Starting phenix.real_space_refine on Sun Aug 24 01:11:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hg1_34731/08_2025/8hg1_34731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg1_34731/08_2025/8hg1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2025/8hg1_34731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2025/8hg1_34731.map" model { file = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2025/8hg1_34731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg1_34731/08_2025/8hg1_34731.cif" } 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-2.0-5787/lib/python3.9/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: 3.63, per 1000 atoms: 0.26 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: 1.20 Conformation dependent library (CDL) restraints added in 614.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.94 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: 2.84 Time building geometry restraints manager: 1.63 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=" C PRO A 592 " pdb=" O PRO A 592 " ideal model delta sigma weight residual 1.240 1.206 0.034 1.12e-02 7.97e+03 9.18e+00 bond pdb=" C5 TTP A1102 " pdb=" C6 TTP A1102 " ideal model delta sigma weight residual 1.390 1.340 0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" N LYS A 661 " pdb=" CA LYS A 661 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.80e+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=" N LYS A 901 " pdb=" CA LYS A 901 " pdb=" C LYS A 901 " ideal model delta sigma weight residual 110.20 103.75 6.45 1.58e+00 4.01e-01 1.67e+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: 1598 0.041 - 0.082: 433 0.082 - 0.123: 144 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.250 Find NCS groups from input model: 0.060 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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= 0.181 Angle : 0.669 21.996 19804 Z= 0.374 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00368 (14536) covalent geometry : angle 0.66860 (19804) hydrogen bonds : bond 0.19327 ( 606) hydrogen bonds : angle 6.23824 ( 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 : 0.572 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: 0.6704 time to fit residues: 273.8502 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 : 0.519 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 204 ASN A 426 ASN A 801 GLN B 59 ASN C 386 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118381 restraints weight = 20568.945| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.05 r_work: 0.3458 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.131 Angle : 0.569 8.524 19804 Z= 0.305 Chirality : 0.042 0.174 2191 Planarity : 0.005 0.079 2388 Dihedral : 14.648 176.721 2232 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.65 % Favored : 95.04 % Rotamer: Outliers : 2.11 % Allowed : 9.11 % 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 aren not related in a simple way. whole: 0.37 (0.21), residues: 1634 helix: 1.49 (0.22), residues: 593 sheet: 0.66 (0.28), residues: 370 loop : -1.15 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 674 TYR 0.013 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 A 839 Details of bonding type rmsd covalent geometry : bond 0.00295 (14536) covalent geometry : angle 0.56904 (19804) hydrogen bonds : bond 0.04591 ( 606) hydrogen bonds : angle 4.68691 ( 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 389 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 357 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8086 (p0) cc_final: 0.7882 (p0) REVERT: A 93 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 361 LEU cc_start: 0.8878 (tp) cc_final: 0.8638 (tt) REVERT: A 362 ASN cc_start: 0.8917 (t0) cc_final: 0.8542 (t0) REVERT: A 367 GLU cc_start: 0.8074 (pp20) cc_final: 0.7678 (pp20) REVERT: A 373 ASP cc_start: 0.7828 (t0) cc_final: 0.7586 (t0) REVERT: A 587 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7810 (pp) REVERT: A 709 ASN cc_start: 0.8181 (m-40) cc_final: 0.7974 (m-40) REVERT: A 986 LYS cc_start: 0.7820 (mppt) cc_final: 0.7478 (mppt) REVERT: C 36 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6692 (mt-10) REVERT: C 72 ASP cc_start: 0.5852 (t0) cc_final: 0.5304 (t0) REVERT: C 122 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7870 (p0) REVERT: C 185 GLU cc_start: 0.7581 (tt0) cc_final: 0.7191 (tt0) REVERT: C 347 LYS cc_start: 0.8608 (tptp) cc_final: 0.8403 (tptp) REVERT: C 355 ASP cc_start: 0.7993 (m-30) cc_final: 0.7633 (m-30) REVERT: C 393 ASN cc_start: 0.8067 (m110) cc_final: 0.7667 (m110) REVERT: C 396 ASN cc_start: 0.8249 (m-40) cc_final: 0.7942 (m-40) outliers start: 32 outliers final: 10 residues processed: 367 average time/residue: 0.6652 time to fit residues: 266.0565 Evaluate side-chains 341 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 329 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 180 ILE 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 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 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: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 225 GLN A 825 ASN B 59 ASN C 386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115458 restraints weight = 20580.148| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.05 r_work: 0.3413 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14536 Z= 0.195 Angle : 0.603 9.567 19804 Z= 0.318 Chirality : 0.044 0.171 2191 Planarity : 0.005 0.081 2388 Dihedral : 14.653 159.564 2232 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 2.97 % Allowed : 13.27 % Favored : 83.76 % 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 aren not related in a simple way. whole: 0.24 (0.21), residues: 1634 helix: 1.42 (0.22), residues: 594 sheet: 0.44 (0.28), residues: 362 loop : -1.14 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 223 TYR 0.016 0.002 TYR A 660 PHE 0.021 0.002 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00465 (14536) covalent geometry : angle 0.60298 (19804) hydrogen bonds : bond 0.05308 ( 606) hydrogen bonds : angle 4.61333 ( 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 406 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 361 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 292 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8273 (mtmt) REVERT: A 310 VAL cc_start: 0.8428 (p) cc_final: 0.8116 (m) REVERT: A 339 GLU cc_start: 0.7708 (pp20) cc_final: 0.7195 (pp20) REVERT: A 341 LEU cc_start: 0.8711 (mt) cc_final: 0.8373 (mt) REVERT: A 361 LEU cc_start: 0.8909 (tp) cc_final: 0.8669 (tt) REVERT: A 362 ASN cc_start: 0.8931 (t0) cc_final: 0.8595 (t0) REVERT: A 367 GLU cc_start: 0.8092 (pp20) cc_final: 0.7697 (pp20) REVERT: A 657 GLN cc_start: 0.8170 (pp30) cc_final: 0.7903 (pp30) REVERT: A 800 MET cc_start: 0.8979 (mmt) cc_final: 0.8670 (mmt) REVERT: A 983 LEU cc_start: 0.7918 (mm) cc_final: 0.7674 (mt) REVERT: A 986 LYS cc_start: 0.7876 (mppt) cc_final: 0.7533 (mppt) REVERT: B 210 ILE cc_start: 0.9060 (mm) cc_final: 0.8852 (mt) REVERT: C 36 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6744 (mt-10) REVERT: C 72 ASP cc_start: 0.6038 (t0) cc_final: 0.5751 (t0) REVERT: C 122 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7945 (p0) REVERT: C 172 GLU cc_start: 0.6727 (pm20) cc_final: 0.6397 (pm20) REVERT: C 185 GLU cc_start: 0.7529 (tt0) cc_final: 0.7277 (tt0) REVERT: C 244 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8030 (mtmm) REVERT: C 355 ASP cc_start: 0.8004 (m-30) cc_final: 0.7607 (m-30) REVERT: C 402 THR cc_start: 0.7920 (m) cc_final: 0.7589 (p) outliers start: 45 outliers final: 19 residues processed: 377 average time/residue: 0.6493 time to fit residues: 267.4002 Evaluate side-chains 362 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 341 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 49 SER 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 446 ASP Chi-restraints excluded: chain A residue 696 LEU 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 B residue 169 LYS Chi-restraints excluded: chain C residue 77 ILE 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 157 GLU Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 246 LEU 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: 8.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 413 ASN A 643 GLN A 825 ASN B 59 ASN C 386 ASN C 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115034 restraints weight = 20521.862| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.05 r_work: 0.3409 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14536 Z= 0.195 Angle : 0.588 8.333 19804 Z= 0.313 Chirality : 0.044 0.172 2191 Planarity : 0.005 0.064 2388 Dihedral : 14.486 141.179 2232 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.92 % Rotamer: Outliers : 3.76 % Allowed : 14.92 % Favored : 81.32 % 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 aren not related in a simple way. whole: 0.18 (0.21), residues: 1634 helix: 1.33 (0.22), residues: 596 sheet: 0.38 (0.28), residues: 357 loop : -1.11 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 207 TYR 0.015 0.001 TYR A 528 PHE 0.022 0.002 PHE A 838 TRP 0.012 0.001 TRP A 470 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00466 (14536) covalent geometry : angle 0.58834 (19804) hydrogen bonds : bond 0.05140 ( 606) hydrogen bonds : angle 4.54781 ( 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 423 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 105 ASP cc_start: 0.8132 (p0) cc_final: 0.7912 (p0) REVERT: A 225 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: A 292 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8243 (mtmt) REVERT: A 310 VAL cc_start: 0.8428 (p) cc_final: 0.8118 (m) REVERT: A 339 GLU cc_start: 0.7725 (pp20) cc_final: 0.7087 (pp20) REVERT: A 340 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7292 (ptmm) REVERT: A 341 LEU cc_start: 0.8724 (mt) cc_final: 0.8320 (mt) REVERT: A 361 LEU cc_start: 0.8909 (tp) cc_final: 0.8666 (tt) REVERT: A 362 ASN cc_start: 0.8915 (t0) cc_final: 0.8622 (t0) REVERT: A 367 GLU cc_start: 0.8100 (pp20) cc_final: 0.7705 (pp20) REVERT: A 639 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8363 (ttmm) REVERT: A 983 LEU cc_start: 0.7901 (mm) cc_final: 0.7680 (mt) REVERT: A 986 LYS cc_start: 0.7899 (mppt) cc_final: 0.7541 (mppt) REVERT: C 36 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6747 (mt-10) REVERT: C 72 ASP cc_start: 0.6206 (t0) cc_final: 0.5847 (t0) REVERT: C 234 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8032 (pp) REVERT: C 355 ASP cc_start: 0.7961 (m-30) cc_final: 0.7558 (m-30) REVERT: C 402 THR cc_start: 0.7965 (m) cc_final: 0.7636 (p) outliers start: 57 outliers final: 28 residues processed: 389 average time/residue: 0.6436 time to fit residues: 274.3105 Evaluate side-chains 394 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 363 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 49 SER 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 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 696 LEU 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 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 ILE 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 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 151 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 467 GLN A 643 GLN B 59 ASN C 386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117226 restraints weight = 20609.838| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.02 r_work: 0.3443 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1967 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= 0.127 Angle : 0.555 9.701 19804 Z= 0.292 Chirality : 0.042 0.173 2191 Planarity : 0.004 0.056 2388 Dihedral : 14.192 138.755 2232 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % Rotamer: Outliers : 2.84 % Allowed : 17.10 % Favored : 80.07 % 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 aren not related in a simple way. whole: 0.32 (0.21), residues: 1634 helix: 1.46 (0.22), residues: 597 sheet: 0.46 (0.28), residues: 355 loop : -1.04 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 223 TYR 0.025 0.001 TYR C 199 PHE 0.019 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 covalent geometry : bond 0.00292 (14536) covalent geometry : angle 0.55536 (19804) hydrogen bonds : bond 0.04162 ( 606) hydrogen bonds : angle 4.36945 ( 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 395 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 105 ASP cc_start: 0.8074 (p0) cc_final: 0.7872 (p0) REVERT: A 292 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8247 (mtmt) REVERT: A 310 VAL cc_start: 0.8422 (p) cc_final: 0.8108 (m) REVERT: A 339 GLU cc_start: 0.7668 (pp20) cc_final: 0.6962 (pp20) REVERT: A 341 LEU cc_start: 0.8663 (mt) cc_final: 0.8229 (mt) REVERT: A 361 LEU cc_start: 0.8892 (tp) cc_final: 0.8628 (tt) REVERT: A 362 ASN cc_start: 0.8881 (t0) cc_final: 0.8569 (t0) REVERT: A 367 GLU cc_start: 0.8095 (pp20) cc_final: 0.7746 (pp20) REVERT: A 495 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7642 (mt-10) REVERT: A 636 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8171 (ttm170) REVERT: A 639 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8325 (ttpp) REVERT: A 745 PHE cc_start: 0.8516 (m-80) cc_final: 0.8292 (m-80) REVERT: A 792 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7725 (mp0) REVERT: A 983 LEU cc_start: 0.7897 (mm) cc_final: 0.7666 (mt) REVERT: A 986 LYS cc_start: 0.7926 (mppt) cc_final: 0.7545 (mppt) REVERT: B 89 ILE cc_start: 0.8230 (tp) cc_final: 0.8021 (tt) REVERT: C 18 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7516 (tppp) REVERT: C 36 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6718 (mt-10) REVERT: C 72 ASP cc_start: 0.6076 (t0) cc_final: 0.5859 (t0) REVERT: C 234 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7958 (pp) REVERT: C 355 ASP cc_start: 0.7893 (m-30) cc_final: 0.7484 (m-30) outliers start: 43 outliers final: 24 residues processed: 367 average time/residue: 0.6394 time to fit residues: 256.6262 Evaluate side-chains 369 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 342 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 49 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER 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 696 LEU 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 169 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 12 GLU 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 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 128 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114956 restraints weight = 20459.875| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.04 r_work: 0.3407 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14536 Z= 0.189 Angle : 0.597 9.713 19804 Z= 0.314 Chirality : 0.044 0.181 2191 Planarity : 0.004 0.050 2388 Dihedral : 14.284 138.263 2232 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.04 % Rotamer: Outliers : 3.43 % Allowed : 17.62 % Favored : 78.94 % 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 aren not related in a simple way. whole: 0.24 (0.21), residues: 1634 helix: 1.37 (0.22), residues: 598 sheet: 0.47 (0.29), residues: 350 loop : -1.10 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.015 0.001 TYR C 158 PHE 0.021 0.002 PHE A 838 TRP 0.011 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00452 (14536) covalent geometry : angle 0.59741 (19804) hydrogen bonds : bond 0.05067 ( 606) hydrogen bonds : angle 4.47838 ( 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 404 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 352 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 105 ASP cc_start: 0.8126 (p0) cc_final: 0.7910 (p0) REVERT: A 225 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: A 282 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 292 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8272 (mtmt) REVERT: A 310 VAL cc_start: 0.8428 (p) cc_final: 0.8134 (m) REVERT: A 339 GLU cc_start: 0.7670 (pp20) cc_final: 0.7047 (pp20) REVERT: A 340 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7237 (ptmm) REVERT: A 341 LEU cc_start: 0.8707 (mt) cc_final: 0.8264 (mt) REVERT: A 361 LEU cc_start: 0.8913 (tp) cc_final: 0.8662 (tt) REVERT: A 362 ASN cc_start: 0.8895 (t0) cc_final: 0.8633 (t0) REVERT: A 367 GLU cc_start: 0.8104 (pp20) cc_final: 0.7703 (pp20) REVERT: A 495 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 636 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8128 (ttm170) REVERT: A 639 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8337 (ttmm) REVERT: A 983 LEU cc_start: 0.7909 (mm) cc_final: 0.7690 (mt) REVERT: A 986 LYS cc_start: 0.7916 (mppt) cc_final: 0.7519 (mppt) REVERT: C 18 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7648 (tppp) REVERT: C 36 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6761 (mt-10) REVERT: C 234 ILE cc_start: 0.8355 (tp) cc_final: 0.8040 (pp) REVERT: C 268 LYS cc_start: 0.8169 (tmmt) cc_final: 0.7964 (tmmt) REVERT: C 355 ASP cc_start: 0.7912 (m-30) cc_final: 0.7531 (m-30) REVERT: C 402 THR cc_start: 0.7919 (m) cc_final: 0.7611 (p) outliers start: 52 outliers final: 35 residues processed: 373 average time/residue: 0.6437 time to fit residues: 262.8596 Evaluate side-chains 386 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 49 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 586 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 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 152 VAL 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 12 GLU 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 246 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 393 ASN 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: 0.6980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 214 GLN C 386 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115071 restraints weight = 20499.363| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.05 r_work: 0.3408 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14536 Z= 0.190 Angle : 0.599 9.935 19804 Z= 0.316 Chirality : 0.044 0.170 2191 Planarity : 0.005 0.048 2388 Dihedral : 14.250 137.942 2232 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.59 % Favored : 95.17 % Rotamer: Outliers : 3.56 % Allowed : 17.69 % Favored : 78.75 % 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 aren not related in a simple way. whole: 0.22 (0.21), residues: 1634 helix: 1.37 (0.22), residues: 598 sheet: 0.47 (0.29), residues: 347 loop : -1.11 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.014 0.001 TYR A 528 PHE 0.022 0.002 PHE A 838 TRP 0.012 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00455 (14536) covalent geometry : angle 0.59854 (19804) hydrogen bonds : bond 0.05001 ( 606) hydrogen bonds : angle 4.49288 ( 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 404 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7746 (mm-30) REVERT: A 225 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: A 282 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 292 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8251 (mtmt) REVERT: A 310 VAL cc_start: 0.8443 (p) cc_final: 0.8150 (m) REVERT: A 339 GLU cc_start: 0.7656 (pp20) cc_final: 0.7037 (pp20) REVERT: A 340 LYS cc_start: 0.8040 (ptmm) cc_final: 0.7202 (ptmm) REVERT: A 341 LEU cc_start: 0.8713 (mt) cc_final: 0.8257 (mt) REVERT: A 361 LEU cc_start: 0.8905 (tp) cc_final: 0.8655 (tt) REVERT: A 362 ASN cc_start: 0.8887 (t0) cc_final: 0.8624 (t0) REVERT: A 367 GLU cc_start: 0.8094 (pp20) cc_final: 0.7722 (pp20) REVERT: A 495 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 636 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8106 (ttm170) REVERT: A 639 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8328 (ttmm) REVERT: A 983 LEU cc_start: 0.7901 (mm) cc_final: 0.7681 (mt) REVERT: A 986 LYS cc_start: 0.7901 (mppt) cc_final: 0.7545 (mppt) REVERT: C 18 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7644 (tppp) REVERT: C 36 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 172 GLU cc_start: 0.6676 (pm20) cc_final: 0.6271 (pm20) REVERT: C 234 ILE cc_start: 0.8353 (tp) cc_final: 0.8036 (pp) REVERT: C 268 LYS cc_start: 0.8200 (tmmt) cc_final: 0.7975 (tmmt) REVERT: C 355 ASP cc_start: 0.7897 (m-30) cc_final: 0.7521 (m-30) REVERT: C 386 ASN cc_start: 0.8043 (t0) cc_final: 0.7747 (t0) REVERT: C 402 THR cc_start: 0.7919 (m) cc_final: 0.7603 (p) outliers start: 54 outliers final: 34 residues processed: 372 average time/residue: 0.6378 time to fit residues: 259.9593 Evaluate side-chains 386 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 349 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 49 SER 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 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 509 LEU 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 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 152 VAL 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 12 GLU 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 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 389 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: 1.9990 chunk 156 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113648 restraints weight = 20449.077| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.04 r_work: 0.3389 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14536 Z= 0.243 Angle : 0.638 9.028 19804 Z= 0.338 Chirality : 0.046 0.171 2191 Planarity : 0.005 0.049 2388 Dihedral : 14.361 138.064 2232 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.61 % Rotamer: Outliers : 3.10 % Allowed : 18.35 % 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 aren not related in a simple way. whole: 0.07 (0.21), residues: 1634 helix: 1.26 (0.22), residues: 595 sheet: 0.45 (0.29), residues: 344 loop : -1.25 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.019 0.002 TYR A 660 PHE 0.028 0.002 PHE C 212 TRP 0.012 0.002 TRP A 470 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00586 (14536) covalent geometry : angle 0.63825 (19804) hydrogen bonds : bond 0.05652 ( 606) hydrogen bonds : angle 4.61718 ( 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 404 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 357 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 225 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: A 282 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 292 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8249 (mtmt) REVERT: A 310 VAL cc_start: 0.8426 (p) cc_final: 0.8143 (m) REVERT: A 339 GLU cc_start: 0.7602 (pp20) cc_final: 0.6920 (pp20) REVERT: A 340 LYS cc_start: 0.8116 (ptmm) cc_final: 0.7275 (ptmm) REVERT: A 341 LEU cc_start: 0.8752 (mt) cc_final: 0.8203 (mt) REVERT: A 361 LEU cc_start: 0.8929 (tp) cc_final: 0.8685 (tt) REVERT: A 362 ASN cc_start: 0.8907 (t0) cc_final: 0.8665 (t0) REVERT: A 367 GLU cc_start: 0.8096 (pp20) cc_final: 0.7700 (pp20) REVERT: A 426 ASN cc_start: 0.8616 (m110) cc_final: 0.8400 (m110) REVERT: A 495 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 509 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8058 (mp) REVERT: A 636 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8066 (ttm170) REVERT: A 639 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8311 (ttmm) REVERT: A 983 LEU cc_start: 0.7917 (mm) cc_final: 0.7703 (mt) REVERT: A 986 LYS cc_start: 0.7905 (mppt) cc_final: 0.7559 (mppt) REVERT: C 18 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7697 (mttt) REVERT: C 36 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6803 (mt-10) REVERT: C 72 ASP cc_start: 0.6376 (t0) cc_final: 0.6091 (t70) REVERT: C 79 LEU cc_start: 0.8080 (mt) cc_final: 0.7875 (pp) REVERT: C 172 GLU cc_start: 0.6737 (pm20) cc_final: 0.6142 (pm20) REVERT: C 177 ASP cc_start: 0.7970 (p0) cc_final: 0.7732 (p0) REVERT: C 234 ILE cc_start: 0.8379 (tp) cc_final: 0.8042 (pp) REVERT: C 268 LYS cc_start: 0.8345 (tmmt) cc_final: 0.8105 (tmmt) REVERT: C 355 ASP cc_start: 0.7876 (m-30) cc_final: 0.7517 (m-30) REVERT: C 386 ASN cc_start: 0.8023 (t0) cc_final: 0.7705 (t0) REVERT: C 402 THR cc_start: 0.7943 (m) cc_final: 0.7642 (p) outliers start: 47 outliers final: 37 residues processed: 376 average time/residue: 0.6489 time to fit residues: 266.8928 Evaluate side-chains 390 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 49 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 576 ASN 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 152 VAL 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 12 GLU 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 194 LYS 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: 0.7980 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 0.0270 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 448 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 214 GLN C 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117133 restraints weight = 20597.283| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.02 r_work: 0.3437 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.131 Angle : 0.572 10.174 19804 Z= 0.302 Chirality : 0.043 0.172 2191 Planarity : 0.004 0.048 2388 Dihedral : 14.083 138.287 2232 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.59 % Favored : 95.17 % Rotamer: Outliers : 2.71 % Allowed : 19.54 % Favored : 77.76 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1634 helix: 1.45 (0.22), residues: 592 sheet: 0.50 (0.29), residues: 347 loop : -1.07 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.015 0.001 TYR C 363 PHE 0.041 0.001 PHE C 410 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00302 (14536) covalent geometry : angle 0.57155 (19804) hydrogen bonds : bond 0.04196 ( 606) hydrogen bonds : angle 4.43054 ( 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 379 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 0.669 Fit side-chains REVERT: A 93 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 225 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: A 282 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 292 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8241 (mtmt) REVERT: A 310 VAL cc_start: 0.8446 (p) cc_final: 0.8133 (m) REVERT: A 339 GLU cc_start: 0.7625 (pp20) cc_final: 0.6849 (pp20) REVERT: A 340 LYS cc_start: 0.8004 (ptmm) cc_final: 0.7100 (ptmm) REVERT: A 341 LEU cc_start: 0.8646 (mt) cc_final: 0.8228 (mt) REVERT: A 361 LEU cc_start: 0.8886 (tp) cc_final: 0.8641 (tt) REVERT: A 362 ASN cc_start: 0.8874 (t0) cc_final: 0.8599 (t0) REVERT: A 367 GLU cc_start: 0.8081 (pp20) cc_final: 0.7722 (pp20) REVERT: A 495 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 636 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8169 (ttm170) REVERT: A 639 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: A 979 ILE cc_start: 0.8359 (mm) cc_final: 0.8130 (mp) REVERT: A 983 LEU cc_start: 0.7906 (mm) cc_final: 0.7688 (mt) REVERT: A 986 LYS cc_start: 0.7881 (mppt) cc_final: 0.7540 (mppt) REVERT: C 18 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7602 (tppp) REVERT: C 36 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6769 (mt-10) REVERT: C 72 ASP cc_start: 0.6281 (t0) cc_final: 0.5913 (t70) REVERT: C 172 GLU cc_start: 0.6677 (pm20) cc_final: 0.6105 (pm20) REVERT: C 177 ASP cc_start: 0.7919 (p0) cc_final: 0.7681 (p0) REVERT: C 234 ILE cc_start: 0.8275 (tp) cc_final: 0.7975 (pp) REVERT: C 268 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7938 (tmmt) REVERT: C 355 ASP cc_start: 0.7865 (m-30) cc_final: 0.7474 (m-30) outliers start: 41 outliers final: 25 residues processed: 356 average time/residue: 0.6407 time to fit residues: 250.2660 Evaluate side-chains 373 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 345 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 418 VAL 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 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 177 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 12 GLU 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 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 376 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 426 ASN B 59 ASN C 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116323 restraints weight = 20623.129| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.01 r_work: 0.3426 rms_B_bonded: 2.60 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: 0.7943 moved from start: 0.2282 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= 0.151 Angle : 0.599 10.653 19804 Z= 0.312 Chirality : 0.043 0.192 2191 Planarity : 0.004 0.047 2388 Dihedral : 14.099 137.791 2232 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.71 % Favored : 95.04 % Rotamer: Outliers : 2.11 % Allowed : 20.66 % Favored : 77.23 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1634 helix: 1.41 (0.22), residues: 599 sheet: 0.53 (0.29), residues: 347 loop : -1.08 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.015 0.001 TYR C 199 PHE 0.041 0.002 PHE C 212 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00356 (14536) covalent geometry : angle 0.59937 (19804) hydrogen bonds : bond 0.04534 ( 606) hydrogen bonds : angle 4.43447 ( 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 376 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 344 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 225 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: A 230 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7418 (tpp) REVERT: A 282 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 292 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8261 (mtmt) REVERT: A 310 VAL cc_start: 0.8442 (p) cc_final: 0.8133 (m) REVERT: A 339 GLU cc_start: 0.7646 (pp20) cc_final: 0.6948 (pp20) REVERT: A 340 LYS cc_start: 0.8012 (ptmm) cc_final: 0.7137 (ptmm) REVERT: A 341 LEU cc_start: 0.8635 (mt) cc_final: 0.8224 (mt) REVERT: A 361 LEU cc_start: 0.8899 (tp) cc_final: 0.8647 (tt) REVERT: A 362 ASN cc_start: 0.8881 (t0) cc_final: 0.8619 (t0) REVERT: A 367 GLU cc_start: 0.8078 (pp20) cc_final: 0.7711 (pp20) REVERT: A 437 ASP cc_start: 0.7609 (p0) cc_final: 0.7256 (p0) REVERT: A 495 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 636 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8145 (ttm170) REVERT: A 639 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: A 845 THR cc_start: 0.8325 (t) cc_final: 0.7994 (p) REVERT: A 979 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 983 LEU cc_start: 0.7915 (mm) cc_final: 0.7694 (mt) REVERT: C 18 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7623 (tppp) REVERT: C 36 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6808 (mt-10) REVERT: C 72 ASP cc_start: 0.6276 (t0) cc_final: 0.5951 (t70) REVERT: C 172 GLU cc_start: 0.6662 (pm20) cc_final: 0.6057 (pm20) REVERT: C 177 ASP cc_start: 0.7938 (p0) cc_final: 0.7698 (p0) REVERT: C 234 ILE cc_start: 0.8312 (tp) cc_final: 0.8003 (pp) REVERT: C 268 LYS cc_start: 0.8299 (tmmt) cc_final: 0.8029 (tmmt) REVERT: C 292 ARG cc_start: 0.7342 (tpm170) cc_final: 0.7042 (tpm170) REVERT: C 355 ASP cc_start: 0.7889 (m-30) cc_final: 0.7497 (m-30) REVERT: C 386 ASN cc_start: 0.7986 (t0) cc_final: 0.7671 (t0) outliers start: 32 outliers final: 25 residues processed: 355 average time/residue: 0.6706 time to fit residues: 259.5174 Evaluate side-chains 368 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 418 VAL 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 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 A residue 979 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 12 GLU 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 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 376 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113517 restraints weight = 20452.820| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.05 r_work: 0.3385 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14536 Z= 0.263 Angle : 0.676 11.142 19804 Z= 0.354 Chirality : 0.047 0.183 2191 Planarity : 0.005 0.049 2388 Dihedral : 14.373 138.169 2232 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.26 % Favored : 94.49 % Rotamer: Outliers : 2.77 % Allowed : 20.33 % Favored : 76.90 % 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 aren not related in a simple way. whole: 0.03 (0.21), residues: 1634 helix: 1.24 (0.22), residues: 593 sheet: 0.40 (0.29), residues: 345 loop : -1.26 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 604 TYR 0.021 0.002 TYR A 660 PHE 0.037 0.002 PHE C 78 TRP 0.011 0.002 TRP A 470 HIS 0.005 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00634 (14536) covalent geometry : angle 0.67615 (19804) hydrogen bonds : bond 0.05921 ( 606) hydrogen bonds : angle 4.66343 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6491.39 seconds wall clock time: 111 minutes 24.59 seconds (6684.59 seconds total)