Starting phenix.real_space_refine on Tue Dec 31 09:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d37_27155/12_2024/8d37_27155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d37_27155/12_2024/8d37_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d37_27155/12_2024/8d37_27155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d37_27155/12_2024/8d37_27155.map" model { file = "/net/cci-nas-00/data/ceres_data/8d37_27155/12_2024/8d37_27155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d37_27155/12_2024/8d37_27155_neut.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.339 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.77, per 1000 atoms: 0.57 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: 4.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.38 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: 6.04 Time building geometry restraints manager: 4.60 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 1.579 1.799 -0.220 1.50e-02 4.44e+03 2.16e+02 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.592 1.706 -0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.443 1.329 0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C4' DCP A1302 " pdb=" C5' DCP A1302 " ideal model delta sigma weight residual 1.508 1.560 -0.052 1.10e-02 8.26e+03 2.25e+01 bond pdb=" C4 DCP A1302 " pdb=" N4 DCP A1302 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.20e-02 6.94e+03 2.08e+01 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 21482 2.58 - 5.17: 125 5.17 - 7.75: 6 7.75 - 10.33: 4 10.33 - 12.91: 3 Bond angle restraints: 21620 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 133.36 6.51 1.00e+00 1.00e+00 4.24e+01 angle pdb=" O2G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 104.48 97.88 6.60 1.14e+00 7.76e-01 3.38e+01 angle pdb=" O2A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.94 116.91 -9.97 1.88e+00 2.83e-01 2.81e+01 angle pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 101.57 93.68 7.89 1.54e+00 4.24e-01 2.64e+01 angle pdb=" O3A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 102.67 91.12 11.55 2.38e+00 1.77e-01 2.36e+01 ... (remaining 21615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 8632 17.05 - 34.10: 477 34.10 - 51.15: 128 51.15 - 68.20: 69 68.20 - 85.25: 6 Dihedral angle restraints: 9312 sinusoidal: 4165 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 9309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1619 0.031 - 0.062: 479 0.062 - 0.094: 133 0.094 - 0.125: 90 0.125 - 0.156: 9 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 -2.50 -2.66 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL B 443 " pdb=" N VAL B 443 " pdb=" C VAL B 443 " pdb=" CB VAL B 443 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-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: 1.750 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 0.220 15798 Z= 0.155 Angle : 0.519 12.913 21620 Z= 0.289 Chirality : 0.037 0.156 2330 Planarity : 0.003 0.037 2604 Dihedral : 12.722 85.251 5987 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS A 138 PHE 0.011 0.001 PHE A 197 TYR 0.009 0.001 TYR A1108 ARG 0.003 0.000 ARG B 328 *********************** 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 : 1.698 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: A 87 ILE cc_start: 0.7104 (mt) cc_final: 0.6750 (mt) REVERT: A 138 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6344 (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: 0.7187 (tp) REVERT: A 602 LEU cc_start: 0.8072 (mt) cc_final: 0.7863 (mt) REVERT: A 818 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7638 (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: 0.7685 (mmm) outliers start: 5 outliers final: 3 residues processed: 528 average time/residue: 1.2987 time to fit residues: 755.1901 Evaluate side-chains 404 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 399 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 152 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A1098 ASN A1110 HIS B 124 GLN B 132 HIS B 216 HIS B 397 GLN C 85 GLN C 216 HIS C 258 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15798 Z= 0.383 Angle : 0.756 9.257 21620 Z= 0.394 Chirality : 0.048 0.260 2330 Planarity : 0.006 0.053 2604 Dihedral : 14.924 89.818 2488 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.75 % Allowed : 12.92 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1758 helix: 0.69 (0.19), residues: 739 sheet: 0.57 (0.30), residues: 245 loop : -0.18 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 918 HIS 0.008 0.002 HIS B 77 PHE 0.028 0.003 PHE A 539 TYR 0.019 0.002 TYR A1108 ARG 0.011 0.001 ARG A 993 *********************** 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 480 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 391 time to evaluate : 1.661 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 87 ILE cc_start: 0.7215 (mt) cc_final: 0.6889 (mt) REVERT: A 280 GLU cc_start: 0.7580 (mp0) cc_final: 0.7296 (mp0) REVERT: A 466 LEU cc_start: 0.7671 (mp) cc_final: 0.7429 (tp) REVERT: A 490 TRP cc_start: 0.7682 (m100) cc_final: 0.7378 (m100) REVERT: A 866 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7699 (mtp-110) REVERT: A 1056 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 74 GLN cc_start: 0.7575 (tt0) cc_final: 0.7314 (tt0) REVERT: B 122 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7544 (mtt-85) REVERT: B 152 THR cc_start: 0.8116 (p) cc_final: 0.7751 (t) REVERT: B 187 HIS cc_start: 0.6263 (OUTLIER) cc_final: 0.6052 (m170) REVERT: B 241 TRP cc_start: 0.5809 (t-100) cc_final: 0.5091 (t-100) REVERT: B 435 MET cc_start: 0.7399 (mtp) cc_final: 0.7070 (ttm) REVERT: C 195 ASN cc_start: 0.7750 (t0) cc_final: 0.7440 (t0) REVERT: C 252 LEU cc_start: 0.8302 (tt) cc_final: 0.8017 (tp) REVERT: C 256 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8067 (tp) REVERT: C 428 LEU cc_start: 0.6996 (tt) cc_final: 0.6624 (tp) outliers start: 89 outliers final: 37 residues processed: 434 average time/residue: 1.3104 time to fit residues: 627.9448 Evaluate side-chains 414 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 381 THR 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 866 ARG 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 1233 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 460 THR 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 303 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER 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 91 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 569 HIS A 803 ASN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15798 Z= 0.352 Angle : 0.724 9.295 21620 Z= 0.379 Chirality : 0.046 0.184 2330 Planarity : 0.006 0.057 2604 Dihedral : 15.117 88.518 2481 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.52 % Allowed : 16.28 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1758 helix: 0.55 (0.18), residues: 739 sheet: 0.47 (0.32), residues: 237 loop : -0.48 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 918 HIS 0.007 0.002 HIS B 454 PHE 0.022 0.002 PHE A 539 TYR 0.018 0.002 TYR A1108 ARG 0.005 0.001 ARG A 193 *********************** 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 489 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 388 time to evaluate : 1.535 Fit side-chains 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: 0.6810 (mt) REVERT: A 138 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6535 (t-90) REVERT: A 280 GLU cc_start: 0.7626 (mp0) cc_final: 0.7341 (mp0) REVERT: A 288 ARG cc_start: 0.7631 (mmt-90) cc_final: 0.7383 (mmt-90) REVERT: A 348 LEU cc_start: 0.8067 (mt) cc_final: 0.7862 (mt) REVERT: A 444 TYR cc_start: 0.7817 (t80) cc_final: 0.7464 (t80) REVERT: A 490 TRP cc_start: 0.7661 (m100) cc_final: 0.7289 (m100) REVERT: A 769 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: A 866 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7828 (mtp-110) REVERT: A 927 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: A 1056 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6882 (mm-30) REVERT: A 1163 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7185 (tpt) REVERT: B 74 GLN cc_start: 0.7635 (tt0) cc_final: 0.7363 (tt0) REVERT: B 122 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7469 (mtt-85) REVERT: B 187 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.6026 (m170) REVERT: B 408 GLU cc_start: 0.7254 (tp30) cc_final: 0.7007 (tp30) REVERT: B 435 MET cc_start: 0.7339 (mtp) cc_final: 0.7056 (ttm) REVERT: C 107 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7490 (mtm-85) REVERT: C 185 LEU cc_start: 0.8243 (mm) cc_final: 0.7941 (mt) REVERT: C 195 ASN cc_start: 0.7816 (t0) cc_final: 0.7491 (t0) REVERT: C 252 LEU cc_start: 0.8354 (tt) cc_final: 0.8086 (tp) REVERT: C 256 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8029 (tp) REVERT: C 349 TYR cc_start: 0.8201 (m-80) cc_final: 0.7970 (m-80) outliers start: 101 outliers final: 54 residues processed: 439 average time/residue: 1.2138 time to fit residues: 590.0654 Evaluate side-chains 430 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 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 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 557 GLU Chi-restraints excluded: chain A residue 581 ASP 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 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 919 MET 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 1163 MET 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 122 ARG Chi-restraints excluded: chain B residue 187 HIS 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 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 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 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 303 LEU 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 413 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 ASN A 922 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15798 Z= 0.400 Angle : 0.763 10.678 21620 Z= 0.402 Chirality : 0.048 0.186 2330 Planarity : 0.007 0.059 2604 Dihedral : 15.349 89.967 2481 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.52 % Allowed : 17.96 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1758 helix: 0.27 (0.18), residues: 738 sheet: 0.27 (0.31), residues: 240 loop : -0.73 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 241 HIS 0.007 0.002 HIS B 454 PHE 0.024 0.003 PHE A 539 TYR 0.015 0.003 TYR A1108 ARG 0.006 0.001 ARG A 193 *********************** 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 474 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 373 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7180 (mt) cc_final: 0.6843 (mt) REVERT: A 348 LEU cc_start: 0.8106 (mt) cc_final: 0.7879 (mt) REVERT: A 430 MET cc_start: 0.7295 (ttp) cc_final: 0.7021 (ttp) REVERT: A 444 TYR cc_start: 0.7830 (t80) cc_final: 0.7458 (t80) REVERT: A 490 TRP cc_start: 0.7650 (m100) cc_final: 0.7355 (m100) REVERT: A 866 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7867 (mtp-110) REVERT: A 927 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7577 (mtm-85) REVERT: A 1163 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7188 (tpt) REVERT: B 74 GLN cc_start: 0.7705 (tt0) cc_final: 0.7445 (tt0) REVERT: B 122 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7436 (mtt-85) REVERT: B 241 TRP cc_start: 0.6132 (t-100) cc_final: 0.4953 (t-100) REVERT: B 408 GLU cc_start: 0.7145 (tp30) cc_final: 0.6926 (tp30) REVERT: B 435 MET cc_start: 0.7348 (mtp) cc_final: 0.7030 (ttm) REVERT: C 185 LEU cc_start: 0.8242 (mm) cc_final: 0.7975 (mt) REVERT: C 197 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8211 (tp) REVERT: C 252 LEU cc_start: 0.8357 (tt) cc_final: 0.8106 (tp) REVERT: C 256 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8033 (tp) outliers start: 101 outliers final: 68 residues processed: 428 average time/residue: 1.2416 time to fit residues: 587.7731 Evaluate side-chains 433 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 359 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 176 THR 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 350 ILE 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 557 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 603 MET 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 799 SER 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 919 MET Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 929 THR 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 1163 MET 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 122 ARG Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL 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 186 LEU Chi-restraints excluded: chain C residue 197 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 303 LEU 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 383 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 803 ASN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 287 ASN B 397 GLN B 400 GLN B 404 ASN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15798 Z= 0.229 Angle : 0.656 11.852 21620 Z= 0.341 Chirality : 0.042 0.152 2330 Planarity : 0.005 0.053 2604 Dihedral : 15.102 85.137 2481 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.56 % Allowed : 19.57 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1758 helix: 0.78 (0.19), residues: 732 sheet: 0.49 (0.32), residues: 237 loop : -0.57 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 220 HIS 0.005 0.001 HIS B 192 PHE 0.019 0.002 PHE C 273 TYR 0.015 0.002 TYR C 429 ARG 0.008 0.001 ARG A 457 *********************** 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 458 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 372 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6856 (OUTLIER) cc_final: 0.6437 (t-90) REVERT: A 348 LEU cc_start: 0.8057 (mt) cc_final: 0.7824 (mt) REVERT: A 430 MET cc_start: 0.7267 (ttp) cc_final: 0.6931 (ttp) REVERT: A 444 TYR cc_start: 0.7818 (t80) cc_final: 0.7531 (t80) REVERT: A 490 TRP cc_start: 0.7607 (m100) cc_final: 0.7261 (m100) REVERT: A 769 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: A 866 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7798 (mtp-110) REVERT: A 927 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7592 (mtm-85) REVERT: A 985 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7211 (tpp) REVERT: A 1163 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7228 (tpt) REVERT: B 74 GLN cc_start: 0.7635 (tt0) cc_final: 0.7386 (tt0) REVERT: B 241 TRP cc_start: 0.6136 (t-100) cc_final: 0.4854 (t-100) REVERT: C 185 LEU cc_start: 0.8145 (mm) cc_final: 0.7901 (mt) REVERT: C 252 LEU cc_start: 0.8295 (tt) cc_final: 0.8065 (tp) REVERT: C 483 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8225 (ttmt) outliers start: 86 outliers final: 40 residues processed: 415 average time/residue: 1.2940 time to fit residues: 595.8968 Evaluate side-chains 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 360 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 195 LEU 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 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 475 SER Chi-restraints excluded: chain A residue 489 GLU 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 866 ARG 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 985 MET 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 1163 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 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 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 319 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 483 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN ** B 210 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15798 Z= 0.213 Angle : 0.656 12.774 21620 Z= 0.338 Chirality : 0.042 0.253 2330 Planarity : 0.005 0.065 2604 Dihedral : 14.999 80.264 2481 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.01 % Allowed : 20.09 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1758 helix: 0.96 (0.19), residues: 734 sheet: 0.70 (0.33), residues: 227 loop : -0.49 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 175 HIS 0.006 0.001 HIS A 565 PHE 0.021 0.002 PHE C 273 TYR 0.025 0.002 TYR C 315 ARG 0.013 0.001 ARG A 650 *********************** 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 464 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 371 time to evaluate : 1.622 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: 0.6835 (OUTLIER) cc_final: 0.6328 (t-90) REVERT: A 348 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 430 MET cc_start: 0.7238 (ttp) cc_final: 0.6885 (ttp) REVERT: A 444 TYR cc_start: 0.7830 (t80) cc_final: 0.7575 (t80) REVERT: A 490 TRP cc_start: 0.7573 (m100) cc_final: 0.7237 (m100) REVERT: A 756 ASP cc_start: 0.8517 (m-30) cc_final: 0.8228 (m-30) REVERT: A 866 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7811 (mtp-110) REVERT: A 927 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7603 (mtm-85) REVERT: A 1163 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7148 (tpt) REVERT: B 74 GLN cc_start: 0.7606 (tt0) cc_final: 0.7355 (tt0) REVERT: B 122 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7427 (mtt-85) REVERT: B 152 THR cc_start: 0.8138 (p) cc_final: 0.7667 (t) REVERT: B 241 TRP cc_start: 0.6093 (t-100) cc_final: 0.4769 (t-100) REVERT: C 252 LEU cc_start: 0.8316 (tt) cc_final: 0.8102 (tp) REVERT: C 256 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 442 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6466 (tp) outliers start: 93 outliers final: 51 residues processed: 419 average time/residue: 1.2950 time to fit residues: 599.5077 Evaluate side-chains 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 LEU 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 299 MET Chi-restraints excluded: chain A residue 348 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 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 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 1136 GLU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 261 GLN 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 332 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL 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 299 LEU 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 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 168 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.0050 chunk 97 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 397 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15798 Z= 0.226 Angle : 0.671 14.568 21620 Z= 0.343 Chirality : 0.043 0.292 2330 Planarity : 0.006 0.072 2604 Dihedral : 14.967 76.253 2481 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.04 % Allowed : 21.45 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1758 helix: 1.01 (0.19), residues: 735 sheet: 0.75 (0.34), residues: 235 loop : -0.48 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 175 HIS 0.005 0.001 HIS A 565 PHE 0.016 0.002 PHE B 126 TYR 0.019 0.002 TYR C 315 ARG 0.019 0.001 ARG B 257 *********************** 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 445 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 367 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6100 (m-80) cc_final: 0.5884 (m-80) REVERT: A 348 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7788 (mt) REVERT: A 430 MET cc_start: 0.7238 (ttp) cc_final: 0.6881 (ttp) REVERT: A 444 TYR cc_start: 0.7808 (t80) cc_final: 0.7548 (t80) REVERT: A 490 TRP cc_start: 0.7563 (m100) cc_final: 0.7263 (m100) REVERT: A 756 ASP cc_start: 0.8514 (m-30) cc_final: 0.8233 (m-30) REVERT: A 866 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7764 (mtp-110) REVERT: A 927 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7644 (mtm-85) REVERT: A 1163 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.6815 (tpt) REVERT: B 74 GLN cc_start: 0.7610 (tt0) cc_final: 0.7378 (tt0) REVERT: B 122 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7407 (mtt-85) REVERT: B 152 THR cc_start: 0.8097 (p) cc_final: 0.7618 (t) REVERT: B 241 TRP cc_start: 0.6087 (t-100) cc_final: 0.4765 (t-100) REVERT: C 256 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7984 (tp) REVERT: C 442 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6503 (tp) outliers start: 78 outliers final: 52 residues processed: 406 average time/residue: 1.2775 time to fit residues: 573.6233 Evaluate side-chains 414 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 355 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 195 LEU 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 299 MET Chi-restraints excluded: chain A residue 348 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 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 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 1094 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 LEU 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 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 299 LEU 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 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 69 optimal weight: 9.9990 chunk 104 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 0.0170 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 258 HIS C 339 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15798 Z= 0.212 Angle : 0.662 14.668 21620 Z= 0.339 Chirality : 0.042 0.184 2330 Planarity : 0.005 0.075 2604 Dihedral : 14.902 72.450 2479 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.72 % Allowed : 22.74 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1758 helix: 1.05 (0.19), residues: 735 sheet: 0.79 (0.34), residues: 235 loop : -0.46 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 175 HIS 0.005 0.001 HIS A 565 PHE 0.012 0.001 PHE A 197 TYR 0.018 0.002 TYR C 315 ARG 0.017 0.001 ARG A 650 *********************** 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 441 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 368 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7765 (mt) REVERT: A 430 MET cc_start: 0.7236 (ttp) cc_final: 0.6869 (ttp) REVERT: A 444 TYR cc_start: 0.7796 (t80) cc_final: 0.7571 (t80) REVERT: A 490 TRP cc_start: 0.7576 (m100) cc_final: 0.7270 (m100) REVERT: A 756 ASP cc_start: 0.8501 (m-30) cc_final: 0.8211 (m-30) REVERT: A 866 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7746 (mtp-110) REVERT: A 1163 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6820 (tpt) REVERT: B 74 GLN cc_start: 0.7596 (tt0) cc_final: 0.7352 (tt0) REVERT: B 122 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7365 (mtt-85) REVERT: B 152 THR cc_start: 0.8071 (p) cc_final: 0.7594 (t) REVERT: B 183 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6875 (tm-30) REVERT: B 185 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.5022 (tt) REVERT: B 241 TRP cc_start: 0.6049 (t-100) cc_final: 0.4790 (t-100) REVERT: C 256 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7955 (tp) REVERT: C 442 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6420 (tp) outliers start: 73 outliers final: 55 residues processed: 408 average time/residue: 1.2413 time to fit residues: 561.9283 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 : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 195 LEU 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 299 MET Chi-restraints excluded: chain A residue 348 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 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 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 1094 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 261 GLN 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 332 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 LEU 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 C residue 120 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 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 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 442 LEU 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 167 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 106 optimal weight: 0.0980 chunk 171 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 210 GLN B 287 ASN B 397 GLN C 258 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15798 Z= 0.209 Angle : 0.685 17.236 21620 Z= 0.346 Chirality : 0.042 0.196 2330 Planarity : 0.005 0.081 2604 Dihedral : 14.872 72.627 2479 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.78 % Allowed : 23.32 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1758 helix: 1.10 (0.19), residues: 735 sheet: 0.86 (0.34), residues: 235 loop : -0.43 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 175 HIS 0.005 0.001 HIS A 565 PHE 0.024 0.002 PHE C 273 TYR 0.018 0.002 TYR C 429 ARG 0.018 0.001 ARG A 650 *********************** 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 440 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 366 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 430 MET cc_start: 0.7223 (ttp) cc_final: 0.6846 (ttp) REVERT: A 444 TYR cc_start: 0.7785 (t80) cc_final: 0.7563 (t80) REVERT: A 490 TRP cc_start: 0.7562 (m100) cc_final: 0.7238 (m100) REVERT: A 756 ASP cc_start: 0.8505 (m-30) cc_final: 0.8204 (m-30) REVERT: A 866 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7672 (mtp-110) REVERT: A 927 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7358 (mtm-85) REVERT: A 1186 ASP cc_start: 0.6834 (t0) cc_final: 0.6496 (t70) REVERT: A 1189 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (mp) REVERT: B 74 GLN cc_start: 0.7582 (tt0) cc_final: 0.7359 (tt0) REVERT: B 122 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7422 (mtt-85) REVERT: B 152 THR cc_start: 0.8068 (p) cc_final: 0.7588 (t) REVERT: B 241 TRP cc_start: 0.6047 (t-100) cc_final: 0.4663 (t-100) REVERT: C 256 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (tp) REVERT: C 442 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6351 (tp) outliers start: 74 outliers final: 54 residues processed: 403 average time/residue: 1.2374 time to fit residues: 551.5197 Evaluate side-chains 414 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 195 LEU 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 350 ILE 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 489 GLU 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 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 1094 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 261 GLN 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 332 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL 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 185 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 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 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 104 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 85 GLN B 287 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 258 HIS C 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 15798 Z= 0.304 Angle : 0.864 59.189 21620 Z= 0.472 Chirality : 0.042 0.169 2330 Planarity : 0.005 0.079 2604 Dihedral : 14.872 72.583 2479 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.39 % Allowed : 23.71 % Favored : 71.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1758 helix: 1.09 (0.19), residues: 735 sheet: 0.87 (0.34), residues: 235 loop : -0.43 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 175 HIS 0.004 0.001 HIS A 565 PHE 0.021 0.002 PHE C 273 TYR 0.017 0.002 TYR C 315 ARG 0.017 0.001 ARG A 650 ********************** 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 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 352 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7780 (mt) REVERT: A 430 MET cc_start: 0.7207 (ttp) cc_final: 0.6850 (ttp) REVERT: A 444 TYR cc_start: 0.7791 (t80) cc_final: 0.7566 (t80) REVERT: A 490 TRP cc_start: 0.7561 (m100) cc_final: 0.7240 (m100) REVERT: A 756 ASP cc_start: 0.8505 (m-30) cc_final: 0.8204 (m-30) REVERT: A 866 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7671 (mtp-110) REVERT: A 927 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7360 (mtm-85) REVERT: A 1186 ASP cc_start: 0.6835 (t0) cc_final: 0.6504 (t70) REVERT: A 1189 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 74 GLN cc_start: 0.7585 (tt0) cc_final: 0.7359 (tt0) REVERT: B 122 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7435 (mtt-85) REVERT: B 152 THR cc_start: 0.8068 (p) cc_final: 0.7590 (t) REVERT: B 241 TRP cc_start: 0.6046 (t-100) cc_final: 0.4666 (t-100) REVERT: C 256 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7951 (tp) REVERT: C 442 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6343 (tp) outliers start: 68 outliers final: 57 residues processed: 388 average time/residue: 1.2101 time to fit residues: 520.5943 Evaluate side-chains 413 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 350 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 195 LEU 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 292 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 ILE 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 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 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 1094 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 LEU 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 185 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 268 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 383 VAL 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 43 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN A 968 GLN A1110 HIS A1157 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.146749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.136937 restraints weight = 29187.510| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.76 r_work: 0.3873 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 15798 Z= 0.304 Angle : 0.864 59.189 21620 Z= 0.471 Chirality : 0.042 0.169 2330 Planarity : 0.005 0.079 2604 Dihedral : 14.872 72.583 2479 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.13 % Allowed : 24.03 % Favored : 71.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1758 helix: 1.09 (0.19), residues: 735 sheet: 0.87 (0.34), residues: 235 loop : -0.43 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 175 HIS 0.004 0.001 HIS A 565 PHE 0.021 0.002 PHE C 273 TYR 0.017 0.002 TYR C 315 ARG 0.017 0.001 ARG A 650 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8005.20 seconds wall clock time: 143 minutes 36.34 seconds (8616.34 seconds total)