Starting phenix.real_space_refine on Sat Sep 12 10:53:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d37_27155/09_2026/8d37_27155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d37_27155/09_2026/8d37_27155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d37_27155/09_2026/8d37_27155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d37_27155/09_2026/8d37_27155_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d37_27155/09_2026/8d37_27155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d37_27155/09_2026/8d37_27155.map" } resolution = 2.65 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= 0.339 sd= 0.592 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 51 5.49 5 S 82 5.16 5 C 9605 2.51 5 N 2690 2.21 5 O 2885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.35, per 1000 atoms: 0.22 Number of scatterers: 15314 At special positions: 0 Unit cell: (113.05, 112.2, 153, 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) Ca 1 19.99 S 82 16.00 P 51 15.00 O 2885 8.00 N 2690 7.00 C 9605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 499.6 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 13 sheets defined 48.9% alpha, 14.4% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.655A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.664A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.898A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.678A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.388A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.703A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 5.183A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.270A pdb=" N ASP A 487 " --> pdb=" O TRP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.561A pdb=" N GLN A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.722A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.797A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.950A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 removed outlier: 3.516A pdb=" N LEU A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 922 " --> pdb=" O TRP A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.514A pdb=" N PHE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 990 Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.617A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1167 removed outlier: 4.520A pdb=" N TYR A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 3.656A pdb=" N VAL A1177 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1209 removed outlier: 4.158A pdb=" N ARG A1208 " --> pdb=" O THR A1204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A1209 " --> pdb=" O GLY A1205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1204 through 1209' Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 removed outlier: 4.284A pdb=" N LEU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 165 through 176 removed outlier: 4.294A pdb=" N ALA B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 removed outlier: 4.573A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.926A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.699A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 468 through 483 removed outlier: 4.447A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 150 through 159 removed outlier: 4.869A pdb=" N ILE C 156 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU C 157 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.809A pdb=" N LEU C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 177 " --> pdb=" O ASN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 4.352A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.622A pdb=" N ASN C 201 " --> pdb=" O ASP C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 244 through 266 removed outlier: 4.495A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.243A pdb=" N LYS C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.559A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.921A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 485 removed outlier: 4.256A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.936A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AA3, first strand: chain 'A' and resid 746 through 751 removed outlier: 6.842A pdb=" N GLY A 746 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.873A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.341A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.867A pdb=" N ARG B 146 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.430A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 5.957A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.231A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4753 1.34 - 1.46: 2701 1.46 - 1.58: 8119 1.58 - 1.70: 95 1.70 - 1.82: 130 Bond restraints: 15798 Sorted by residual: bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.654 1.799 -0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" O3A DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.632 1.528 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.746 1.648 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.413 1.329 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1' DC P 7 " pdb=" N1 DC P 7 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.78e+00 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 21577 3.55 - 7.11: 37 7.11 - 10.66: 4 10.66 - 14.21: 1 14.21 - 17.76: 1 Bond angle restraints: 21620 Sorted by residual: angle pdb=" O1A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.39 124.15 -17.76 3.00e+00 1.11e-01 3.51e+01 angle pdb=" N3 DT T 23 " pdb=" C4 DT T 23 " pdb=" O4 DT T 23 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT T 25 " pdb=" C4 DT T 25 " pdb=" O4 DT T 25 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT T 20 " pdb=" C4 DT T 20 " pdb=" O4 DT T 20 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT T 6 " pdb=" C4 DT T 6 " pdb=" O4 DT T 6 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 21615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 8636 17.05 - 34.10: 478 34.10 - 51.15: 133 51.15 - 68.20: 67 68.20 - 85.25: 5 Dihedral angle restraints: 9319 sinusoidal: 4172 harmonic: 5147 Sorted by residual: dihedral pdb=" CA ASP B 159 " pdb=" C ASP B 159 " pdb=" N LYS B 160 " pdb=" CA LYS B 160 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS C 164 " pdb=" C LYS C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 125.77 -32.77 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 9316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1642 0.033 - 0.065: 453 0.065 - 0.098: 107 0.098 - 0.131: 91 0.131 - 0.164: 37 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' DCP A1302 " pdb=" C3' DCP A1302 " pdb=" C5' DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False -2.49 -2.66 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" C3' DA P 4 " pdb=" C4' DA P 4 " pdb=" O3' DA P 4 " pdb=" C2' DA P 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" C3' DA P 9 " pdb=" C4' DA P 9 " pdb=" O3' DA P 9 " pdb=" C2' DA P 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 2327 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 435 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO A 436 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A1200 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 8 " 0.017 2.00e-02 2.50e+03 6.96e-03 1.45e+00 pdb=" N9 DG P 8 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG P 8 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG P 8 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG P 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG P 8 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG P 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG P 8 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG P 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 8 " -0.002 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 116 2.55 - 3.14: 12136 3.14 - 3.72: 23713 3.72 - 4.31: 33213 4.31 - 4.90: 54634 Nonbonded interactions: 123812 Sorted by model distance: nonbonded pdb=" OD1 ASP A 904 " pdb=" OG1 THR A 914 " model vdw 1.962 3.040 nonbonded pdb=" OE1 GLU A 895 " pdb=" OH TYR A 955 " model vdw 2.040 3.040 nonbonded pdb=" NZ LYS A 461 " pdb=" O LYS B 265 " model vdw 2.130 3.120 nonbonded pdb=" O MET C 435 " pdb=" OG SER C 436 " model vdw 2.137 3.040 nonbonded pdb=" O THR B 460 " pdb=" OG1 THR B 461 " model vdw 2.165 3.040 ... (remaining 123807 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.003 0.145 15799 Z= 0.226 Angle : 0.543 17.763 21622 Z= 0.337 Chirality : 0.041 0.164 2330 Planarity : 0.003 0.037 2604 Dihedral : 12.679 85.251 5994 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.32 % Allowed : 2.07 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1758 helix: 1.14 (0.21), residues: 713 sheet: 0.81 (0.32), residues: 240 loop : 0.24 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.009 0.001 TYR A1108 PHE 0.011 0.001 PHE A 197 TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.23 (15798) covalent geometry : angle 0.54277 / 0.34 (21620) SS BOND : bond 0.00444 / 0.23 ( 1) SS BOND : angle 0.81653 / 0.45 ( 2) hydrogen bonds : bond 0.16061 / 11.28 ( 727) hydrogen bonds : angle 6.41772 / 4.62 ( 1978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7104 (mt) cc_final: 0.6750 (mt) REVERT: A 138 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6343 (t-90) REVERT: A 296 SER cc_start: 0.8246 (p) cc_final: 0.7896 (m) REVERT: A 382 MET cc_start: 0.8198 (tpp) cc_final: 0.7757 (tpt) REVERT: A 466 LEU cc_start: 0.7422 (mp) cc_final: 0.7188 (tp) REVERT: A 602 LEU cc_start: 0.8072 (mt) cc_final: 0.7864 (mt) REVERT: A 818 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7639 (ttm-80) REVERT: B 74 GLN cc_start: 0.7384 (tt0) cc_final: 0.6979 (tp40) REVERT: B 152 THR cc_start: 0.8107 (p) cc_final: 0.7691 (t) REVERT: B 241 TRP cc_start: 0.5727 (t-100) cc_final: 0.5098 (t-100) REVERT: B 259 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7305 (mmp-170) REVERT: B 411 ILE cc_start: 0.8489 (mt) cc_final: 0.8252 (mm) REVERT: B 435 MET cc_start: 0.7375 (mtp) cc_final: 0.7141 (mtm) REVERT: B 465 MET cc_start: 0.8500 (mmm) cc_final: 0.7686 (mmm) outliers start: 5 outliers final: 3 residues processed: 528 average time/residue: 0.5277 time to fit residues: 308.7028 Evaluate side-chains 403 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 398 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 ASN A1098 ASN A1110 HIS B 124 GLN B 132 HIS B 216 HIS B 397 GLN B 400 GLN B 404 ASN C 85 GLN C 258 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.147164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.137353 restraints weight = 29295.641| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.77 r_work: 0.3880 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15799 Z= 0.194 Angle : 0.690 8.421 21622 Z= 0.364 Chirality : 0.046 0.231 2330 Planarity : 0.006 0.047 2604 Dihedral : 14.375 66.906 2495 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.43 % Allowed : 12.40 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1758 helix: 1.19 (0.19), residues: 730 sheet: 0.74 (0.30), residues: 249 loop : 0.07 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 993 TYR 0.016 0.002 TYR A1108 PHE 0.019 0.002 PHE A 539 TRP 0.015 0.002 TRP A 918 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (15798) covalent geometry : angle 0.69004 / 0.36 (21620) SS BOND : bond 0.00491 / 0.26 ( 1) SS BOND : angle 0.80075 / 0.44 ( 2) hydrogen bonds : bond 0.05741 / 3.96 ( 727) hydrogen bonds : angle 5.09395 / 3.59 ( 1978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 403 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7165 (mt) cc_final: 0.6784 (mt) REVERT: A 138 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6525 (t-90) REVERT: A 292 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8264 (tt) REVERT: A 297 MET cc_start: 0.7509 (mtm) cc_final: 0.7276 (mtm) REVERT: A 466 LEU cc_start: 0.7576 (mp) cc_final: 0.7323 (tp) REVERT: A 490 TRP cc_start: 0.7657 (m100) cc_final: 0.7417 (m100) REVERT: B 74 GLN cc_start: 0.7891 (tt0) cc_final: 0.7686 (tt0) REVERT: B 152 THR cc_start: 0.7996 (p) cc_final: 0.7596 (t) REVERT: B 241 TRP cc_start: 0.5697 (t-100) cc_final: 0.5109 (t-100) REVERT: B 243 THR cc_start: 0.2738 (OUTLIER) cc_final: 0.2505 (t) REVERT: B 259 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7539 (mmp-170) REVERT: B 407 LEU cc_start: 0.7608 (mt) cc_final: 0.7324 (tp) REVERT: B 435 MET cc_start: 0.7603 (mtp) cc_final: 0.7288 (ttm) REVERT: C 252 LEU cc_start: 0.8441 (tt) cc_final: 0.8159 (tp) REVERT: C 256 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7971 (tp) REVERT: C 428 LEU cc_start: 0.6908 (tt) cc_final: 0.6566 (tp) outliers start: 84 outliers final: 36 residues processed: 441 average time/residue: 0.5249 time to fit residues: 256.7804 Evaluate side-chains 423 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 382 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 431 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 468 ASN A 569 HIS A 968 GLN A1059 ASN A1110 HIS B 124 GLN B 261 GLN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137880 restraints weight = 29313.630| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.79 r_work: 0.3888 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15799 Z= 0.149 Angle : 0.633 9.165 21622 Z= 0.332 Chirality : 0.043 0.225 2330 Planarity : 0.005 0.047 2604 Dihedral : 14.585 71.195 2493 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.68 % Allowed : 14.86 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1758 helix: 1.21 (0.19), residues: 737 sheet: 0.76 (0.31), residues: 245 loop : -0.04 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 279 TYR 0.015 0.002 TYR B 432 PHE 0.018 0.002 PHE B 219 TRP 0.013 0.001 TRP A 220 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (15798) covalent geometry : angle 0.63256 / 0.33 (21620) SS BOND : bond 0.00366 / 0.19 ( 1) SS BOND : angle 0.46505 / 0.26 ( 2) hydrogen bonds : bond 0.05014 / 3.45 ( 727) hydrogen bonds : angle 4.89180 / 3.44 ( 1978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 394 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6904 (OUTLIER) cc_final: 0.6513 (t-90) REVERT: A 466 LEU cc_start: 0.7529 (mp) cc_final: 0.7278 (tp) REVERT: A 490 TRP cc_start: 0.7628 (m100) cc_final: 0.7353 (m100) REVERT: B 74 GLN cc_start: 0.7907 (tt0) cc_final: 0.7694 (tt0) REVERT: B 151 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7300 (mt-10) REVERT: B 152 THR cc_start: 0.8014 (p) cc_final: 0.7532 (t) REVERT: B 259 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7347 (mmp-170) REVERT: B 407 LEU cc_start: 0.7499 (mt) cc_final: 0.7280 (tp) REVERT: B 408 GLU cc_start: 0.7569 (tp30) cc_final: 0.7313 (tp30) REVERT: B 435 MET cc_start: 0.7547 (mtp) cc_final: 0.7308 (ttm) REVERT: C 185 LEU cc_start: 0.8106 (mm) cc_final: 0.7755 (mt) REVERT: C 252 LEU cc_start: 0.8440 (tt) cc_final: 0.8176 (tp) REVERT: C 256 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7981 (tp) REVERT: C 428 LEU cc_start: 0.6805 (tt) cc_final: 0.6496 (tp) REVERT: C 433 ASP cc_start: 0.7565 (m-30) cc_final: 0.7348 (m-30) outliers start: 88 outliers final: 44 residues processed: 433 average time/residue: 0.4962 time to fit residues: 239.0271 Evaluate side-chains 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 174 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 179 optimal weight: 9.9990 chunk 106 optimal weight: 0.0000 chunk 95 optimal weight: 0.0870 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.6566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 GLN A1110 HIS B 124 GLN B 397 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.147724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.137719 restraints weight = 29185.041| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.78 r_work: 0.3884 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15799 Z= 0.148 Angle : 0.633 9.983 21622 Z= 0.331 Chirality : 0.042 0.231 2330 Planarity : 0.005 0.046 2604 Dihedral : 14.732 72.929 2492 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.91 % Allowed : 18.15 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1758 helix: 1.26 (0.19), residues: 734 sheet: 0.94 (0.31), residues: 236 loop : -0.10 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 257 TYR 0.019 0.002 TYR C 315 PHE 0.018 0.002 PHE A 197 TRP 0.019 0.001 TRP B 241 HIS 0.006 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (15798) covalent geometry : angle 0.63291 / 0.33 (21620) SS BOND : bond 0.00354 / 0.19 ( 1) SS BOND : angle 0.52401 / 0.29 ( 2) hydrogen bonds : bond 0.04818 / 3.30 ( 727) hydrogen bonds : angle 4.83932 / 3.40 ( 1978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 386 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6481 (t-90) REVERT: A 178 TYR cc_start: 0.6202 (m-80) cc_final: 0.6002 (m-80) REVERT: A 466 LEU cc_start: 0.7523 (mp) cc_final: 0.7291 (tp) REVERT: A 490 TRP cc_start: 0.7677 (m100) cc_final: 0.7379 (m100) REVERT: A 769 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: A 922 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: B 74 GLN cc_start: 0.7870 (tt0) cc_final: 0.7655 (tt0) REVERT: B 151 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7308 (mt-10) REVERT: B 152 THR cc_start: 0.8071 (p) cc_final: 0.7577 (t) REVERT: B 259 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7508 (mmp-170) REVERT: B 407 LEU cc_start: 0.7369 (mt) cc_final: 0.7159 (tp) REVERT: B 408 GLU cc_start: 0.7525 (tp30) cc_final: 0.7277 (tp30) REVERT: B 435 MET cc_start: 0.7545 (mtp) cc_final: 0.7322 (ttm) REVERT: C 185 LEU cc_start: 0.8058 (mm) cc_final: 0.7711 (mt) REVERT: C 252 LEU cc_start: 0.8434 (tt) cc_final: 0.8185 (tp) REVERT: C 256 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7949 (tp) REVERT: C 428 LEU cc_start: 0.6851 (tt) cc_final: 0.6549 (tp) REVERT: C 433 ASP cc_start: 0.7622 (m-30) cc_final: 0.7359 (m-30) outliers start: 76 outliers final: 42 residues processed: 420 average time/residue: 0.5120 time to fit residues: 239.7893 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 375 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 165 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 50 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 95 optimal weight: 0.0370 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS A 968 GLN A1110 HIS B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.148093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138022 restraints weight = 29302.893| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.79 r_work: 0.3887 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15799 Z= 0.138 Angle : 0.628 11.720 21622 Z= 0.327 Chirality : 0.042 0.233 2330 Planarity : 0.005 0.051 2604 Dihedral : 14.805 74.083 2492 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.91 % Allowed : 18.48 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1758 helix: 1.30 (0.19), residues: 741 sheet: 0.95 (0.33), residues: 224 loop : -0.15 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 328 TYR 0.022 0.002 TYR C 315 PHE 0.016 0.002 PHE B 403 TRP 0.026 0.001 TRP B 241 HIS 0.005 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (15798) covalent geometry : angle 0.62824 / 0.33 (21620) SS BOND : bond 0.00352 / 0.19 ( 1) SS BOND : angle 0.43649 / 0.24 ( 2) hydrogen bonds : bond 0.04595 / 3.15 ( 727) hydrogen bonds : angle 4.78793 / 3.36 ( 1978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 378 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6439 (t-90) REVERT: A 280 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7500 (mp0) REVERT: A 490 TRP cc_start: 0.7664 (m100) cc_final: 0.7336 (m100) REVERT: A 922 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6507 (mt0) REVERT: B 74 GLN cc_start: 0.7877 (tt0) cc_final: 0.7659 (tt0) REVERT: B 152 THR cc_start: 0.8043 (p) cc_final: 0.7682 (t) REVERT: B 183 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 259 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7445 (mmp-170) REVERT: B 407 LEU cc_start: 0.7205 (mt) cc_final: 0.6997 (tp) REVERT: B 408 GLU cc_start: 0.7432 (tp30) cc_final: 0.7218 (tp30) REVERT: C 195 ASN cc_start: 0.7971 (t0) cc_final: 0.7668 (t0) REVERT: C 252 LEU cc_start: 0.8458 (tt) cc_final: 0.8234 (tp) REVERT: C 256 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7938 (tp) REVERT: C 428 LEU cc_start: 0.6843 (tt) cc_final: 0.6545 (tp) REVERT: C 433 ASP cc_start: 0.7643 (m-30) cc_final: 0.7397 (m-30) outliers start: 76 outliers final: 47 residues processed: 413 average time/residue: 0.5142 time to fit residues: 235.9810 Evaluate side-chains 414 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 GLN A1110 HIS B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 216 HIS C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.148315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138222 restraints weight = 29134.227| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.79 r_work: 0.3890 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15799 Z= 0.137 Angle : 0.622 12.374 21622 Z= 0.323 Chirality : 0.042 0.233 2330 Planarity : 0.005 0.067 2604 Dihedral : 14.843 74.674 2492 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.84 % Allowed : 19.06 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1758 helix: 1.39 (0.19), residues: 735 sheet: 0.92 (0.33), residues: 228 loop : -0.05 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 650 TYR 0.016 0.002 TYR C 315 PHE 0.016 0.001 PHE A 197 TRP 0.027 0.001 TRP B 241 HIS 0.005 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15798) covalent geometry : angle 0.62216 / 0.32 (21620) SS BOND : bond 0.00326 / 0.17 ( 1) SS BOND : angle 0.46947 / 0.26 ( 2) hydrogen bonds : bond 0.04499 / 3.09 ( 727) hydrogen bonds : angle 4.75859 / 3.35 ( 1978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 381 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6473 (t-90) REVERT: A 490 TRP cc_start: 0.7662 (m100) cc_final: 0.7332 (m100) REVERT: A 922 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6498 (mt0) REVERT: B 74 GLN cc_start: 0.7855 (tt0) cc_final: 0.7635 (tt0) REVERT: B 152 THR cc_start: 0.8144 (p) cc_final: 0.7645 (t) REVERT: B 259 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7478 (mmp-170) REVERT: B 407 LEU cc_start: 0.7128 (mt) cc_final: 0.6921 (tp) REVERT: B 408 GLU cc_start: 0.7399 (tp30) cc_final: 0.7180 (tp30) REVERT: C 185 LEU cc_start: 0.8047 (mm) cc_final: 0.7714 (mt) REVERT: C 195 ASN cc_start: 0.7972 (t0) cc_final: 0.7669 (t0) REVERT: C 252 LEU cc_start: 0.8455 (tt) cc_final: 0.8235 (tp) REVERT: C 256 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7913 (tp) REVERT: C 428 LEU cc_start: 0.6829 (tt) cc_final: 0.6531 (tp) REVERT: C 433 ASP cc_start: 0.7642 (m-30) cc_final: 0.7367 (m-30) outliers start: 75 outliers final: 51 residues processed: 417 average time/residue: 0.5008 time to fit residues: 232.9972 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 367 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 132 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 78 optimal weight: 0.0670 overall best weight: 2.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 922 GLN A 968 GLN A1110 HIS B 124 GLN B 287 ASN B 397 GLN B 400 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.146080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.136084 restraints weight = 28964.029| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.78 r_work: 0.3864 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15799 Z= 0.182 Angle : 0.687 13.888 21622 Z= 0.357 Chirality : 0.044 0.240 2330 Planarity : 0.006 0.064 2604 Dihedral : 14.985 74.072 2492 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.04 % Allowed : 19.90 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1758 helix: 1.14 (0.19), residues: 733 sheet: 0.68 (0.32), residues: 243 loop : -0.14 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 650 TYR 0.018 0.002 TYR C 315 PHE 0.017 0.002 PHE A 539 TRP 0.025 0.002 TRP B 241 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (15798) covalent geometry : angle 0.68723 / 0.36 (21620) SS BOND : bond 0.00448 / 0.24 ( 1) SS BOND : angle 0.65910 / 0.35 ( 2) hydrogen bonds : bond 0.05098 / 3.50 ( 727) hydrogen bonds : angle 4.91695 / 3.46 ( 1978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 377 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6510 (t-90) REVERT: A 280 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7521 (mp0) REVERT: A 444 TYR cc_start: 0.7951 (t80) cc_final: 0.7679 (t80) REVERT: A 490 TRP cc_start: 0.7698 (m100) cc_final: 0.7405 (m100) REVERT: A 834 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 927 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7884 (mtm-85) REVERT: B 74 GLN cc_start: 0.7947 (tt0) cc_final: 0.7731 (tt0) REVERT: C 185 LEU cc_start: 0.8083 (mm) cc_final: 0.7761 (mt) REVERT: C 195 ASN cc_start: 0.8009 (t0) cc_final: 0.7706 (t0) REVERT: C 252 LEU cc_start: 0.8435 (tt) cc_final: 0.8230 (tp) REVERT: C 256 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7962 (tp) REVERT: C 428 LEU cc_start: 0.7031 (tt) cc_final: 0.6738 (tp) REVERT: C 433 ASP cc_start: 0.7729 (m-30) cc_final: 0.7449 (m-30) outliers start: 78 outliers final: 50 residues processed: 415 average time/residue: 0.5431 time to fit residues: 250.5328 Evaluate side-chains 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 362 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 119 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 0.0050 chunk 163 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 968 GLN A1110 HIS B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 216 HIS C 258 HIS C 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.145450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135440 restraints weight = 29242.949| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.79 r_work: 0.3853 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15799 Z= 0.197 Angle : 0.718 15.632 21622 Z= 0.371 Chirality : 0.046 0.357 2330 Planarity : 0.006 0.086 2604 Dihedral : 15.067 74.092 2488 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.52 % Allowed : 21.12 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1758 helix: 0.89 (0.19), residues: 736 sheet: 0.61 (0.32), residues: 243 loop : -0.30 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 389 TYR 0.017 0.002 TYR C 429 PHE 0.019 0.002 PHE C 273 TRP 0.020 0.002 TRP B 241 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (15798) covalent geometry : angle 0.71807 / 0.37 (21620) SS BOND : bond 0.00479 / 0.25 ( 1) SS BOND : angle 0.59638 / 0.32 ( 2) hydrogen bonds : bond 0.05223 / 3.58 ( 727) hydrogen bonds : angle 5.01388 / 3.53 ( 1978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 364 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6534 (t-90) REVERT: A 280 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7557 (mp0) REVERT: A 444 TYR cc_start: 0.7950 (t80) cc_final: 0.7665 (t80) REVERT: A 490 TRP cc_start: 0.7704 (m100) cc_final: 0.7368 (m100) REVERT: A 748 TRP cc_start: 0.7153 (m-90) cc_final: 0.6838 (m-90) REVERT: A 922 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6510 (mt0) REVERT: A 927 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7894 (mtm-85) REVERT: B 74 GLN cc_start: 0.7893 (tt0) cc_final: 0.7669 (tt0) REVERT: B 394 GLU cc_start: 0.6580 (mp0) cc_final: 0.5548 (mp0) REVERT: C 185 LEU cc_start: 0.8089 (mm) cc_final: 0.7792 (mt) REVERT: C 195 ASN cc_start: 0.8017 (t0) cc_final: 0.7720 (t0) REVERT: C 252 LEU cc_start: 0.8419 (tt) cc_final: 0.8203 (tp) REVERT: C 256 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7983 (tp) REVERT: C 433 ASP cc_start: 0.7746 (m-30) cc_final: 0.7472 (m-30) outliers start: 70 outliers final: 55 residues processed: 400 average time/residue: 0.5105 time to fit residues: 226.8612 Evaluate side-chains 405 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 174 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 736 ASN A 968 GLN A1110 HIS ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.136492 restraints weight = 29174.943| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.78 r_work: 0.3867 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15799 Z= 0.160 Angle : 0.697 17.339 21622 Z= 0.358 Chirality : 0.044 0.232 2330 Planarity : 0.006 0.091 2604 Dihedral : 15.033 74.635 2488 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.13 % Allowed : 22.03 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1758 helix: 0.96 (0.19), residues: 738 sheet: 0.67 (0.33), residues: 241 loop : -0.26 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 650 TYR 0.020 0.002 TYR C 429 PHE 0.028 0.002 PHE C 273 TRP 0.020 0.002 TRP B 241 HIS 0.006 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (15798) covalent geometry : angle 0.69724 / 0.36 (21620) SS BOND : bond 0.00369 / 0.19 ( 1) SS BOND : angle 0.29532 / 0.16 ( 2) hydrogen bonds : bond 0.04850 / 3.31 ( 727) hydrogen bonds : angle 4.94937 / 3.49 ( 1978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 355 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6549 (t-90) REVERT: A 280 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7509 (mp0) REVERT: A 444 TYR cc_start: 0.7977 (t80) cc_final: 0.7687 (t80) REVERT: A 490 TRP cc_start: 0.7726 (m100) cc_final: 0.7399 (m100) REVERT: A 866 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7667 (mtp-110) REVERT: A 922 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6467 (mt0) REVERT: A 927 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7908 (mtm-85) REVERT: B 74 GLN cc_start: 0.7919 (tt0) cc_final: 0.7694 (tt0) REVERT: B 408 GLU cc_start: 0.7331 (tp30) cc_final: 0.7123 (tp30) REVERT: C 185 LEU cc_start: 0.8077 (mm) cc_final: 0.7767 (mt) REVERT: C 195 ASN cc_start: 0.7986 (t0) cc_final: 0.7685 (t0) REVERT: C 252 LEU cc_start: 0.8434 (tt) cc_final: 0.8232 (tp) REVERT: C 256 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7960 (tp) REVERT: C 433 ASP cc_start: 0.7714 (m-30) cc_final: 0.7436 (m-30) REVERT: C 442 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6607 (tp) outliers start: 64 outliers final: 51 residues processed: 389 average time/residue: 0.5171 time to fit residues: 223.5905 Evaluate side-chains 403 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 124 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 79 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 968 GLN A1110 HIS B 85 GLN B 124 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 258 HIS C 339 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.147181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.137151 restraints weight = 29293.526| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.79 r_work: 0.3876 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15799 Z= 0.149 Angle : 0.703 17.894 21622 Z= 0.356 Chirality : 0.044 0.390 2330 Planarity : 0.005 0.089 2604 Dihedral : 15.021 75.181 2488 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.01 % Allowed : 22.55 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1758 helix: 1.00 (0.19), residues: 740 sheet: 0.70 (0.33), residues: 241 loop : -0.21 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 650 TYR 0.019 0.002 TYR C 429 PHE 0.022 0.002 PHE C 273 TRP 0.023 0.001 TRP A 175 HIS 0.009 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (15798) covalent geometry : angle 0.70335 / 0.36 (21620) SS BOND : bond 0.00332 / 0.17 ( 1) SS BOND : angle 0.45861 / 0.24 ( 2) hydrogen bonds : bond 0.04629 / 3.17 ( 727) hydrogen bonds : angle 4.90524 / 3.46 ( 1978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7032 (pp20) cc_final: 0.6787 (pp20) REVERT: A 138 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6510 (t-90) REVERT: A 280 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7421 (mp0) REVERT: A 444 TYR cc_start: 0.7911 (t80) cc_final: 0.7627 (t80) REVERT: A 490 TRP cc_start: 0.7719 (m100) cc_final: 0.7392 (m100) REVERT: A 866 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7662 (mtp-110) REVERT: A 922 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: B 74 GLN cc_start: 0.7902 (tt0) cc_final: 0.7698 (tt0) REVERT: B 408 GLU cc_start: 0.7350 (tp30) cc_final: 0.7110 (tp30) REVERT: C 185 LEU cc_start: 0.8066 (mm) cc_final: 0.7750 (mt) REVERT: C 195 ASN cc_start: 0.7976 (t0) cc_final: 0.7678 (t0) REVERT: C 252 LEU cc_start: 0.8420 (tt) cc_final: 0.8178 (tp) REVERT: C 256 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7932 (tp) REVERT: C 433 ASP cc_start: 0.7625 (m-30) cc_final: 0.7353 (m-30) outliers start: 62 outliers final: 48 residues processed: 392 average time/residue: 0.5068 time to fit residues: 221.1068 Evaluate side-chains 406 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 354 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 GLN A1059 ASN A1110 HIS B 124 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.148897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.138857 restraints weight = 29116.457| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.79 r_work: 0.3897 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15799 Z= 0.130 Angle : 0.682 18.459 21622 Z= 0.345 Chirality : 0.043 0.259 2330 Planarity : 0.005 0.086 2604 Dihedral : 14.992 75.846 2488 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.42 % Allowed : 23.64 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1758 helix: 1.11 (0.19), residues: 740 sheet: 0.93 (0.34), residues: 231 loop : -0.17 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 650 TYR 0.019 0.001 TYR C 429 PHE 0.022 0.001 PHE C 273 TRP 0.028 0.001 TRP A 175 HIS 0.004 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15798) covalent geometry : angle 0.68171 / 0.35 (21620) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 0.32344 / 0.19 ( 2) hydrogen bonds : bond 0.04280 / 2.94 ( 727) hydrogen bonds : angle 4.82755 / 3.41 ( 1978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6227.19 seconds wall clock time: 106 minutes 30.12 seconds (6390.12 seconds total)