.930 175.763 2232 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.71 % Favored : 95.04 % Rotamer: Outliers : 2.64 % Allowed : 12.67 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1634 helix: 1.39 (0.22), residues: 598 sheet: 0.49 (0.27), residues: 376 loop : -1.25 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 223 TYR 0.016 0.002 TYR A 528 PHE 0.025 0.002 PHE A 838 TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (14536) covalent geometry : angle 0.61721 / 0.33 (19804) hydrogen bonds : bond 0.05690 / 3.81 ( 606) hydrogen bonds : angle 4.75796 / 3.26 ( 1707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 360 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 223 ARG cc_start: 0.8489 (ttt-90) cc_final: 0.8264 (ttt-90) REVERT: A 292 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8269 (mtmt) REVERT: A 310 VAL cc_start: 0.8449 (p) cc_final: 0.8152 (m) REVERT: A 361 LEU cc_start: 0.8914 (tp) cc_final: 0.8697 (tt) REVERT: A 362 ASN cc_start: 0.8929 (t0) cc_final: 0.8613 (t0) REVERT: A 367 GLU cc_start: 0.8069 (pp20) cc_final: 0.7683 (pp20) REVERT: A 373 ASP cc_start: 0.7786 (t0) cc_final: 0.7519 (t0) REVERT: A 467 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: A 497 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7966 (mtt90) REVERT: A 509 LEU cc_start: 0.8383 (tp) cc_final: 0.8163 (tp) REVERT: A 587 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7885 (tt) REVERT: A 709 ASN cc_start: 0.8216 (m-40) cc_final: 0.8005 (m-40) REVERT: A 800 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8698 (mmt) REVERT: A 842 MET cc_start: 0.7839 (tpp) cc_final: 0.7632 (mmm) REVERT: A 983 LEU cc_start: 0.7924 (mm) cc_final: 0.7708 (mt) REVERT: A 986 LYS cc_start: 0.7874 (mppt) cc_final: 0.7518 (mppt) REVERT: B 54 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7517 (mmmm) REVERT: C 36 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6782 (mt-10) REVERT: C 72 ASP cc_start: 0.5963 (t0) cc_final: 0.5625 (t0) REVERT: C 78 PHE cc_start: 0.7319 (m-10) cc_final: 0.6973 (m-10) REVERT: C 172 GLU cc_start: 0.6633 (pm20) cc_final: 0.6355 (pm20) REVERT: C 185 GLU cc_start: 0.7680 (tt0) cc_final: 0.7338 (tt0) REVERT: C 206 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7772 (mmmt) REVERT: C 355 ASP cc_start: 0.7970 (m-30) cc_final: 0.7625 (m-30) REVERT: C 384 VAL cc_start: 0.7850 (p) cc_final: 0.7634 (t) REVERT: C 393 ASN cc_start: 0.8097 (m110) cc_final: 0.7682 (m110) REVERT: C 396 ASN cc_start: 0.8289 (m-40) cc_final: 0.7991 (m-40) outliers start: 40 outliers final: 18 residues processed: 373 average time/residue: 0.5310 time to fit residues: 216.6837 Evaluate side-chains 363 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 341 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 326 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN A 48 GLN A 225 GLN A 467 GLN A 643 GLN A 825 ASN B 59 ASN C 386 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116305 restraints weight = 20538.537| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.04 r_work: 0.3427 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14536 Z= 0.153 Angle : 0.584 8.516 19804 Z= 0.313 Chirality : 0.043 0.172 2191 Planarity : 0.005 0.085 2388 Dihedral : 14.866 167.405 2232 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % Rotamer: Outliers : 2.71 % Allowed : 14.52 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1634 helix: 1.50 (0.22), residues: 586 sheet: 0.42 (0.28), residues: 361 loop : -1.17 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 674 TYR 0.017 0.001 TYR C 158 PHE 0.022 0.001 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (14536) covalent geometry : angle 0.58350 / 0.31 (19804) hydrogen bonds : bond 0.04943 / 3.30 ( 606) hydrogen bonds : angle 4.60715 / 3.16 ( 1707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 350 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 223 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8234 (ttt-90) REVERT: A 292 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8258 (mtmt) REVERT: A 310 VAL cc_start: 0.8431 (p) cc_final: 0.8118 (m) REVERT: A 339 GLU cc_start: 0.7682 (pp20) cc_final: 0.7228 (pp20) REVERT: A 361 LEU cc_start: 0.8900 (tp) cc_final: 0.8652 (tt) REVERT: A 362 ASN cc_start: 0.8908 (t0) cc_final: 0.8603 (t0) REVERT: A 367 GLU cc_start: 0.8090 (pp20) cc_final: 0.7766 (pp20) REVERT: A 497 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7915 (mtt90) REVERT: A 509 LEU cc_start: 0.8362 (tp) cc_final: 0.8154 (tp) REVERT: A 636 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8171 (ttm170) REVERT: A 800 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8794 (mmt) REVERT: A 983 LEU cc_start: 0.7898 (mm) cc_final: 0.7667 (mt) REVERT: A 986 LYS cc_start: 0.7868 (mppt) cc_final: 0.7501 (mppt) REVERT: C 36 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6757 (mt-10) REVERT: C 72 ASP cc_start: 0.5907 (t0) cc_final: 0.5454 (t0) REVERT: C 122 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7936 (p0) REVERT: C 172 GLU cc_start: 0.6620 (pm20) cc_final: 0.6364 (pm20) REVERT: C 244 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7902 (mtmm) REVERT: C 355 ASP cc_start: 0.8008 (m-30) cc_final: 0.7595 (m-30) REVERT: C 384 VAL cc_start: 0.7749 (p) cc_final: 0.7513 (t) REVERT: C 393 ASN cc_start: 0.8114 (m110) cc_final: 0.7675 (m110) REVERT: C 396 ASN cc_start: 0.8316 (m-40) cc_final: 0.8022 (m-40) outliers start: 41 outliers final: 18 residues processed: 362 average time/residue: 0.4968 time to fit residues: 196.4895 Evaluate side-chains 364 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 342 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 244 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 151 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 225 GLN A 413 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116581 restraints weight = 20510.528| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.02 r_work: 0.3428 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14536 Z= 0.149 Angle : 0.581 10.125 19804 Z= 0.310 Chirality : 0.043 0.178 2191 Planarity : 0.005 0.070 2388 Dihedral : 14.802 161.299 2232 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 3.04 % Allowed : 15.31 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1634 helix: 1.50 (0.22), residues: 588 sheet: 0.40 (0.28), residues: 361 loop : -1.16 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 674 TYR 0.012 0.001 TYR A 528 PHE 0.023 0.001 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14536) covalent geometry : angle 0.58065 / 0.31 (19804) hydrogen bonds : bond 0.04770 / 3.19 ( 606) hydrogen bonds : angle 4.54025 / 3.12 ( 1707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 357 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7806 (t0) cc_final: 0.7586 (t0) REVERT: A 93 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 292 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8230 (mtmt) REVERT: A 310 VAL cc_start: 0.8423 (p) cc_final: 0.8100 (m) REVERT: A 339 GLU cc_start: 0.7695 (pp20) cc_final: 0.7016 (pp20) REVERT: A 341 LEU cc_start: 0.8676 (mt) cc_final: 0.8266 (mt) REVERT: A 361 LEU cc_start: 0.8889 (tp) cc_final: 0.8630 (tt) REVERT: A 362 ASN cc_start: 0.8908 (t0) cc_final: 0.8615 (t0) REVERT: A 367 GLU cc_start: 0.8082 (pp20) cc_final: 0.7765 (pp20) REVERT: A 373 ASP cc_start: 0.7792 (t0) cc_final: 0.7562 (t0) REVERT: A 587 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7838 (tt) REVERT: A 636 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8153 (ttm170) REVERT: A 983 LEU cc_start: 0.7893 (mm) cc_final: 0.7660 (mt) REVERT: A 986 LYS cc_start: 0.7873 (mppt) cc_final: 0.7528 (mppt) REVERT: C 36 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6740 (mt-10) REVERT: C 177 ASP cc_start: 0.7933 (p0) cc_final: 0.7706 (p0) REVERT: C 206 LYS cc_start: 0.7934 (mmmm) cc_final: 0.7733 (mmmt) REVERT: C 234 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7970 (pp) REVERT: C 244 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7961 (mtmm) REVERT: C 355 ASP cc_start: 0.7973 (m-30) cc_final: 0.7563 (m-30) REVERT: C 384 VAL cc_start: 0.7710 (p) cc_final: 0.7456 (t) REVERT: C 402 THR cc_start: 0.7863 (m) cc_final: 0.7537 (p) outliers start: 46 outliers final: 23 residues processed: 373 average time/residue: 0.4923 time to fit residues: 201.2552 Evaluate side-chains 379 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 352 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 326 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 225 GLN A 413 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114921 restraints weight = 20455.984| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.05 r_work: 0.3408 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14536 Z= 0.214 Angle : 0.618 9.398 19804 Z= 0.329 Chirality : 0.045 0.169 2191 Planarity : 0.005 0.061 2388 Dihedral : 14.823 156.195 2232 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.08 % Favored : 94.74 % Rotamer: Outliers : 3.17 % Allowed : 16.44 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1634 helix: 1.36 (0.22), residues: 596 sheet: 0.33 (0.28), residues: 361 loop : -1.18 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.016 0.002 TYR A 660 PHE 0.026 0.002 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (14536) covalent geometry : angle 0.61832 / 0.33 (19804) hydrogen bonds : bond 0.05347 / 3.57 ( 606) hydrogen bonds : angle 4.57486 / 3.15 ( 1707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7790 (t0) cc_final: 0.7576 (t0) REVERT: A 93 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 292 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8274 (mtmt) REVERT: A 310 VAL cc_start: 0.8433 (p) cc_final: 0.8125 (m) REVERT: A 339 GLU cc_start: 0.7718 (pp20) cc_final: 0.7088 (pp20) REVERT: A 341 LEU cc_start: 0.8711 (mt) cc_final: 0.8265 (mt) REVERT: A 361 LEU cc_start: 0.8908 (tp) cc_final: 0.8666 (tt) REVERT: A 362 ASN cc_start: 0.8927 (t0) cc_final: 0.8647 (t0) REVERT: A 367 GLU cc_start: 0.8092 (pp20) cc_final: 0.7770 (pp20) REVERT: A 657 GLN cc_start: 0.8192 (pp30) cc_final: 0.7821 (pp30) REVERT: A 712 LEU cc_start: 0.8593 (tp) cc_final: 0.8326 (tt) REVERT: A 983 LEU cc_start: 0.7932 (mm) cc_final: 0.7713 (mt) REVERT: A 986 LYS cc_start: 0.7913 (mppt) cc_final: 0.7549 (mppt) REVERT: C 36 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6776 (mt-10) REVERT: C 72 ASP cc_start: 0.6119 (t0) cc_final: 0.5746 (t0) REVERT: C 199 TYR cc_start: 0.7703 (p90) cc_final: 0.7285 (p90) REVERT: C 234 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8037 (pp) REVERT: C 355 ASP cc_start: 0.7976 (m-30) cc_final: 0.7564 (m-30) REVERT: C 378 LYS cc_start: 0.7719 (tttm) cc_final: 0.7469 (tttm) REVERT: C 384 VAL cc_start: 0.7745 (p) cc_final: 0.7478 (t) REVERT: C 402 THR cc_start: 0.7941 (m) cc_final: 0.7615 (p) outliers start: 48 outliers final: 33 residues processed: 376 average time/residue: 0.5020 time to fit residues: 207.3845 Evaluate side-chains 386 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 352 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 403 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 225 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN C 386 ASN C 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115274 restraints weight = 20506.676| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.03 r_work: 0.3413 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14536 Z= 0.186 Angle : 0.610 9.192 19804 Z= 0.324 Chirality : 0.044 0.169 2191 Planarity : 0.005 0.060 2388 Dihedral : 14.771 150.473 2232 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.83 % Favored : 94.98 % Rotamer: Outliers : 3.30 % Allowed : 16.90 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1634 helix: 1.34 (0.22), residues: 596 sheet: 0.35 (0.28), residues: 357 loop : -1.16 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.014 0.002 TYR A 528 PHE 0.029 0.002 PHE C 78 TRP 0.012 0.001 TRP A 470 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (14536) covalent geometry : angle 0.61017 / 0.32 (19804) hydrogen bonds : bond 0.05109 / 3.41 ( 606) hydrogen bonds : angle 4.54832 / 3.14 ( 1707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7805 (t0) cc_final: 0.7587 (t0) REVERT: A 93 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 292 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8268 (mtmt) REVERT: A 310 VAL cc_start: 0.8423 (p) cc_final: 0.8118 (m) REVERT: A 339 GLU cc_start: 0.7683 (pp20) cc_final: 0.7032 (pp20) REVERT: A 341 LEU cc_start: 0.8698 (mt) cc_final: 0.8219 (mt) REVERT: A 361 LEU cc_start: 0.8905 (tp) cc_final: 0.8660 (tt) REVERT: A 362 ASN cc_start: 0.8916 (t0) cc_final: 0.8654 (t0) REVERT: A 367 GLU cc_start: 0.8088 (pp20) cc_final: 0.7771 (pp20) REVERT: A 657 GLN cc_start: 0.8169 (pp30) cc_final: 0.7814 (pp30) REVERT: A 712 LEU cc_start: 0.8608 (tp) cc_final: 0.8342 (tt) REVERT: A 983 LEU cc_start: 0.7911 (mm) cc_final: 0.7694 (mt) REVERT: A 986 LYS cc_start: 0.7910 (mppt) cc_final: 0.7532 (mppt) REVERT: C 36 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6740 (mt-10) REVERT: C 72 ASP cc_start: 0.6094 (t0) cc_final: 0.5730 (t0) REVERT: C 157 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: C 234 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8029 (pp) REVERT: C 355 ASP cc_start: 0.7970 (m-30) cc_final: 0.7547 (m-30) REVERT: C 378 LYS cc_start: 0.7724 (tttm) cc_final: 0.7476 (tttm) REVERT: C 384 VAL cc_start: 0.7744 (p) cc_final: 0.7474 (t) REVERT: C 402 THR cc_start: 0.7945 (m) cc_final: 0.7614 (p) outliers start: 50 outliers final: 36 residues processed: 379 average time/residue: 0.5129 time to fit residues: 212.8796 Evaluate side-chains 387 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 349 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 403 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 225 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115788 restraints weight = 20489.948| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.02 r_work: 0.3419 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14536 Z= 0.166 Angle : 0.603 9.678 19804 Z= 0.321 Chirality : 0.044 0.169 2191 Planarity : 0.005 0.058 2388 Dihedral : 14.719 145.680 2232 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.83 % Favored : 94.98 % Rotamer: Outliers : 3.43 % Allowed : 17.49 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1634 helix: 1.37 (0.22), residues: 598 sheet: 0.35 (0.28), residues: 357 loop : -1.13 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 223 TYR 0.014 0.001 TYR A 528 PHE 0.023 0.001 PHE C 78 TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (14536) covalent geometry : angle 0.60260 / 0.32 (19804) hydrogen bonds : bond 0.04917 / 3.27 ( 606) hydrogen bonds : angle 4.50808 / 3.11 ( 1707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 359 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7831 (t0) cc_final: 0.7607 (t0) REVERT: A 93 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 292 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8244 (mtmt) REVERT: A 310 VAL cc_start: 0.8438 (p) cc_final: 0.8129 (m) REVERT: A 339 GLU cc_start: 0.7681 (pp20) cc_final: 0.7037 (pp20) REVERT: A 341 LEU cc_start: 0.8697 (mt) cc_final: 0.8232 (mt) REVERT: A 361 LEU cc_start: 0.8905 (tp) cc_final: 0.8655 (tt) REVERT: A 362 ASN cc_start: 0.8917 (t0) cc_final: 0.8640 (t0) REVERT: A 367 GLU cc_start: 0.8083 (pp20) cc_final: 0.7766 (pp20) REVERT: A 636 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8133 (ttm170) REVERT: A 657 GLN cc_start: 0.8158 (pp30) cc_final: 0.7798 (pp30) REVERT: A 712 LEU cc_start: 0.8605 (tp) cc_final: 0.8347 (tt) REVERT: A 983 LEU cc_start: 0.7913 (mm) cc_final: 0.7696 (mt) REVERT: A 986 LYS cc_start: 0.7915 (mppt) cc_final: 0.7537 (mppt) REVERT: C 36 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6726 (mt-10) REVERT: C 72 ASP cc_start: 0.6109 (t0) cc_final: 0.5758 (t0) REVERT: C 157 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: C 177 ASP cc_start: 0.7916 (p0) cc_final: 0.7683 (p0) REVERT: C 234 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8022 (pp) REVERT: C 355 ASP cc_start: 0.7926 (m-30) cc_final: 0.7509 (m-30) REVERT: C 378 LYS cc_start: 0.7717 (tttm) cc_final: 0.7468 (tttm) REVERT: C 384 VAL cc_start: 0.7733 (p) cc_final: 0.7455 (t) REVERT: C 402 THR cc_start: 0.7941 (m) cc_final: 0.7603 (p) outliers start: 52 outliers final: 36 residues processed: 378 average time/residue: 0.4852 time to fit residues: 201.2889 Evaluate side-chains 381 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 342 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 403 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 225 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116247 restraints weight = 20556.120| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.03 r_work: 0.3426 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14536 Z= 0.143 Angle : 0.594 9.377 19804 Z= 0.315 Chirality : 0.043 0.170 2191 Planarity : 0.004 0.052 2388 Dihedral : 14.614 138.940 2232 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % Rotamer: Outliers : 2.84 % Allowed : 18.61 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1634 helix: 1.47 (0.22), residues: 591 sheet: 0.40 (0.28), residues: 355 loop : -1.10 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 407 TYR 0.013 0.001 TYR A 528 PHE 0.021 0.001 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14536) covalent geometry : angle 0.59422 / 0.32 (19804) hydrogen bonds : bond 0.04574 / 3.03 ( 606) hydrogen bonds : angle 4.44684 / 3.07 ( 1707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 360 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7827 (t0) cc_final: 0.7596 (t0) REVERT: A 93 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 292 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8243 (mtmt) REVERT: A 310 VAL cc_start: 0.8431 (p) cc_final: 0.8116 (m) REVERT: A 339 GLU cc_start: 0.7674 (pp20) cc_final: 0.6974 (pp20) REVERT: A 340 LYS cc_start: 0.7996 (ptmm) cc_final: 0.7138 (ptmm) REVERT: A 341 LEU cc_start: 0.8667 (mt) cc_final: 0.8202 (mt) REVERT: A 361 LEU cc_start: 0.8900 (tp) cc_final: 0.8644 (tt) REVERT: A 362 ASN cc_start: 0.8902 (t0) cc_final: 0.8628 (t0) REVERT: A 367 GLU cc_start: 0.8089 (pp20) cc_final: 0.7776 (pp20) REVERT: A 636 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8184 (ttm170) REVERT: A 657 GLN cc_start: 0.8153 (pp30) cc_final: 0.7785 (pp30) REVERT: A 694 MET cc_start: 0.8557 (mmm) cc_final: 0.8296 (mmt) REVERT: A 712 LEU cc_start: 0.8593 (tp) cc_final: 0.8340 (tt) REVERT: A 983 LEU cc_start: 0.7914 (mm) cc_final: 0.7699 (mt) REVERT: A 986 LYS cc_start: 0.7935 (mppt) cc_final: 0.7551 (mppt) REVERT: C 36 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6706 (mt-10) REVERT: C 72 ASP cc_start: 0.6100 (t0) cc_final: 0.5749 (t0) REVERT: C 157 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: C 177 ASP cc_start: 0.7903 (p0) cc_final: 0.7678 (p0) REVERT: C 234 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8002 (pp) REVERT: C 355 ASP cc_start: 0.7905 (m-30) cc_final: 0.7492 (m-30) REVERT: C 378 LYS cc_start: 0.7711 (tttm) cc_final: 0.7458 (tttm) REVERT: C 384 VAL cc_start: 0.7711 (p) cc_final: 0.7421 (t) REVERT: C 402 THR cc_start: 0.7893 (m) cc_final: 0.7546 (p) outliers start: 43 outliers final: 30 residues processed: 375 average time/residue: 0.5044 time to fit residues: 207.6706 Evaluate side-chains 384 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.0020 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 825 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 = 0.3808 r_free = 0.3808 target = 0.136497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116579 restraints weight = 20560.167| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.02 r_work: 0.3432 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14536 Z= 0.135 Angle : 0.600 14.109 19804 Z= 0.316 Chirality : 0.043 0.198 2191 Planarity : 0.004 0.047 2388 Dihedral : 14.555 138.901 2232 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.35 % Rotamer: Outliers : 2.38 % Allowed : 19.21 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1634 helix: 1.52 (0.22), residues: 591 sheet: 0.45 (0.29), residues: 352 loop : -1.07 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 407 TYR 0.024 0.001 TYR C 158 PHE 0.022 0.001 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14536) covalent geometry : angle 0.59999 / 0.32 (19804) hydrogen bonds : bond 0.04439 / 2.95 ( 606) hydrogen bonds : angle 4.42495 / 3.06 ( 1707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 352 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7809 (t0) cc_final: 0.7578 (t0) REVERT: A 93 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 292 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8240 (mtmt) REVERT: A 310 VAL cc_start: 0.8428 (p) cc_final: 0.8114 (m) REVERT: A 339 GLU cc_start: 0.7667 (pp20) cc_final: 0.6980 (pp20) REVERT: A 341 LEU cc_start: 0.8648 (mt) cc_final: 0.8185 (mt) REVERT: A 361 LEU cc_start: 0.8896 (tp) cc_final: 0.8629 (tt) REVERT: A 362 ASN cc_start: 0.8904 (t0) cc_final: 0.8631 (t0) REVERT: A 367 GLU cc_start: 0.8090 (pp20) cc_final: 0.7779 (pp20) REVERT: A 636 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8172 (ttm170) REVERT: A 694 MET cc_start: 0.8548 (mmm) cc_final: 0.8324 (mmm) REVERT: A 712 LEU cc_start: 0.8584 (tp) cc_final: 0.8327 (tt) REVERT: A 983 LEU cc_start: 0.7907 (mm) cc_final: 0.7692 (mt) REVERT: A 986 LYS cc_start: 0.7935 (mppt) cc_final: 0.7548 (mppt) REVERT: C 36 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6702 (mt-10) REVERT: C 72 ASP cc_start: 0.6105 (t0) cc_final: 0.5729 (t0) REVERT: C 157 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7418 (pp20) REVERT: C 177 ASP cc_start: 0.7920 (p0) cc_final: 0.7698 (p0) REVERT: C 234 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7989 (pp) REVERT: C 355 ASP cc_start: 0.7926 (m-30) cc_final: 0.7513 (m-30) REVERT: C 378 LYS cc_start: 0.7680 (tttm) cc_final: 0.7431 (tttm) REVERT: C 384 VAL cc_start: 0.7691 (p) cc_final: 0.7398 (t) outliers start: 36 outliers final: 30 residues processed: 369 average time/residue: 0.4821 time to fit residues: 195.8511 Evaluate side-chains 384 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 934 CYS Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114713 restraints weight = 20517.316| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.02 r_work: 0.3404 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14536 Z= 0.219 Angle : 0.641 11.221 19804 Z= 0.339 Chirality : 0.046 0.196 2191 Planarity : 0.005 0.048 2388 Dihedral : 14.618 138.997 2232 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.61 % Rotamer: Outliers : 2.24 % Allowed : 19.60 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1634 helix: 1.37 (0.22), residues: 596 sheet: 0.43 (0.29), residues: 352 loop : -1.18 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.021 0.002 TYR C 158 PHE 0.027 0.002 PHE A 838 TRP 0.011 0.002 TRP A 940 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (14536) covalent geometry : angle 0.64126 / 0.34 (19804) hydrogen bonds : bond 0.05343 / 3.55 ( 606) hydrogen bonds : angle 4.55501 / 3.15 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5055.97 seconds wall clock time: 86 minutes 33.02 seconds (5193.02 seconds total)