Starting phenix.real_space_refine on Fri Jun 13 20:16:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d37_27155/06_2025/8d37_27155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d37_27155/06_2025/8d37_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_27155/06_2025/8d37_27155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d37_27155/06_2025/8d37_27155.map" model { file = "/net/cci-nas-00/data/ceres_data/8d37_27155/06_2025/8d37_27155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d37_27155/06_2025/8d37_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.13, per 1000 atoms: 0.66 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: 5.90 Conformation dependent library (CDL) restraints added in 2.2 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: 7.78 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: 10.33 Time building geometry restraints manager: 6.20 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: 0.010 Normalize map: mean=0, sd=1: 2.600 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 49.700 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.190 ------------------------------------------------------------------------------- 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 15799 Z= 0.210 Angle : 0.519 12.913 21622 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 Details of bonding type rmsd hydrogen bonds : bond 0.16061 ( 727) hydrogen bonds : angle 6.41772 ( 1978) SS BOND : bond 0.00444 ( 1) SS BOND : angle 0.81653 ( 2) covalent geometry : bond 0.00320 (15798) covalent geometry : angle 0.51900 (21620) *********************** 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 : 1.782 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: 1.2980 time to fit residues: 759.2901 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 : 1.699 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.144071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.134299 restraints weight = 29173.113| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.76 r_work: 0.3836 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 15799 Z= 0.266 Angle : 0.756 9.257 21622 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 Details of bonding type rmsd hydrogen bonds : bond 0.06316 ( 727) hydrogen bonds : angle 5.25869 ( 1978) SS BOND : bond 0.00574 ( 1) SS BOND : angle 0.59911 ( 2) covalent geometry : bond 0.00596 (15798) covalent geometry : angle 0.75555 (21620) *********************** 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 : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7297 (mt) cc_final: 0.6961 (mt) REVERT: A 280 GLU cc_start: 0.7557 (mp0) cc_final: 0.7324 (mp0) REVERT: A 466 LEU cc_start: 0.7673 (mp) cc_final: 0.7429 (tp) REVERT: A 490 TRP cc_start: 0.7772 (m100) cc_final: 0.7489 (m100) REVERT: A 866 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7697 (mtp-110) REVERT: A 1056 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6985 (mm-30) REVERT: B 74 GLN cc_start: 0.7872 (tt0) cc_final: 0.7654 (tt0) REVERT: B 122 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7655 (mtt-85) REVERT: B 152 THR cc_start: 0.8082 (p) cc_final: 0.7746 (t) REVERT: B 187 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.6278 (m170) REVERT: B 241 TRP cc_start: 0.5767 (t-100) cc_final: 0.5051 (t-100) REVERT: B 435 MET cc_start: 0.7605 (mtp) cc_final: 0.7304 (ttm) REVERT: C 195 ASN cc_start: 0.7915 (t0) cc_final: 0.7640 (t0) REVERT: C 197 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8052 (tt) REVERT: C 252 LEU cc_start: 0.8428 (tt) cc_final: 0.8142 (tp) REVERT: C 256 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8024 (tp) REVERT: C 277 ASP cc_start: 0.6440 (p0) cc_final: 0.6119 (p0) REVERT: C 428 LEU cc_start: 0.6935 (tt) cc_final: 0.6576 (tp) outliers start: 89 outliers final: 37 residues processed: 434 average time/residue: 1.2298 time to fit residues: 589.7008 Evaluate side-chains 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 373 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 197 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 52 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 B 400 GLN B 404 ASN C 85 GLN C 216 HIS C 258 HIS C 339 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.144440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.134473 restraints weight = 28954.515| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.76 r_work: 0.3838 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15799 Z= 0.223 Angle : 0.705 9.332 21622 Z= 0.368 Chirality : 0.045 0.184 2330 Planarity : 0.006 0.047 2604 Dihedral : 15.055 87.676 2481 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 6.27 % Allowed : 16.41 % Favored : 77.33 % 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: 0.18 (0.20), residues: 1758 helix: 0.65 (0.19), residues: 739 sheet: 0.40 (0.31), residues: 249 loop : -0.39 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 918 HIS 0.006 0.001 HIS B 454 PHE 0.021 0.002 PHE A 539 TYR 0.017 0.002 TYR A1108 ARG 0.005 0.001 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 727) hydrogen bonds : angle 5.15514 ( 1978) SS BOND : bond 0.00456 ( 1) SS BOND : angle 0.56536 ( 2) covalent geometry : bond 0.00505 (15798) covalent geometry : angle 0.70479 (21620) *********************** 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 485 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 388 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7237 (mt) cc_final: 0.6870 (mt) REVERT: A 138 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6650 (t-90) REVERT: A 444 TYR cc_start: 0.7983 (t80) cc_final: 0.7621 (t80) REVERT: A 490 TRP cc_start: 0.7727 (m100) cc_final: 0.7373 (m100) REVERT: A 748 TRP cc_start: 0.7211 (m-90) cc_final: 0.6919 (m-90) REVERT: A 769 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: A 866 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7760 (mtp-110) REVERT: A 927 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7890 (mtm-85) REVERT: A 1163 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7254 (tpt) REVERT: B 74 GLN cc_start: 0.7944 (tt0) cc_final: 0.7714 (tt0) REVERT: B 187 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.6212 (m170) REVERT: B 280 ASP cc_start: 0.6036 (t0) cc_final: 0.5701 (t70) REVERT: B 408 GLU cc_start: 0.7688 (tp30) cc_final: 0.7411 (tp30) REVERT: B 435 MET cc_start: 0.7563 (mtp) cc_final: 0.7309 (ttm) REVERT: C 107 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7809 (mtm-85) REVERT: C 185 LEU cc_start: 0.8133 (mm) cc_final: 0.7800 (mt) REVERT: C 195 ASN cc_start: 0.8029 (t0) cc_final: 0.7731 (t0) REVERT: C 252 LEU cc_start: 0.8441 (tt) cc_final: 0.8175 (tp) REVERT: C 256 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7995 (tp) REVERT: C 349 TYR cc_start: 0.8291 (m-80) cc_final: 0.7995 (m-80) outliers start: 97 outliers final: 53 residues processed: 434 average time/residue: 1.1702 time to fit residues: 562.4063 Evaluate side-chains 428 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 368 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 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 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 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 197 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 460 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 16 optimal weight: 0.0770 chunk 166 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 0.0030 chunk 88 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.7952 ------------------------------------------------------------------------------- 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 B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.148039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.138205 restraints weight = 29219.219| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.76 r_work: 0.3890 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15799 Z= 0.127 Angle : 0.616 11.907 21622 Z= 0.319 Chirality : 0.041 0.153 2330 Planarity : 0.005 0.049 2604 Dihedral : 14.802 77.684 2481 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.26 % Allowed : 19.12 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.20), residues: 1758 helix: 1.22 (0.19), residues: 735 sheet: 0.98 (0.33), residues: 216 loop : -0.24 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 175 HIS 0.004 0.001 HIS A 138 PHE 0.020 0.001 PHE B 403 TYR 0.013 0.001 TYR C 429 ARG 0.007 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 727) hydrogen bonds : angle 4.80630 ( 1978) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.38353 ( 2) covalent geometry : bond 0.00275 (15798) covalent geometry : angle 0.61601 (21620) *********************** 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 452 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 386 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.6455 (t-90) REVERT: A 430 MET cc_start: 0.7462 (ttp) cc_final: 0.7188 (ttp) REVERT: A 490 TRP cc_start: 0.7647 (m100) cc_final: 0.7239 (m100) REVERT: A 756 ASP cc_start: 0.8529 (m-30) cc_final: 0.8250 (m-30) REVERT: A 1163 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7206 (tpt) REVERT: B 74 GLN cc_start: 0.7865 (tt0) cc_final: 0.7638 (tt0) REVERT: B 187 HIS cc_start: 0.6353 (OUTLIER) cc_final: 0.6129 (m170) REVERT: B 241 TRP cc_start: 0.5988 (t-100) cc_final: 0.4748 (t-100) REVERT: B 407 LEU cc_start: 0.7173 (mt) cc_final: 0.6961 (tp) REVERT: B 408 GLU cc_start: 0.7403 (tp30) cc_final: 0.7199 (tp30) REVERT: C 107 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7692 (mtm-85) REVERT: C 185 LEU cc_start: 0.7988 (mm) cc_final: 0.7661 (mt) REVERT: C 195 ASN cc_start: 0.7921 (t0) cc_final: 0.7623 (t0) REVERT: C 197 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8077 (tp) REVERT: C 252 LEU cc_start: 0.8408 (tt) cc_final: 0.8168 (tp) REVERT: C 256 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7931 (tp) REVERT: C 433 ASP cc_start: 0.7622 (m-30) cc_final: 0.7390 (m-30) REVERT: C 437 ILE cc_start: 0.6816 (mt) cc_final: 0.6513 (mt) outliers start: 66 outliers final: 29 residues processed: 419 average time/residue: 1.4200 time to fit residues: 659.2057 Evaluate side-chains 399 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 365 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL 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 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 306 LEU 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 C residue 175 LEU Chi-restraints excluded: chain C residue 197 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 423 SER 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 116 optimal weight: 0.8980 chunk 163 optimal weight: 0.0000 chunk 119 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.9866 ------------------------------------------------------------------------------- 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 184 ASN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.148634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138598 restraints weight = 29476.279| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.79 r_work: 0.3896 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15799 Z= 0.128 Angle : 0.621 11.592 21622 Z= 0.318 Chirality : 0.041 0.283 2330 Planarity : 0.005 0.055 2604 Dihedral : 14.718 72.933 2481 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.52 % Allowed : 20.16 % Favored : 75.32 % 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: 0.90 (0.20), residues: 1758 helix: 1.36 (0.19), residues: 742 sheet: 0.84 (0.34), residues: 231 loop : -0.14 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 175 HIS 0.005 0.001 HIS A 565 PHE 0.021 0.002 PHE B 126 TYR 0.022 0.001 TYR C 315 ARG 0.014 0.001 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 727) hydrogen bonds : angle 4.69169 ( 1978) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.39170 ( 2) covalent geometry : bond 0.00283 (15798) covalent geometry : angle 0.62115 (21620) *********************** 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 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 378 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6431 (t-90) REVERT: A 178 TYR cc_start: 0.6062 (m-80) cc_final: 0.5813 (m-80) REVERT: A 430 MET cc_start: 0.7449 (ttp) cc_final: 0.7127 (ttp) REVERT: A 456 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8075 (mm110) REVERT: A 490 TRP cc_start: 0.7690 (m100) cc_final: 0.7342 (m100) REVERT: A 866 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7567 (mtp-110) REVERT: B 74 GLN cc_start: 0.7872 (tt0) cc_final: 0.7660 (tt0) REVERT: B 151 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 152 THR cc_start: 0.8095 (p) cc_final: 0.7566 (t) REVERT: B 187 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.6158 (m170) REVERT: B 241 TRP cc_start: 0.5920 (t-100) cc_final: 0.4702 (t-100) REVERT: B 407 LEU cc_start: 0.7075 (mt) cc_final: 0.6862 (tp) REVERT: B 408 GLU cc_start: 0.7428 (tp30) cc_final: 0.7221 (tp30) REVERT: C 195 ASN cc_start: 0.7990 (t0) cc_final: 0.7696 (t0) REVERT: C 197 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8059 (tp) REVERT: C 252 LEU cc_start: 0.8411 (tt) cc_final: 0.8207 (tp) REVERT: C 256 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7881 (tp) REVERT: C 277 ASP cc_start: 0.6337 (p0) cc_final: 0.6063 (p0) REVERT: C 433 ASP cc_start: 0.7579 (m-30) cc_final: 0.7350 (m-30) REVERT: C 437 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5935 (mt) outliers start: 70 outliers final: 35 residues processed: 415 average time/residue: 1.2268 time to fit residues: 565.1544 Evaluate side-chains 409 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 887 VAL 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 1136 GLU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 175 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 319 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 14 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 A1157 ASN B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 216 HIS C 258 HIS C 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130987 restraints weight = 29331.134| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.77 r_work: 0.3790 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 15799 Z= 0.379 Angle : 0.880 13.036 21622 Z= 0.462 Chirality : 0.053 0.331 2330 Planarity : 0.008 0.082 2604 Dihedral : 15.555 86.977 2481 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.40 % Allowed : 19.06 % Favored : 74.55 % 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: -0.43 (0.19), residues: 1758 helix: 0.08 (0.18), residues: 743 sheet: 0.36 (0.32), residues: 236 loop : -0.74 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 484 HIS 0.011 0.002 HIS B 454 PHE 0.033 0.004 PHE A 539 TYR 0.022 0.003 TYR C 315 ARG 0.014 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.07058 ( 727) hydrogen bonds : angle 5.47852 ( 1978) SS BOND : bond 0.00645 ( 1) SS BOND : angle 0.84730 ( 2) covalent geometry : bond 0.00858 (15798) covalent geometry : angle 0.88003 (21620) *********************** 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 471 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 372 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7327 (mt) cc_final: 0.6997 (mt) REVERT: A 430 MET cc_start: 0.7669 (ttp) cc_final: 0.7311 (ttp) REVERT: A 444 TYR cc_start: 0.7945 (t80) cc_final: 0.7498 (t80) REVERT: A 490 TRP cc_start: 0.7726 (m100) cc_final: 0.7505 (m100) REVERT: A 866 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7771 (mtp-110) REVERT: A 927 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7803 (mtm-85) REVERT: B 74 GLN cc_start: 0.8003 (tt0) cc_final: 0.7800 (tt0) REVERT: B 229 LYS cc_start: 0.5661 (OUTLIER) cc_final: 0.5414 (ptmt) REVERT: C 252 LEU cc_start: 0.8447 (tt) cc_final: 0.8235 (tp) REVERT: C 256 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 277 ASP cc_start: 0.6551 (p0) cc_final: 0.6281 (p0) REVERT: C 433 ASP cc_start: 0.7652 (m-30) cc_final: 0.7422 (m-30) REVERT: C 437 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6687 (mt) outliers start: 99 outliers final: 60 residues processed: 427 average time/residue: 1.1788 time to fit residues: 558.1584 Evaluate side-chains 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 355 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain A residue 350 ILE 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 581 ASP 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 910 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 1136 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 256 LEU 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 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 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 299 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 758 ASN A 803 ASN A 922 GLN A 968 GLN A1110 HIS B 124 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 323 HIS B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.146064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.136257 restraints weight = 29299.023| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.76 r_work: 0.3866 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15799 Z= 0.141 Angle : 0.673 13.768 21622 Z= 0.345 Chirality : 0.042 0.241 2330 Planarity : 0.005 0.053 2604 Dihedral : 15.051 79.389 2481 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.94 % Allowed : 23.26 % Favored : 72.80 % 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 (0.20), residues: 1758 helix: 0.84 (0.19), residues: 741 sheet: 0.86 (0.33), residues: 224 loop : -0.52 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 220 HIS 0.005 0.001 HIS A 565 PHE 0.020 0.002 PHE B 403 TYR 0.018 0.002 TYR C 315 ARG 0.009 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 727) hydrogen bonds : angle 4.96427 ( 1978) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.38758 ( 2) covalent geometry : bond 0.00309 (15798) covalent geometry : angle 0.67308 (21620) *********************** 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 428 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.6458 (t-90) REVERT: A 430 MET cc_start: 0.7595 (ttp) cc_final: 0.7210 (ttp) REVERT: A 444 TYR cc_start: 0.7958 (t80) cc_final: 0.7679 (t80) REVERT: A 490 TRP cc_start: 0.7645 (m100) cc_final: 0.7373 (m100) REVERT: A 756 ASP cc_start: 0.8588 (m-30) cc_final: 0.8386 (m-30) REVERT: A 866 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7694 (mtp-110) REVERT: A 1185 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7980 (mm) REVERT: B 74 GLN cc_start: 0.7895 (tt0) cc_final: 0.7685 (tt0) REVERT: B 113 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 151 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7312 (mm-30) REVERT: B 152 THR cc_start: 0.8180 (p) cc_final: 0.7693 (t) REVERT: B 241 TRP cc_start: 0.6042 (t-100) cc_final: 0.4843 (t-100) REVERT: B 408 GLU cc_start: 0.7449 (tp30) cc_final: 0.7216 (tp30) REVERT: C 185 LEU cc_start: 0.8039 (mm) cc_final: 0.7729 (mt) REVERT: C 256 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 277 ASP cc_start: 0.6401 (p0) cc_final: 0.6116 (p0) REVERT: C 442 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6451 (tp) outliers start: 61 outliers final: 37 residues processed: 399 average time/residue: 1.2411 time to fit residues: 549.2316 Evaluate side-chains 395 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 353 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL 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 489 GLU Chi-restraints excluded: chain A residue 605 LEU 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 887 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 229 LYS 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 C residue 168 VAL Chi-restraints excluded: chain C residue 175 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 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 107 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 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 B 400 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.145291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135501 restraints weight = 29036.197| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.74 r_work: 0.3855 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15799 Z= 0.167 Angle : 0.693 15.819 21622 Z= 0.355 Chirality : 0.043 0.188 2330 Planarity : 0.006 0.083 2604 Dihedral : 15.004 75.699 2481 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.52 % Allowed : 22.42 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.20), residues: 1758 helix: 0.77 (0.19), residues: 747 sheet: 0.84 (0.34), residues: 224 loop : -0.54 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 175 HIS 0.005 0.001 HIS B 192 PHE 0.022 0.002 PHE C 273 TYR 0.018 0.002 TYR C 315 ARG 0.017 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 727) hydrogen bonds : angle 4.97926 ( 1978) SS BOND : bond 0.00325 ( 1) SS BOND : angle 0.40356 ( 2) covalent geometry : bond 0.00378 (15798) covalent geometry : angle 0.69267 (21620) *********************** 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 432 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 362 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.7589 (ttp) cc_final: 0.7190 (ttp) REVERT: A 444 TYR cc_start: 0.7968 (t80) cc_final: 0.7711 (t80) REVERT: A 490 TRP cc_start: 0.7648 (m100) cc_final: 0.7386 (m100) REVERT: A 756 ASP cc_start: 0.8598 (m-30) cc_final: 0.8377 (m-30) REVERT: A 866 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7782 (mtp-110) REVERT: A 927 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7786 (mtm-85) REVERT: A 1185 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 74 GLN cc_start: 0.7889 (tt0) cc_final: 0.7687 (tt0) REVERT: B 151 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7315 (mm-30) REVERT: B 152 THR cc_start: 0.8186 (p) cc_final: 0.7701 (t) REVERT: B 241 TRP cc_start: 0.6060 (t-100) cc_final: 0.4749 (t-100) REVERT: B 476 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7695 (pt) REVERT: C 185 LEU cc_start: 0.8077 (mm) cc_final: 0.7760 (mt) REVERT: C 256 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 277 ASP cc_start: 0.6465 (p0) cc_final: 0.6145 (p0) REVERT: C 442 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6484 (tp) outliers start: 70 outliers final: 44 residues processed: 398 average time/residue: 1.1991 time to fit residues: 528.2322 Evaluate side-chains 398 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 370 GLU 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 489 GLU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 277 ASP 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 476 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 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 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 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 262 GLN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.142075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.132305 restraints weight = 29179.690| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.76 r_work: 0.3809 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15799 Z= 0.275 Angle : 0.803 16.609 21622 Z= 0.414 Chirality : 0.048 0.201 2330 Planarity : 0.007 0.102 2604 Dihedral : 15.319 83.394 2479 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.91 % Allowed : 22.61 % Favored : 72.48 % 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: -0.22 (0.20), residues: 1758 helix: 0.27 (0.18), residues: 745 sheet: 0.51 (0.33), residues: 236 loop : -0.66 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 918 HIS 0.007 0.002 HIS B 454 PHE 0.024 0.003 PHE A 539 TYR 0.021 0.003 TYR C 315 ARG 0.017 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 727) hydrogen bonds : angle 5.28402 ( 1978) SS BOND : bond 0.00454 ( 1) SS BOND : angle 0.68779 ( 2) covalent geometry : bond 0.00624 (15798) covalent geometry : angle 0.80296 (21620) *********************** 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 432 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.7672 (ttp) cc_final: 0.7280 (ttp) REVERT: A 444 TYR cc_start: 0.7953 (t80) cc_final: 0.7629 (t80) REVERT: A 490 TRP cc_start: 0.7764 (m100) cc_final: 0.7543 (m100) REVERT: A 732 TYR cc_start: 0.5596 (m-80) cc_final: 0.5219 (m-80) REVERT: A 834 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 866 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7795 (mtp-110) REVERT: A 927 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7801 (mtm-85) REVERT: B 74 GLN cc_start: 0.7945 (tt0) cc_final: 0.7740 (tt0) REVERT: B 187 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6360 (m170) REVERT: B 229 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5370 (ttmt) REVERT: B 241 TRP cc_start: 0.6083 (t-100) cc_final: 0.4844 (t-100) REVERT: B 476 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7787 (pt) REVERT: C 185 LEU cc_start: 0.8137 (mm) cc_final: 0.7803 (mt) REVERT: C 256 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 433 ASP cc_start: 0.7706 (m-30) cc_final: 0.7504 (m-30) outliers start: 76 outliers final: 52 residues processed: 395 average time/residue: 1.1903 time to fit residues: 523.0587 Evaluate side-chains 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 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 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 1153 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 256 LEU 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 476 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 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 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 ILE 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 45 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 264 GLN A 803 ASN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 85 GLN B 124 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.146320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.136501 restraints weight = 29234.804| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.77 r_work: 0.3868 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15799 Z= 0.146 Angle : 0.713 18.093 21622 Z= 0.361 Chirality : 0.043 0.170 2330 Planarity : 0.005 0.082 2604 Dihedral : 15.014 77.237 2479 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.17 % Allowed : 24.81 % Favored : 72.03 % 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: 0.22 (0.20), residues: 1758 helix: 0.78 (0.19), residues: 740 sheet: 0.74 (0.33), residues: 227 loop : -0.57 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 175 HIS 0.004 0.001 HIS A1110 PHE 0.016 0.002 PHE C 273 TYR 0.017 0.002 TYR C 315 ARG 0.019 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 727) hydrogen bonds : angle 4.99129 ( 1978) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.50388 ( 2) covalent geometry : bond 0.00331 (15798) covalent geometry : angle 0.71256 (21620) ********************** 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 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.7589 (ttp) cc_final: 0.7187 (ttp) REVERT: A 444 TYR cc_start: 0.7946 (t80) cc_final: 0.7698 (t80) REVERT: A 490 TRP cc_start: 0.7672 (m100) cc_final: 0.7391 (m100) REVERT: A 732 TYR cc_start: 0.5420 (m-80) cc_final: 0.4973 (m-80) REVERT: A 748 TRP cc_start: 0.7014 (m-90) cc_final: 0.6808 (m-90) REVERT: A 866 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7752 (mtp-110) REVERT: A 916 PHE cc_start: 0.7609 (t80) cc_final: 0.7344 (t80) REVERT: A 1186 ASP cc_start: 0.6872 (t0) cc_final: 0.6616 (t70) REVERT: B 151 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7363 (mm-30) REVERT: B 152 THR cc_start: 0.8166 (p) cc_final: 0.7693 (t) REVERT: B 183 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 241 TRP cc_start: 0.5994 (t-100) cc_final: 0.4602 (t-100) REVERT: B 408 GLU cc_start: 0.7325 (tp30) cc_final: 0.7118 (tp30) REVERT: B 476 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7693 (pt) REVERT: C 185 LEU cc_start: 0.8040 (mm) cc_final: 0.7726 (mt) REVERT: C 256 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7947 (tp) outliers start: 49 outliers final: 35 residues processed: 387 average time/residue: 1.2680 time to fit residues: 544.5578 Evaluate side-chains 385 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 347 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR 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 432 VAL 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 992 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 256 LEU 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 441 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 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 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 44 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 0.0170 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.145899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.136144 restraints weight = 29086.528| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.75 r_work: 0.3865 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 15799 Z= 0.248 Angle : 1.009 59.200 21622 Z= 0.585 Chirality : 0.044 0.217 2330 Planarity : 0.006 0.102 2604 Dihedral : 15.017 77.303 2479 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.29 % Allowed : 24.48 % Favored : 72.22 % Cbeta Deviations : 0.12 % 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: 0.19 (0.20), residues: 1758 helix: 0.73 (0.19), residues: 746 sheet: 0.75 (0.33), residues: 227 loop : -0.59 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 175 HIS 0.004 0.001 HIS A 565 PHE 0.014 0.002 PHE C 273 TYR 0.018 0.002 TYR C 315 ARG 0.016 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 727) hydrogen bonds : angle 4.99098 ( 1978) SS BOND : bond 0.00410 ( 1) SS BOND : angle 0.56626 ( 2) covalent geometry : bond 0.00547 (15798) covalent geometry : angle 1.00873 (21620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13737.03 seconds wall clock time: 237 minutes 5.47 seconds (14225.47 seconds total)