Starting phenix.real_space_refine on Wed Mar 4 19:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4f_72481/03_2026/9y4f_72481_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4f_72481/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9y4f_72481/03_2026/9y4f_72481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4f_72481/03_2026/9y4f_72481.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4f_72481/03_2026/9y4f_72481_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4f_72481/03_2026/9y4f_72481_neut.cif" } 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-5986/lib/python3.9/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, 31 Unusual residues: {' CA': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.18, per 1000 atoms: 0.21 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: 1.51 Conformation dependent library (CDL) restraints added in 700.9 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: 2.01 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: 2.77 Time building geometry restraints manager: 1.94 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: 21551 3.16 - 6.32: 101 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=" O2A DTP A4002 " pdb=" PA DTP A4002 " pdb=" O5' DTP A4002 " ideal model delta sigma weight residual 108.07 94.54 13.53 2.65e+00 1.42e-01 2.60e+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 - 0.033: 1561 0.033 - 0.067: 517 0.067 - 0.100: 160 0.100 - 0.134: 80 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 2.510 nonbonded pdb=" OD1 ASP A 890 " pdb="CA CA A4001 " model vdw 2.363 2.510 nonbonded pdb="CA CA A4001 " pdb=" O2G DTP A4002 " model vdw 2.377 2.510 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 2.510 ... (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: 0.010 Normalize map: mean=0, sd=1: 3.150 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: 0.030 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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= 0.237 Angle : 0.663 15.803 21676 Z= 0.356 Chirality : 0.041 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 covalent geometry : bond 0.00395 (15811) covalent geometry : angle 0.66213 (21674) SS BOND : bond 0.01473 ( 1) SS BOND : angle 2.93522 ( 2) hydrogen bonds : bond 0.20790 ( 705) hydrogen bonds : angle 6.33056 ( 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 : 0.540 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: 0.5388 time to fit residues: 206.5331 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 : 0.606 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3630 r_free = 0.3630 target = 0.115459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097529 restraints weight = 25846.566| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.76 r_work: 0.3247 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0869 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= 0.117 Angle : 0.538 8.577 21676 Z= 0.288 Chirality : 0.039 0.181 2322 Planarity : 0.004 0.050 2575 Dihedral : 16.530 143.691 2615 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.82 % Allowed : 24.04 % Favored : 72.13 % 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: 1.67 (0.20), residues: 706 sheet: 1.12 (0.33), residues: 229 loop : -0.14 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 927 TYR 0.011 0.001 TYR A 434 PHE 0.009 0.001 PHE C 403 TRP 0.018 0.001 TRP A 918 HIS 0.005 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00236 (15811) covalent geometry : angle 0.53705 (21674) SS BOND : bond 0.01303 ( 1) SS BOND : angle 2.71768 ( 2) hydrogen bonds : bond 0.05160 ( 705) hydrogen bonds : angle 4.87555 ( 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 394 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 336 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7480 (ptp90) REVERT: A 90 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: A 376 LEU cc_start: 0.9008 (mt) cc_final: 0.8789 (mp) REVERT: A 544 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8120 (mtp) REVERT: A 873 GLU cc_start: 0.8453 (pm20) cc_final: 0.8244 (pm20) REVERT: A 965 LEU cc_start: 0.8770 (mm) cc_final: 0.8482 (mt) REVERT: A 1055 SER cc_start: 0.8548 (p) cc_final: 0.8227 (m) REVERT: A 1057 MET cc_start: 0.8235 (ppp) cc_final: 0.7978 (tmm) REVERT: A 1206 MET cc_start: 0.8438 (mmt) cc_final: 0.8109 (mmt) REVERT: B 74 GLN cc_start: 0.8561 (mt0) cc_final: 0.8254 (mt0) REVERT: B 366 ASN cc_start: 0.7573 (p0) cc_final: 0.7256 (t0) REVERT: B 393 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8678 (tm) REVERT: B 407 LEU cc_start: 0.8252 (mt) cc_final: 0.8006 (mt) REVERT: C 394 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: C 427 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7963 (mt0) outliers start: 58 outliers final: 22 residues processed: 369 average time/residue: 0.5289 time to fit residues: 215.8641 Evaluate side-chains 325 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 476 ILE 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 427 GLN 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: 3.9990 chunk 98 optimal weight: 0.0060 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 overall best weight: 2.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A1157 ASN B 404 ASN C 133 HIS C 192 HIS C 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092543 restraints weight = 26019.404| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.76 r_work: 0.3159 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15812 Z= 0.222 Angle : 0.656 9.046 21676 Z= 0.353 Chirality : 0.044 0.176 2322 Planarity : 0.005 0.056 2575 Dihedral : 16.524 144.752 2567 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.20 % Allowed : 23.91 % Favored : 70.88 % 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: 0.72 (0.20), residues: 1726 helix: 1.32 (0.20), residues: 713 sheet: 1.04 (0.33), residues: 217 loop : -0.41 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 389 TYR 0.015 0.002 TYR A 837 PHE 0.016 0.002 PHE A1164 TRP 0.018 0.002 TRP A 918 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00509 (15811) covalent geometry : angle 0.65473 (21674) SS BOND : bond 0.02068 ( 1) SS BOND : angle 3.51207 ( 2) hydrogen bonds : bond 0.07445 ( 705) hydrogen bonds : angle 4.95152 ( 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 396 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7507 (ptp90) REVERT: A 90 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: A 544 MET cc_start: 0.8518 (tpp) cc_final: 0.8145 (mtp) REVERT: A 965 LEU cc_start: 0.8818 (mm) cc_final: 0.8513 (mt) REVERT: A 1206 MET cc_start: 0.8508 (mmt) cc_final: 0.8241 (mmt) REVERT: A 1226 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 74 GLN cc_start: 0.8666 (mt0) cc_final: 0.8319 (mt0) REVERT: B 329 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7842 (mmtm) REVERT: B 393 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8668 (tm) REVERT: B 428 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 83 LYS cc_start: 0.7684 (mtpp) cc_final: 0.7347 (mtpp) REVERT: C 394 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5765 (mt-10) REVERT: C 463 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8518 (mptt) REVERT: C 465 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7619 (mmm) outliers start: 79 outliers final: 47 residues processed: 357 average time/residue: 0.5178 time to fit residues: 204.7092 Evaluate side-chains 355 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 430 MET 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 976 GLN Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1066 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 92 LEU Chi-restraints excluded: chain B residue 104 VAL 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 258 HIS Chi-restraints excluded: chain B residue 319 VAL 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 385 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL 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 B residue 468 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 106 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 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 Chi-restraints excluded: chain C residue 463 LYS Chi-restraints excluded: chain C residue 465 MET 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: 6.9990 chunk 100 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 55 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A1157 ASN B 366 ASN C 133 HIS C 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096501 restraints weight = 25701.934| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.77 r_work: 0.3228 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1114 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= 0.116 Angle : 0.535 7.472 21676 Z= 0.286 Chirality : 0.039 0.178 2322 Planarity : 0.004 0.051 2575 Dihedral : 16.209 143.095 2562 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.02 % Allowed : 24.90 % Favored : 71.08 % 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: 1.16 (0.20), residues: 1726 helix: 1.77 (0.20), residues: 699 sheet: 1.27 (0.32), residues: 232 loop : -0.26 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 389 TYR 0.012 0.001 TYR A 951 PHE 0.011 0.001 PHE C 403 TRP 0.016 0.001 TRP A 918 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00240 (15811) covalent geometry : angle 0.53400 (21674) SS BOND : bond 0.01783 ( 1) SS BOND : angle 2.71852 ( 2) hydrogen bonds : bond 0.04718 ( 705) hydrogen bonds : angle 4.62611 ( 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 390 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7429 (ptp90) REVERT: A 90 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: A 544 MET cc_start: 0.8424 (tpp) cc_final: 0.8095 (mtp) REVERT: A 873 GLU cc_start: 0.8442 (pm20) cc_final: 0.8240 (pm20) REVERT: A 965 LEU cc_start: 0.8792 (mm) cc_final: 0.8512 (mt) REVERT: A 1055 SER cc_start: 0.8600 (p) cc_final: 0.8270 (m) REVERT: A 1206 MET cc_start: 0.8416 (mmt) cc_final: 0.8088 (mmt) REVERT: A 1226 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8101 (tt) REVERT: B 74 GLN cc_start: 0.8567 (mt0) cc_final: 0.8241 (mt0) REVERT: B 257 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8106 (mtm-85) REVERT: B 366 ASN cc_start: 0.7611 (p0) cc_final: 0.7294 (t0) REVERT: B 386 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7828 (t0) REVERT: B 393 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8553 (tm) REVERT: B 428 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8596 (mp) REVERT: C 195 ASN cc_start: 0.8370 (m-40) cc_final: 0.8146 (m-40) REVERT: C 394 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5772 (mp0) outliers start: 61 outliers final: 30 residues processed: 365 average time/residue: 0.5325 time to fit residues: 214.6921 Evaluate side-chains 339 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 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 235 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 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 413 VAL 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 C residue 105 GLU 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 437 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: 0.7980 chunk 137 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 103 optimal weight: 0.0170 chunk 78 optimal weight: 6.9990 chunk 140 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.0040 chunk 106 optimal weight: 0.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A1157 ASN C 74 GLN C 133 HIS C 192 HIS C 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098151 restraints weight = 25873.951| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.75 r_work: 0.3257 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15812 Z= 0.111 Angle : 0.529 9.473 21676 Z= 0.280 Chirality : 0.039 0.176 2322 Planarity : 0.004 0.052 2575 Dihedral : 16.091 142.631 2562 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.35 % Allowed : 25.23 % 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: 1.35 (0.21), residues: 1726 helix: 1.98 (0.20), residues: 700 sheet: 1.33 (0.33), residues: 231 loop : -0.20 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 389 TYR 0.011 0.001 TYR A 951 PHE 0.011 0.001 PHE C 403 TRP 0.025 0.001 TRP A 918 HIS 0.003 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00233 (15811) covalent geometry : angle 0.52812 (21674) SS BOND : bond 0.01205 ( 1) SS BOND : angle 2.69834 ( 2) hydrogen bonds : bond 0.04088 ( 705) hydrogen bonds : angle 4.44856 ( 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 387 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7484 (ptp90) REVERT: A 90 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: A 229 VAL cc_start: 0.9110 (t) cc_final: 0.8902 (p) REVERT: A 544 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8092 (mtp) REVERT: A 965 LEU cc_start: 0.8800 (mm) cc_final: 0.8508 (mt) REVERT: A 1057 MET cc_start: 0.8256 (ppp) cc_final: 0.8029 (tmm) REVERT: A 1206 MET cc_start: 0.8364 (mmt) cc_final: 0.7960 (mmt) REVERT: A 1226 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 74 GLN cc_start: 0.8558 (mt0) cc_final: 0.8241 (mt0) REVERT: B 366 ASN cc_start: 0.7545 (p0) cc_final: 0.7240 (t0) REVERT: B 386 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (t0) REVERT: B 393 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8505 (tm) REVERT: C 195 ASN cc_start: 0.8348 (m-40) cc_final: 0.8136 (m-40) REVERT: C 394 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5638 (mp0) outliers start: 66 outliers final: 35 residues processed: 357 average time/residue: 0.5337 time to fit residues: 210.1255 Evaluate side-chains 352 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 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 A residue 1226 LEU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 LEU 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 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 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 393 LEU Chi-restraints excluded: chain C residue 394 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN A1157 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 = 0.3585 r_free = 0.3585 target = 0.112446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094331 restraints weight = 25749.805| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.74 r_work: 0.3192 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15812 Z= 0.170 Angle : 0.605 8.749 21676 Z= 0.322 Chirality : 0.042 0.173 2322 Planarity : 0.005 0.069 2575 Dihedral : 16.257 143.553 2562 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.28 % Allowed : 25.96 % Favored : 69.76 % 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: 710 sheet: 1.13 (0.33), residues: 222 loop : -0.38 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 389 TYR 0.013 0.002 TYR A 951 PHE 0.011 0.001 PHE A1164 TRP 0.026 0.001 TRP A 918 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00386 (15811) covalent geometry : angle 0.60422 (21674) SS BOND : bond 0.01494 ( 1) SS BOND : angle 3.11371 ( 2) hydrogen bonds : bond 0.05979 ( 705) hydrogen bonds : angle 4.61026 ( 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 388 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 323 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8385 (ttp80) cc_final: 0.7494 (ptp90) REVERT: A 90 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: A 544 MET cc_start: 0.8443 (tpp) cc_final: 0.8159 (mtp) REVERT: A 596 MET cc_start: 0.8657 (mtp) cc_final: 0.8454 (mtt) REVERT: A 965 LEU cc_start: 0.8819 (mm) cc_final: 0.8533 (mt) REVERT: A 1206 MET cc_start: 0.8378 (mmt) cc_final: 0.8060 (mmt) REVERT: A 1226 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 74 GLN cc_start: 0.8634 (mt0) cc_final: 0.8297 (mt0) REVERT: B 386 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7839 (t0) REVERT: B 393 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8572 (tm) REVERT: C 195 ASN cc_start: 0.8419 (m-40) cc_final: 0.8146 (m-40) REVERT: C 394 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5781 (mp0) REVERT: C 426 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7975 (mp0) outliers start: 65 outliers final: 43 residues processed: 355 average time/residue: 0.5389 time to fit residues: 211.1633 Evaluate side-chains 347 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 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 993 ARG 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 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG 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 437 ILE 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 236 GLU 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 426 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 128 optimal weight: 0.0030 chunk 142 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A1157 ASN B 404 ASN C 133 HIS C 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096976 restraints weight = 25707.567| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.73 r_work: 0.3237 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15812 Z= 0.117 Angle : 0.549 9.205 21676 Z= 0.290 Chirality : 0.039 0.172 2322 Planarity : 0.004 0.072 2575 Dihedral : 16.119 142.596 2562 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.89 % Allowed : 26.68 % 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: 1.30 (0.20), residues: 1726 helix: 1.99 (0.20), residues: 700 sheet: 1.18 (0.33), residues: 229 loop : -0.24 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 389 TYR 0.010 0.001 TYR A 951 PHE 0.010 0.001 PHE C 403 TRP 0.034 0.001 TRP A 918 HIS 0.023 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00248 (15811) covalent geometry : angle 0.54850 (21674) SS BOND : bond 0.01252 ( 1) SS BOND : angle 2.79817 ( 2) hydrogen bonds : bond 0.04502 ( 705) hydrogen bonds : angle 4.45003 ( 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 374 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8382 (ttp80) cc_final: 0.7491 (ptp90) REVERT: A 90 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: A 544 MET cc_start: 0.8368 (tpp) cc_final: 0.8108 (mtp) REVERT: A 596 MET cc_start: 0.8642 (mtp) cc_final: 0.8437 (mtt) REVERT: A 965 LEU cc_start: 0.8805 (mm) cc_final: 0.8527 (mt) REVERT: A 1057 MET cc_start: 0.8301 (ppp) cc_final: 0.8043 (tmm) REVERT: A 1206 MET cc_start: 0.8349 (mmt) cc_final: 0.7964 (mmt) REVERT: A 1226 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8099 (tt) REVERT: B 74 GLN cc_start: 0.8558 (mt0) cc_final: 0.8237 (mt0) REVERT: B 366 ASN cc_start: 0.7578 (p0) cc_final: 0.7280 (t0) REVERT: B 393 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8469 (tm) REVERT: B 407 LEU cc_start: 0.8402 (mt) cc_final: 0.8180 (mt) REVERT: C 195 ASN cc_start: 0.8401 (m-40) cc_final: 0.8116 (m-40) REVERT: C 394 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5629 (mp0) outliers start: 59 outliers final: 40 residues processed: 350 average time/residue: 0.5242 time to fit residues: 202.8969 Evaluate side-chains 346 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 937 THR 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 A residue 1226 LEU 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 258 HIS Chi-restraints excluded: chain B residue 334 CYS 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 420 THR Chi-restraints excluded: chain B residue 437 ILE 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 247 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 138 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A1157 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 = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096769 restraints weight = 25903.269| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.77 r_work: 0.3234 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1357 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= 0.122 Angle : 0.558 8.921 21676 Z= 0.294 Chirality : 0.039 0.168 2322 Planarity : 0.005 0.077 2575 Dihedral : 16.077 142.718 2562 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.56 % Allowed : 27.54 % 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: 1.31 (0.20), residues: 1726 helix: 2.01 (0.20), residues: 700 sheet: 1.19 (0.33), residues: 229 loop : -0.23 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 389 TYR 0.011 0.001 TYR A 951 PHE 0.010 0.001 PHE C 403 TRP 0.025 0.001 TRP A 918 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00265 (15811) covalent geometry : angle 0.55753 (21674) SS BOND : bond 0.01271 ( 1) SS BOND : angle 2.81309 ( 2) hydrogen bonds : bond 0.04544 ( 705) hydrogen bonds : angle 4.41073 ( 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 364 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7420 (ptp90) REVERT: A 90 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: A 544 MET cc_start: 0.8345 (tpp) cc_final: 0.8091 (mtp) REVERT: A 596 MET cc_start: 0.8638 (mtp) cc_final: 0.8437 (mtt) REVERT: A 631 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5738 (tp) REVERT: A 965 LEU cc_start: 0.8807 (mm) cc_final: 0.8525 (mt) REVERT: A 1057 MET cc_start: 0.8278 (ppp) cc_final: 0.8007 (tmm) REVERT: A 1164 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 1206 MET cc_start: 0.8334 (mmt) cc_final: 0.7930 (mmt) REVERT: A 1226 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 74 GLN cc_start: 0.8569 (mt0) cc_final: 0.8251 (mt0) REVERT: B 366 ASN cc_start: 0.7592 (p0) cc_final: 0.7290 (t0) REVERT: B 393 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8472 (tm) REVERT: C 195 ASN cc_start: 0.8411 (m-40) cc_final: 0.8151 (m-40) REVERT: C 394 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5574 (mp0) REVERT: C 426 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7914 (mp0) outliers start: 54 outliers final: 36 residues processed: 342 average time/residue: 0.5205 time to fit residues: 197.7319 Evaluate side-chains 345 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 631 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 937 THR 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 A residue 1164 PHE Chi-restraints excluded: chain A residue 1226 LEU 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 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG 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 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 394 GLU Chi-restraints excluded: chain C residue 426 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 74 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN A1157 ASN B 404 ASN C 133 HIS C 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094240 restraints weight = 25631.448| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.74 r_work: 0.3189 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1278 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= 0.172 Angle : 0.628 11.334 21676 Z= 0.331 Chirality : 0.042 0.176 2322 Planarity : 0.005 0.094 2575 Dihedral : 16.184 143.444 2560 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.02 % Allowed : 27.27 % 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: 0.96 (0.20), residues: 1726 helix: 1.65 (0.20), residues: 717 sheet: 1.00 (0.32), residues: 230 loop : -0.41 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 389 TYR 0.013 0.002 TYR A 951 PHE 0.010 0.002 PHE A1129 TRP 0.035 0.001 TRP A 918 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00388 (15811) covalent geometry : angle 0.62724 (21674) SS BOND : bond 0.01504 ( 1) SS BOND : angle 3.06440 ( 2) hydrogen bonds : bond 0.06006 ( 705) hydrogen bonds : angle 4.61794 ( 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 368 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8404 (ttp80) cc_final: 0.7457 (ptp90) REVERT: A 90 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: A 544 MET cc_start: 0.8411 (tpp) cc_final: 0.8151 (mtp) REVERT: A 596 MET cc_start: 0.8680 (mtp) cc_final: 0.8466 (mtt) REVERT: A 965 LEU cc_start: 0.8810 (mm) cc_final: 0.8523 (mt) REVERT: A 1057 MET cc_start: 0.8352 (ppp) cc_final: 0.8128 (tmm) REVERT: A 1164 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 1206 MET cc_start: 0.8387 (mmt) cc_final: 0.8026 (mmt) REVERT: A 1226 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8150 (tt) REVERT: B 74 GLN cc_start: 0.8642 (mt0) cc_final: 0.8301 (mt0) REVERT: B 366 ASN cc_start: 0.7648 (p0) cc_final: 0.7357 (t0) REVERT: B 428 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 195 ASN cc_start: 0.8439 (m-40) cc_final: 0.8165 (m-40) REVERT: C 394 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5722 (mp0) REVERT: C 426 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7930 (mp0) outliers start: 61 outliers final: 39 residues processed: 343 average time/residue: 0.5137 time to fit residues: 195.7732 Evaluate side-chains 351 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 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 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 393 MET 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 937 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE 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 258 HIS Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 363 ARG 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 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 426 GLU 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 44 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.0000 chunk 47 optimal weight: 0.0270 chunk 25 optimal weight: 0.9980 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A1157 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 = 0.3632 r_free = 0.3632 target = 0.115648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097651 restraints weight = 25841.937| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.75 r_work: 0.3248 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15812 Z= 0.118 Angle : 0.576 9.794 21676 Z= 0.301 Chirality : 0.040 0.175 2322 Planarity : 0.005 0.085 2575 Dihedral : 15.990 142.318 2558 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.64 % Allowed : 28.66 % 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: 1.28 (0.20), residues: 1726 helix: 1.96 (0.20), residues: 699 sheet: 1.18 (0.33), residues: 229 loop : -0.22 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 389 TYR 0.013 0.001 TYR A 951 PHE 0.011 0.001 PHE C 403 TRP 0.035 0.001 TRP A 918 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00253 (15811) covalent geometry : angle 0.57547 (21674) SS BOND : bond 0.01449 ( 1) SS BOND : angle 2.06096 ( 2) hydrogen bonds : bond 0.04223 ( 705) hydrogen bonds : angle 4.45203 ( 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 354 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8378 (ttp80) cc_final: 0.7449 (ptp90) REVERT: A 90 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: A 229 VAL cc_start: 0.9125 (t) cc_final: 0.8905 (p) REVERT: A 464 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: A 544 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8097 (mtp) REVERT: A 596 MET cc_start: 0.8646 (mtp) cc_final: 0.8443 (mtt) REVERT: A 631 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5769 (tp) REVERT: A 965 LEU cc_start: 0.8801 (mm) cc_final: 0.8539 (mt) REVERT: A 1164 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 1206 MET cc_start: 0.8333 (mmt) cc_final: 0.7986 (mmt) REVERT: A 1226 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8128 (tt) REVERT: B 74 GLN cc_start: 0.8556 (mt0) cc_final: 0.8245 (mt0) REVERT: B 366 ASN cc_start: 0.7581 (p0) cc_final: 0.7288 (t0) REVERT: B 389 ARG cc_start: 0.6618 (mmm160) cc_final: 0.6222 (mmm160) REVERT: C 195 ASN cc_start: 0.8394 (m-40) cc_final: 0.8124 (m-40) REVERT: C 394 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: C 449 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7610 (tm-30) outliers start: 40 outliers final: 30 residues processed: 339 average time/residue: 0.5136 time to fit residues: 192.8565 Evaluate side-chains 338 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 301 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 582 ASP 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 937 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR 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 420 THR 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 394 GLU 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 18 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 663 GLN A1157 ASN C 133 HIS C 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095574 restraints weight = 25648.333| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.76 r_work: 0.3214 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1353 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= 0.152 Angle : 0.613 10.667 21676 Z= 0.320 Chirality : 0.041 0.179 2322 Planarity : 0.005 0.079 2575 Dihedral : 16.035 142.919 2558 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.83 % Allowed : 28.59 % Favored : 68.58 % 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: 1.15 (0.20), residues: 1726 helix: 1.82 (0.20), residues: 706 sheet: 1.09 (0.33), residues: 232 loop : -0.28 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 389 TYR 0.012 0.001 TYR A 951 PHE 0.012 0.001 PHE A 949 TRP 0.045 0.001 TRP A 918 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00344 (15811) covalent geometry : angle 0.61214 (21674) SS BOND : bond 0.01545 ( 1) SS BOND : angle 2.89140 ( 2) hydrogen bonds : bond 0.05185 ( 705) hydrogen bonds : angle 4.50877 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.37 seconds wall clock time: 107 minutes 4.92 seconds (6424.92 seconds total)