Starting phenix.real_space_refine on Fri Jul 3 19:09:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4f_72481/07_2026/9y4f_72481_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4f_72481/07_2026/9y4f_72481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y4f_72481/07_2026/9y4f_72481_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4f_72481/07_2026/9y4f_72481_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y4f_72481/07_2026/9y4f_72481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4f_72481/07_2026/9y4f_72481.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.222 sd= 0.767 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 61 5.49 5 S 82 5.16 5 C 9558 2.51 5 N 2706 2.21 5 O 2895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15303 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8225 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 67, 'TRANS': 960} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2977 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 352} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2883 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 3 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: "D" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1187 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.99, per 1000 atoms: 0.20 Number of scatterers: 15303 At special positions: 0 Unit cell: (101.48, 106.64, 159.96, 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 61 15.00 O 2895 8.00 N 2706 7.00 C 9558 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 533.1 milliseconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 12 sheets defined 47.6% alpha, 14.2% beta 26 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 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 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.041A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.814A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.952A 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 317 removed outlier: 3.815A pdb=" N GLN A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.524A pdb=" N ILE A 350 " --> pdb=" O TRP A 347 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 418 removed outlier: 6.089A pdb=" N GLN A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.261A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 4.064A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 4.037A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.914A pdb=" N GLN A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.704A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.510A pdb=" N LYS A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 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 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.279A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.943A 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 removed outlier: 4.028A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) No H-bonds generated for '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 923 removed outlier: 3.977A pdb=" N GLY A 923 " --> pdb=" O MET A 919 " (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 Processing helix chain 'A' and resid 974 through 988 removed outlier: 4.747A pdb=" N ALA A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1001 No H-bonds generated for 'chain 'A' and resid 999 through 1001' Processing helix chain 'A' and resid 1002 through 1009 Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.694A pdb=" N GLU A1031 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A1034 " --> pdb=" O ARG A1030 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.603A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.793A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A1104 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.887A pdb=" N ALA A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1211 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.605A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.642A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.528A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (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 removed outlier: 3.619A pdb=" N MET B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.877A pdb=" N LYS B 321 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.578A pdb=" N ASN B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 366' Processing helix chain 'B' and resid 391 through 408 removed outlier: 4.124A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 407 " --> pdb=" O PHE B 403 " (cutoff:3.500A) 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 434 removed outlier: 3.780A pdb=" N GLU B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 470 through 481 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 185 through 192 removed outlier: 3.865A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.559A pdb=" N LEU C 197 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 198 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 3.562A pdb=" N ASP C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 4.270A 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 319 through 323 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 394 through 409 removed outlier: 3.706A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 435 removed outlier: 3.550A pdb=" N LEU C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 451 removed outlier: 4.159A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 485 removed outlier: 3.582A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.073A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 174 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 211 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.177A 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 removed outlier: 3.542A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 612 through 615 Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.705A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1019 through 1020 removed outlier: 3.558A pdb=" N TRP A 994 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A1046 " --> pdb=" O ARG A 996 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.613A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.760A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.005A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 454 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.560A pdb=" N TYR C 206 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 218 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 230 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.878A 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 removed outlier: 3.505A pdb=" N LYS C 134 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.583A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.55 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: 4837 1.34 - 1.47: 4073 1.47 - 1.59: 6659 1.59 - 1.72: 113 1.72 - 1.85: 129 Bond restraints: 15811 Sorted by residual: bond pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 1.579 1.766 -0.187 1.10e-02 8.26e+03 2.90e+02 bond pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " ideal model delta sigma weight residual 1.443 1.347 0.096 1.00e-02 1.00e+04 9.27e+01 bond pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 1.592 1.671 -0.079 1.10e-02 8.26e+03 5.22e+01 bond pdb=" C6 DTP A4002 " pdb=" N6 DTP A4002 " ideal model delta sigma weight residual 1.337 1.382 -0.045 1.10e-02 8.26e+03 1.67e+01 bond pdb=" C8 DTP A4002 " pdb=" N7 DTP A4002 " ideal model delta sigma weight residual 1.310 1.347 -0.037 1.00e-02 1.00e+04 1.40e+01 ... (remaining 15806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 21546 3.16 - 6.32: 106 6.32 - 9.48: 12 9.48 - 12.64: 5 12.64 - 15.80: 5 Bond angle restraints: 21674 Sorted by residual: angle pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 136.83 122.71 14.12 1.00e+00 1.00e+00 1.99e+02 angle pdb=" O2A DTP A4002 " pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 106.94 121.50 -14.56 1.88e+00 2.83e-01 6.00e+01 angle pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 121.27 114.98 6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" O1B DTP A4002 " pdb=" PB DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 111.24 95.44 15.80 2.72e+00 1.35e-01 3.38e+01 angle pdb=" N3 DT D 3 " pdb=" C4 DT D 3 " pdb=" O4 DT D 3 " ideal model delta sigma weight residual 119.90 123.23 -3.33 6.00e-01 2.78e+00 3.08e+01 ... (remaining 21669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.92: 8395 28.92 - 57.84: 794 57.84 - 86.76: 63 86.76 - 115.68: 8 115.68 - 144.60: 1 Dihedral angle restraints: 9261 sinusoidal: 4207 harmonic: 5054 Sorted by residual: dihedral pdb=" CA CYS A1077 " pdb=" C CYS A1077 " pdb=" N CYS A1078 " pdb=" CA CYS A1078 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+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 55.10 37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" C4' DG D 12 " pdb=" C3' DG D 12 " pdb=" O3' DG D 12 " pdb=" P DA D 13 " ideal model delta sinusoidal sigma weight residual 220.00 75.40 144.60 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 9258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1490 0.034 - 0.067: 543 0.067 - 0.100: 198 0.100 - 0.134: 87 0.134 - 0.167: 4 Chirality restraints: 2322 Sorted by residual: 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 2.60 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA ILE A1131 " pdb=" N ILE A1131 " pdb=" C ILE A1131 " pdb=" CB ILE A1131 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA GLU B 408 " pdb=" N GLU B 408 " pdb=" C GLU B 408 " pdb=" CB GLU B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 2319 not shown) Planarity restraints: 2575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 389 " -0.197 9.50e-02 1.11e+02 8.91e-02 6.09e+00 pdb=" NE ARG B 389 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 389 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 389 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 389 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 918 " -0.016 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP A 918 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 918 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 918 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 918 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 918 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 918 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 918 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 918 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 918 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 408 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" CD GLU B 408 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 408 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 408 " -0.012 2.00e-02 2.50e+03 ... (remaining 2572 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4890 2.85 - 3.36: 12768 3.36 - 3.87: 24386 3.87 - 4.39: 27539 4.39 - 4.90: 46475 Nonbonded interactions: 116058 Sorted by model distance: nonbonded pdb=" O VAL A 891 " pdb="CA CA A4001 " model vdw 2.335 3.250 nonbonded pdb=" OD1 ASP A 890 " pdb="CA CA A4001 " model vdw 2.363 3.250 nonbonded pdb="CA CA A4001 " pdb=" O2G DTP A4002 " model vdw 2.377 3.250 nonbonded pdb=" O SER A 302 " pdb=" OG SER A 302 " model vdw 2.418 3.040 nonbonded pdb="CA CA A4001 " pdb=" O1A DTP A4002 " model vdw 2.436 3.250 ... (remaining 116053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.400 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 15812 Z= 0.318 Angle : 0.690 15.803 21676 Z= 0.429 Chirality : 0.043 0.167 2322 Planarity : 0.005 0.089 2575 Dihedral : 20.006 144.598 5998 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.64 % Allowed : 26.94 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1726 helix: 1.26 (0.20), residues: 698 sheet: 0.34 (0.34), residues: 222 loop : -0.24 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 389 TYR 0.011 0.001 TYR A 434 PHE 0.010 0.001 PHE A1164 TRP 0.039 0.001 TRP A 918 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.32 (15811) covalent geometry : angle 0.68954 / 0.43 (21674) SS BOND : bond 0.01473 / 0.78 ( 1) SS BOND : angle 2.93522 / 1.56 ( 2) hydrogen bonds : bond 0.20790 / 14.17 ( 705) hydrogen bonds : angle 6.33056 / 4.39 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7421 (ptp90) REVERT: A 376 LEU cc_start: 0.9055 (mt) cc_final: 0.8831 (mp) REVERT: A 544 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8078 (mtp) REVERT: A 873 GLU cc_start: 0.8527 (pm20) cc_final: 0.8317 (pm20) REVERT: A 965 LEU cc_start: 0.8766 (mm) cc_final: 0.8467 (mt) REVERT: A 1055 SER cc_start: 0.8611 (p) cc_final: 0.8243 (m) REVERT: A 1191 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8693 (mttm) REVERT: A 1206 MET cc_start: 0.8701 (mmt) cc_final: 0.8309 (mmt) REVERT: A 1226 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 74 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 329 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7892 (mmtm) REVERT: B 366 ASN cc_start: 0.7795 (p0) cc_final: 0.7387 (t0) REVERT: B 393 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (tm) REVERT: C 328 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6123 (mmp-170) REVERT: C 394 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: C 395 LEU cc_start: 0.9032 (mt) cc_final: 0.8757 (mp) REVERT: C 426 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8379 (mp0) outliers start: 40 outliers final: 28 residues processed: 347 average time/residue: 0.5010 time to fit residues: 192.8997 Evaluate side-chains 359 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 305 ASN B 397 GLN B 409 ASN C 133 HIS C 192 HIS C 195 ASN C 323 HIS C 339 ASN C 397 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096993 restraints weight = 25822.612| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.78 r_work: 0.3240 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15812 Z= 0.129 Angle : 0.566 7.835 21676 Z= 0.311 Chirality : 0.041 0.189 2322 Planarity : 0.004 0.051 2575 Dihedral : 16.791 144.957 2615 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.35 % Allowed : 24.31 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1726 helix: 1.69 (0.20), residues: 705 sheet: 1.18 (0.32), residues: 239 loop : -0.10 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 389 TYR 0.013 0.001 TYR A 221 PHE 0.009 0.001 PHE C 403 TRP 0.018 0.001 TRP A 918 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (15811) covalent geometry : angle 0.56558 / 0.31 (21674) SS BOND : bond 0.01195 / 0.63 ( 1) SS BOND : angle 2.73037 / 1.44 ( 2) hydrogen bonds : bond 0.05666 / 3.86 ( 705) hydrogen bonds : angle 4.97974 / 3.46 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 336 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7481 (ptp90) REVERT: A 90 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: A 376 LEU cc_start: 0.9009 (mt) cc_final: 0.8778 (mp) REVERT: A 544 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8103 (mtp) REVERT: A 873 GLU cc_start: 0.8450 (pm20) cc_final: 0.8231 (pm20) REVERT: A 965 LEU cc_start: 0.8772 (mm) cc_final: 0.8482 (mt) REVERT: A 993 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7783 (tpt170) REVERT: A 1055 SER cc_start: 0.8550 (p) cc_final: 0.8211 (m) REVERT: A 1206 MET cc_start: 0.8459 (mmt) cc_final: 0.8212 (mmt) REVERT: B 74 GLN cc_start: 0.8567 (mt0) cc_final: 0.8251 (mt0) REVERT: B 310 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 366 ASN cc_start: 0.7584 (p0) cc_final: 0.7264 (t0) REVERT: B 393 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8789 (tm) REVERT: C 394 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: C 395 LEU cc_start: 0.8699 (mt) cc_final: 0.8491 (mp) outliers start: 66 outliers final: 23 residues processed: 373 average time/residue: 0.5255 time to fit residues: 217.7605 Evaluate side-chains 331 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 111 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 404 ASN C 133 HIS C 192 HIS C 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.113169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095033 restraints weight = 26104.103| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.78 r_work: 0.3204 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15812 Z= 0.150 Angle : 0.582 8.560 21676 Z= 0.319 Chirality : 0.042 0.176 2322 Planarity : 0.004 0.048 2575 Dihedral : 16.581 145.763 2568 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.87 % Allowed : 24.44 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1726 helix: 1.67 (0.20), residues: 707 sheet: 1.25 (0.33), residues: 225 loop : -0.21 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 389 TYR 0.012 0.002 TYR A 951 PHE 0.010 0.001 PHE A1164 TRP 0.021 0.001 TRP A 918 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15811) covalent geometry : angle 0.58103 / 0.32 (21674) SS BOND : bond 0.01599 / 0.84 ( 1) SS BOND : angle 2.96486 / 1.65 ( 2) hydrogen bonds : bond 0.06146 / 4.23 ( 705) hydrogen bonds : angle 4.82095 / 3.35 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 311 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7459 (ptp90) REVERT: A 90 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: A 544 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: A 965 LEU cc_start: 0.8808 (mm) cc_final: 0.8518 (mt) REVERT: A 1055 SER cc_start: 0.8640 (p) cc_final: 0.8309 (m) REVERT: A 1206 MET cc_start: 0.8460 (mmt) cc_final: 0.8176 (mmt) REVERT: A 1226 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8065 (tt) REVERT: B 74 GLN cc_start: 0.8593 (mt0) cc_final: 0.8269 (mt0) REVERT: B 257 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8146 (mtm-85) REVERT: B 366 ASN cc_start: 0.7616 (p0) cc_final: 0.7308 (t0) REVERT: B 393 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8671 (tm) REVERT: B 407 LEU cc_start: 0.8349 (mt) cc_final: 0.8085 (mt) REVERT: B 428 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8633 (mp) REVERT: C 394 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5844 (mt-10) REVERT: C 395 LEU cc_start: 0.8715 (mt) cc_final: 0.8460 (mp) outliers start: 74 outliers final: 40 residues processed: 350 average time/residue: 0.5221 time to fit residues: 203.0483 Evaluate side-chains 342 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 55 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN C 133 HIS C 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097201 restraints weight = 25814.360| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.77 r_work: 0.3243 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15812 Z= 0.116 Angle : 0.532 6.853 21676 Z= 0.292 Chirality : 0.040 0.170 2322 Planarity : 0.004 0.050 2575 Dihedral : 16.542 144.799 2565 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.02 % Allowed : 25.30 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1726 helix: 1.85 (0.20), residues: 706 sheet: 1.38 (0.32), residues: 229 loop : -0.19 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 389 TYR 0.012 0.001 TYR A 951 PHE 0.010 0.001 PHE C 403 TRP 0.023 0.001 TRP A 918 HIS 0.003 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (15811) covalent geometry : angle 0.53129 / 0.29 (21674) SS BOND : bond 0.01239 / 0.65 ( 1) SS BOND : angle 2.71257 / 1.45 ( 2) hydrogen bonds : bond 0.04792 / 3.30 ( 705) hydrogen bonds : angle 4.60199 / 3.20 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7472 (ptp90) REVERT: A 90 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: A 544 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8095 (mtp) REVERT: A 873 GLU cc_start: 0.8445 (pm20) cc_final: 0.8238 (pm20) REVERT: A 965 LEU cc_start: 0.8795 (mm) cc_final: 0.8504 (mt) REVERT: A 1055 SER cc_start: 0.8560 (p) cc_final: 0.8250 (m) REVERT: A 1206 MET cc_start: 0.8404 (mmt) cc_final: 0.8067 (mmt) REVERT: A 1226 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8025 (tt) REVERT: B 74 GLN cc_start: 0.8567 (mt0) cc_final: 0.8245 (mt0) REVERT: B 257 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8132 (mtm-85) REVERT: B 366 ASN cc_start: 0.7580 (p0) cc_final: 0.7267 (t0) REVERT: B 393 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8551 (tm) REVERT: B 407 LEU cc_start: 0.8214 (mt) cc_final: 0.7995 (mt) REVERT: B 428 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 198 ASP cc_start: 0.7844 (m-30) cc_final: 0.7598 (t70) REVERT: C 394 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5952 (mp0) outliers start: 61 outliers final: 34 residues processed: 353 average time/residue: 0.5277 time to fit residues: 206.4545 Evaluate side-chains 338 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 413 LEU 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 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 129 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.0980 chunk 106 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN C 133 HIS C 192 HIS C 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096995 restraints weight = 25980.451| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.78 r_work: 0.3239 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15812 Z= 0.121 Angle : 0.545 7.700 21676 Z= 0.297 Chirality : 0.040 0.158 2322 Planarity : 0.004 0.050 2575 Dihedral : 16.545 144.801 2565 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.22 % Allowed : 24.84 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1726 helix: 1.97 (0.20), residues: 700 sheet: 1.30 (0.32), residues: 229 loop : -0.21 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 389 TYR 0.011 0.001 TYR A 951 PHE 0.010 0.001 PHE C 403 TRP 0.023 0.001 TRP A 918 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (15811) covalent geometry : angle 0.54436 / 0.30 (21674) SS BOND : bond 0.01279 / 0.67 ( 1) SS BOND : angle 2.74872 / 1.46 ( 2) hydrogen bonds : bond 0.04801 / 3.32 ( 705) hydrogen bonds : angle 4.56299 / 3.18 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7479 (ptp90) REVERT: A 90 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: A 544 MET cc_start: 0.8404 (tpp) cc_final: 0.8093 (mtp) REVERT: A 873 GLU cc_start: 0.8463 (pm20) cc_final: 0.8257 (pm20) REVERT: A 965 LEU cc_start: 0.8796 (mm) cc_final: 0.8522 (mt) REVERT: A 1055 SER cc_start: 0.8581 (p) cc_final: 0.8265 (m) REVERT: A 1206 MET cc_start: 0.8348 (mmt) cc_final: 0.8004 (mmt) REVERT: A 1226 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8038 (tt) REVERT: B 74 GLN cc_start: 0.8573 (mt0) cc_final: 0.8250 (mt0) REVERT: B 257 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8110 (mtm-85) REVERT: B 366 ASN cc_start: 0.7580 (p0) cc_final: 0.7280 (t0) REVERT: B 386 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7782 (t0) REVERT: B 393 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8562 (tm) REVERT: B 407 LEU cc_start: 0.8215 (mt) cc_final: 0.8005 (mt) REVERT: B 428 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8599 (mp) REVERT: C 198 ASP cc_start: 0.7843 (m-30) cc_final: 0.7614 (t70) REVERT: C 394 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5862 (mp0) outliers start: 64 outliers final: 41 residues processed: 345 average time/residue: 0.5131 time to fit residues: 196.0908 Evaluate side-chains 341 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 0.0980 chunk 136 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN C 133 HIS C 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095399 restraints weight = 25841.647| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.76 r_work: 0.3211 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15812 Z= 0.146 Angle : 0.573 9.159 21676 Z= 0.312 Chirality : 0.042 0.169 2322 Planarity : 0.005 0.055 2575 Dihedral : 16.583 145.180 2562 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.01 % Allowed : 24.97 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1726 helix: 1.81 (0.20), residues: 711 sheet: 1.18 (0.32), residues: 231 loop : -0.34 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 389 TYR 0.011 0.002 TYR A 951 PHE 0.010 0.001 PHE A1164 TRP 0.026 0.001 TRP A 918 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (15811) covalent geometry : angle 0.57266 / 0.31 (21674) SS BOND : bond 0.01410 / 0.74 ( 1) SS BOND : angle 2.93224 / 1.56 ( 2) hydrogen bonds : bond 0.05565 / 3.85 ( 705) hydrogen bonds : angle 4.60799 / 3.21 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7484 (ptp90) REVERT: A 90 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: A 376 LEU cc_start: 0.9020 (mt) cc_final: 0.8782 (mp) REVERT: A 464 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (ttp) REVERT: A 544 MET cc_start: 0.8463 (tpp) cc_final: 0.8167 (mtp) REVERT: A 873 GLU cc_start: 0.8476 (pm20) cc_final: 0.8270 (pm20) REVERT: A 965 LEU cc_start: 0.8813 (mm) cc_final: 0.8529 (mt) REVERT: A 1206 MET cc_start: 0.8363 (mmt) cc_final: 0.8000 (mmt) REVERT: A 1226 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 74 GLN cc_start: 0.8573 (mt0) cc_final: 0.8245 (mt0) REVERT: B 257 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8102 (mtm-85) REVERT: B 386 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7807 (t0) REVERT: B 393 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8552 (tm) REVERT: B 428 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8630 (mp) REVERT: C 394 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5732 (mp0) outliers start: 76 outliers final: 48 residues processed: 348 average time/residue: 0.4946 time to fit residues: 190.6758 Evaluate side-chains 355 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 430 MET 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 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN C 133 HIS C 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096715 restraints weight = 25794.603| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.77 r_work: 0.3235 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15812 Z= 0.122 Angle : 0.556 9.860 21676 Z= 0.301 Chirality : 0.040 0.173 2322 Planarity : 0.004 0.063 2575 Dihedral : 16.528 144.477 2562 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.28 % Allowed : 26.28 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1726 helix: 1.96 (0.20), residues: 700 sheet: 1.21 (0.32), residues: 231 loop : -0.27 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 389 TYR 0.012 0.001 TYR C 193 PHE 0.010 0.001 PHE C 403 TRP 0.032 0.001 TRP A 918 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (15811) covalent geometry : angle 0.55565 / 0.30 (21674) SS BOND : bond 0.01233 / 0.65 ( 1) SS BOND : angle 2.78367 / 1.47 ( 2) hydrogen bonds : bond 0.04822 / 3.34 ( 705) hydrogen bonds : angle 4.51997 / 3.14 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 306 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7437 (ptp90) REVERT: A 90 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: A 464 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8514 (ttp) REVERT: A 544 MET cc_start: 0.8423 (tpp) cc_final: 0.8157 (mtp) REVERT: A 631 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5803 (tp) REVERT: A 873 GLU cc_start: 0.8459 (pm20) cc_final: 0.8251 (pm20) REVERT: A 965 LEU cc_start: 0.8800 (mm) cc_final: 0.8524 (mt) REVERT: A 1055 SER cc_start: 0.8577 (p) cc_final: 0.8252 (m) REVERT: A 1206 MET cc_start: 0.8322 (mmt) cc_final: 0.7951 (mmt) REVERT: A 1226 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8069 (tt) REVERT: B 74 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: B 257 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8087 (mtm-85) REVERT: B 366 ASN cc_start: 0.7570 (p0) cc_final: 0.7254 (t0) REVERT: B 386 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7793 (t0) REVERT: B 393 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8500 (tm) REVERT: B 407 LEU cc_start: 0.8375 (mt) cc_final: 0.8114 (mt) REVERT: B 445 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: C 394 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5732 (mp0) REVERT: C 449 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7686 (tm-30) outliers start: 65 outliers final: 43 residues processed: 344 average time/residue: 0.5127 time to fit residues: 195.7411 Evaluate side-chains 350 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 138 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 404 ASN C 133 HIS C 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096857 restraints weight = 25980.801| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.76 r_work: 0.3236 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15812 Z= 0.124 Angle : 0.555 10.226 21676 Z= 0.301 Chirality : 0.040 0.169 2322 Planarity : 0.004 0.051 2575 Dihedral : 16.505 144.396 2562 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.74 % Allowed : 25.69 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1726 helix: 1.98 (0.20), residues: 700 sheet: 1.22 (0.32), residues: 231 loop : -0.26 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 927 TYR 0.012 0.001 TYR C 193 PHE 0.010 0.001 PHE C 403 TRP 0.024 0.001 TRP A 918 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15811) covalent geometry : angle 0.55478 / 0.30 (21674) SS BOND : bond 0.01289 / 0.68 ( 1) SS BOND : angle 2.74865 / 1.45 ( 2) hydrogen bonds : bond 0.04795 / 3.32 ( 705) hydrogen bonds : angle 4.48786 / 3.12 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7416 (ptp90) REVERT: A 90 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: A 464 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: A 544 MET cc_start: 0.8365 (tpp) cc_final: 0.8129 (mtp) REVERT: A 631 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5742 (tp) REVERT: A 873 GLU cc_start: 0.8461 (pm20) cc_final: 0.8257 (pm20) REVERT: A 965 LEU cc_start: 0.8803 (mm) cc_final: 0.8524 (mt) REVERT: A 1206 MET cc_start: 0.8332 (mmt) cc_final: 0.7917 (mmt) REVERT: A 1226 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 74 GLN cc_start: 0.8558 (mt0) cc_final: 0.8240 (mt0) REVERT: B 257 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8067 (mtm-85) REVERT: B 366 ASN cc_start: 0.7595 (p0) cc_final: 0.7262 (t0) REVERT: B 386 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7781 (t0) REVERT: B 393 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8487 (tm) REVERT: B 407 LEU cc_start: 0.8384 (mt) cc_final: 0.8123 (mt) REVERT: C 198 ASP cc_start: 0.7866 (m-30) cc_final: 0.7624 (t70) REVERT: C 394 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5683 (mp0) outliers start: 72 outliers final: 47 residues processed: 346 average time/residue: 0.5102 time to fit residues: 195.9607 Evaluate side-chains 350 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU 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 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 74 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 122 optimal weight: 0.0030 chunk 151 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 137 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN C 133 HIS C 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.113899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095747 restraints weight = 25787.700| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.78 r_work: 0.3217 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15812 Z= 0.145 Angle : 0.590 10.361 21676 Z= 0.317 Chirality : 0.042 0.170 2322 Planarity : 0.005 0.070 2575 Dihedral : 16.536 144.709 2562 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.28 % Allowed : 26.61 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1726 helix: 1.86 (0.20), residues: 706 sheet: 1.17 (0.32), residues: 231 loop : -0.30 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 389 TYR 0.013 0.001 TYR C 193 PHE 0.009 0.001 PHE A1164 TRP 0.019 0.001 TRP A 918 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15811) covalent geometry : angle 0.58982 / 0.32 (21674) SS BOND : bond 0.01369 / 0.72 ( 1) SS BOND : angle 2.84049 / 1.51 ( 2) hydrogen bonds : bond 0.05324 / 3.69 ( 705) hydrogen bonds : angle 4.53856 / 3.16 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7437 (ptp90) REVERT: A 90 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: A 464 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8565 (ttp) REVERT: A 544 MET cc_start: 0.8379 (tpp) cc_final: 0.8153 (mtp) REVERT: A 873 GLU cc_start: 0.8468 (pm20) cc_final: 0.8266 (pm20) REVERT: A 965 LEU cc_start: 0.8809 (mm) cc_final: 0.8524 (mt) REVERT: A 1055 SER cc_start: 0.8600 (p) cc_final: 0.8272 (m) REVERT: A 1206 MET cc_start: 0.8348 (mmt) cc_final: 0.7964 (mmt) REVERT: A 1226 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 74 GLN cc_start: 0.8587 (mt0) cc_final: 0.8262 (mt0) REVERT: B 257 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8126 (mtm-85) REVERT: B 366 ASN cc_start: 0.7628 (p0) cc_final: 0.7295 (t0) REVERT: B 386 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7797 (t0) REVERT: B 393 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (tm) REVERT: C 394 GLU cc_start: 0.6475 (pm20) cc_final: 0.5710 (mp0) outliers start: 65 outliers final: 52 residues processed: 340 average time/residue: 0.5480 time to fit residues: 206.5417 Evaluate side-chains 354 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 296 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 430 MET 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 464 MET Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 133 HIS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 404 ASN C 133 HIS C 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094833 restraints weight = 25851.532| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.77 r_work: 0.3200 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15812 Z= 0.167 Angle : 0.628 11.114 21676 Z= 0.337 Chirality : 0.043 0.174 2322 Planarity : 0.005 0.055 2575 Dihedral : 16.485 144.890 2559 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.22 % Allowed : 26.88 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1726 helix: 1.78 (0.20), residues: 706 sheet: 1.10 (0.32), residues: 229 loop : -0.35 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 389 TYR 0.013 0.002 TYR C 193 PHE 0.010 0.001 PHE A1164 TRP 0.017 0.001 TRP A 918 HIS 0.019 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15811) covalent geometry : angle 0.62668 / 0.34 (21674) SS BOND : bond 0.01905 / 1.00 ( 1) SS BOND : angle 3.73547 / 2.17 ( 2) hydrogen bonds : bond 0.05813 / 4.03 ( 705) hydrogen bonds : angle 4.58628 / 3.19 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7484 (ptp90) REVERT: A 90 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: A 544 MET cc_start: 0.8430 (tpp) cc_final: 0.8197 (mtp) REVERT: A 965 LEU cc_start: 0.8810 (mm) cc_final: 0.8523 (mt) REVERT: A 1055 SER cc_start: 0.8621 (p) cc_final: 0.8277 (m) REVERT: A 1206 MET cc_start: 0.8369 (mmt) cc_final: 0.8007 (mmt) REVERT: A 1226 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 74 GLN cc_start: 0.8647 (mt0) cc_final: 0.8303 (mt0) REVERT: B 257 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8124 (mtm-85) REVERT: B 366 ASN cc_start: 0.7647 (p0) cc_final: 0.7322 (t0) REVERT: B 386 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 393 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (tm) REVERT: C 394 GLU cc_start: 0.6521 (pm20) cc_final: 0.5713 (mp0) outliers start: 64 outliers final: 50 residues processed: 339 average time/residue: 0.5389 time to fit residues: 202.9307 Evaluate side-chains 351 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 476 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 18 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 173 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 216 HIS C 133 HIS C 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095090 restraints weight = 25674.199| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.76 r_work: 0.3205 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15812 Z= 0.152 Angle : 0.615 11.140 21676 Z= 0.330 Chirality : 0.042 0.168 2322 Planarity : 0.005 0.095 2575 Dihedral : 16.439 144.747 2556 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.22 % Allowed : 27.08 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1726 helix: 1.76 (0.20), residues: 706 sheet: 1.09 (0.32), residues: 229 loop : -0.37 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 389 TYR 0.013 0.002 TYR C 193 PHE 0.009 0.001 PHE A1164 TRP 0.018 0.001 TRP A 918 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (15811) covalent geometry : angle 0.61454 / 0.33 (21674) SS BOND : bond 0.01659 / 0.87 ( 1) SS BOND : angle 3.10550 / 1.78 ( 2) hydrogen bonds : bond 0.05608 / 3.89 ( 705) hydrogen bonds : angle 4.56953 / 3.18 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6118.19 seconds wall clock time: 104 minutes 31.53 seconds (6271.53 seconds total)