Starting phenix.real_space_refine on Tue Nov 18 20:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5zqz_6940/11_2025/5zqz_6940.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zqz_6940/11_2025/5zqz_6940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5zqz_6940/11_2025/5zqz_6940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zqz_6940/11_2025/5zqz_6940.map" model { file = "/net/cci-nas-00/data/ceres_data/5zqz_6940/11_2025/5zqz_6940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zqz_6940/11_2025/5zqz_6940.cif" } resolution = 4.2 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10916 2.51 5 N 2944 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5410 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 33, 'TRANS': 677} Chain breaks: 2 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3177 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5410 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 33, 'TRANS': 677} Chain breaks: 2 Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3177 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Time building chain proxies: 4.04, per 1000 atoms: 0.24 Number of scatterers: 17174 At special positions: 0 Unit cell: (109.56, 183.48, 104.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3214 8.00 N 2944 7.00 C 10916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.56 Conformation dependent library (CDL) restraints added in 841.3 milliseconds 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 16 sheets defined 43.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 4.977A pdb=" N GLU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.578A pdb=" N ALA A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.503A pdb=" N SER A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.839A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 183 through 186 removed outlier: 3.633A pdb=" N GLN A 186 " --> pdb=" O GLY A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 193 through 202 removed outlier: 4.171A pdb=" N ASP A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.346A pdb=" N LYS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 removed outlier: 3.790A pdb=" N LEU A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.657A pdb=" N TYR A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.564A pdb=" N ILE A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.684A pdb=" N LEU A 321 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 removed outlier: 4.327A pdb=" N GLY A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.695A pdb=" N VAL A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 removed outlier: 3.785A pdb=" N ALA A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.680A pdb=" N GLN A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.841A pdb=" N ASP A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.512A pdb=" N ARG A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.635A pdb=" N ARG A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.554A pdb=" N VAL A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.664A pdb=" N ILE A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 562' Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.576A pdb=" N ASP A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 592 removed outlier: 4.115A pdb=" N GLY A 592 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.597A pdb=" N ALA A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 4.009A pdb=" N LYS A 625 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.648A pdb=" N LYS A 631 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.981A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 688 Processing helix chain 'A' and resid 696 through 699 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.609A pdb=" N ALA A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 720 removed outlier: 3.977A pdb=" N PHE A 720 " --> pdb=" O PRO A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.921A pdb=" N ALA A 751 " --> pdb=" O CYS A 747 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.898A pdb=" N ASP B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.724A pdb=" N ARG B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 4.358A pdb=" N GLU B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 194 through 201 removed outlier: 3.874A pdb=" N SER B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.986A pdb=" N SER B 226 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 4.428A pdb=" N TYR B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 354 through 357 removed outlier: 3.775A pdb=" N TYR B 357 " --> pdb=" O GLY B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.838A pdb=" N GLU B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 438 through 448 removed outlier: 4.319A pdb=" N ARG B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 81 removed outlier: 4.977A pdb=" N GLU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.578A pdb=" N ALA C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.504A pdb=" N SER C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.839A pdb=" N LEU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 183 through 186 removed outlier: 3.633A pdb=" N GLN C 186 " --> pdb=" O GLY C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 193 through 202 removed outlier: 4.171A pdb=" N ASP C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 4.345A pdb=" N LYS C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 253 removed outlier: 3.789A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.657A pdb=" N TYR C 283 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.564A pdb=" N ILE C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL C 307 " --> pdb=" O LYS C 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.684A pdb=" N LEU C 321 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 removed outlier: 4.327A pdb=" N GLY C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.694A pdb=" N VAL C 379 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 396 removed outlier: 3.785A pdb=" N ALA C 396 " --> pdb=" O THR C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 393 through 396' Processing helix chain 'C' and resid 397 through 405 removed outlier: 3.679A pdb=" N GLN C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 removed outlier: 3.840A pdb=" N ASP C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS C 411 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 427 removed outlier: 3.511A pdb=" N ARG C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 462 removed outlier: 3.635A pdb=" N ARG C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS C 460 " --> pdb=" O HIS C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.553A pdb=" N VAL C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Proline residue: C 553 - end of helix Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.664A pdb=" N ILE C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 562' Processing helix chain 'C' and resid 568 through 579 removed outlier: 3.575A pdb=" N ASP C 572 " --> pdb=" O PRO C 568 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 removed outlier: 4.115A pdb=" N GLY C 592 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.596A pdb=" N ALA C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS C 598 " --> pdb=" O ASP C 594 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU C 603 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 626 removed outlier: 4.009A pdb=" N LYS C 625 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY C 626 " --> pdb=" O MET C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.648A pdb=" N LYS C 631 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 removed outlier: 3.982A pdb=" N ILE C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 656 " --> pdb=" O MET C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 688 Processing helix chain 'C' and resid 696 through 699 Processing helix chain 'C' and resid 700 through 705 removed outlier: 3.610A pdb=" N ALA C 704 " --> pdb=" O GLY C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 720 removed outlier: 3.977A pdb=" N PHE C 720 " --> pdb=" O PRO C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 736 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.920A pdb=" N ALA C 751 " --> pdb=" O CYS C 747 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.898A pdb=" N ASP D 73 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.724A pdb=" N ARG D 81 " --> pdb=" O HIS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 122 removed outlier: 4.358A pdb=" N GLU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 194 through 201 removed outlier: 3.875A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.985A pdb=" N SER D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 259 removed outlier: 4.427A pdb=" N TYR D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 354 through 357 removed outlier: 3.776A pdb=" N TYR D 357 " --> pdb=" O GLY D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 357' Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.839A pdb=" N GLU D 364 " --> pdb=" O PRO D 360 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 392 Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 438 through 448 removed outlier: 4.320A pdb=" N ARG D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN A 42 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 46 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN A 42 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 88 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 removed outlier: 6.459A pdb=" N CYS A 145 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.604A pdb=" N ALA A 161 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA6, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.889A pdb=" N VAL B 161 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 132 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS D 132 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 161 " --> pdb=" O TYR D 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 336 removed outlier: 3.777A pdb=" N ALA B 335 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU B 319 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 161 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 132 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS D 132 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 161 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 319 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 335 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 341 removed outlier: 6.788A pdb=" N GLU B 377 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N CYS B 458 " --> pdb=" O GLU B 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN C 42 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 46 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.534A pdb=" N ASN C 42 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 88 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.459A pdb=" N CYS C 145 " --> pdb=" O GLY C 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.604A pdb=" N ALA C 161 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB6, first strand: chain 'C' and resid 496 through 498 Processing sheet with id=AB7, first strand: chain 'D' and resid 340 through 341 removed outlier: 6.788A pdb=" N GLU D 377 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N CYS D 458 " --> pdb=" O GLU D 377 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5119 1.33 - 1.45: 2905 1.45 - 1.57: 9269 1.57 - 1.69: 3 1.69 - 1.81: 170 Bond restraints: 17466 Sorted by residual: bond pdb=" CA GLU C 67 " pdb=" C GLU C 67 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.38e-02 5.25e+03 1.06e+01 bond pdb=" CA GLU A 67 " pdb=" C GLU A 67 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.38e-02 5.25e+03 1.02e+01 bond pdb=" CB MET D 136 " pdb=" CG MET D 136 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.97e+00 bond pdb=" CB MET B 136 " pdb=" CG MET B 136 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.90e+00 bond pdb=" CG1 ILE D 102 " pdb=" CD1 ILE D 102 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.09e+00 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 22954 3.77 - 7.55: 517 7.55 - 11.32: 63 11.32 - 15.09: 12 15.09 - 18.87: 6 Bond angle restraints: 23552 Sorted by residual: angle pdb=" CA GLU B 118 " pdb=" CB GLU B 118 " pdb=" CG GLU B 118 " ideal model delta sigma weight residual 114.10 132.97 -18.87 2.00e+00 2.50e-01 8.90e+01 angle pdb=" CA GLU D 118 " pdb=" CB GLU D 118 " pdb=" CG GLU D 118 " ideal model delta sigma weight residual 114.10 132.94 -18.84 2.00e+00 2.50e-01 8.88e+01 angle pdb=" CB GLU D 118 " pdb=" CG GLU D 118 " pdb=" CD GLU D 118 " ideal model delta sigma weight residual 112.60 126.54 -13.94 1.70e+00 3.46e-01 6.72e+01 angle pdb=" CB GLU B 118 " pdb=" CG GLU B 118 " pdb=" CD GLU B 118 " ideal model delta sigma weight residual 112.60 126.49 -13.89 1.70e+00 3.46e-01 6.68e+01 angle pdb=" CA ARG A 159 " pdb=" CB ARG A 159 " pdb=" CG ARG A 159 " ideal model delta sigma weight residual 114.10 128.96 -14.86 2.00e+00 2.50e-01 5.52e+01 ... (remaining 23547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9728 17.92 - 35.84: 751 35.84 - 53.76: 176 53.76 - 71.68: 37 71.68 - 89.60: 8 Dihedral angle restraints: 10700 sinusoidal: 4264 harmonic: 6436 Sorted by residual: dihedral pdb=" CA PHE B 376 " pdb=" C PHE B 376 " pdb=" N GLU B 377 " pdb=" CA GLU B 377 " ideal model delta harmonic sigma weight residual 180.00 139.38 40.62 0 5.00e+00 4.00e-02 6.60e+01 dihedral pdb=" CA PHE D 376 " pdb=" C PHE D 376 " pdb=" N GLU D 377 " pdb=" CA GLU D 377 " ideal model delta harmonic sigma weight residual 180.00 139.41 40.59 0 5.00e+00 4.00e-02 6.59e+01 dihedral pdb=" CA ASN D 142 " pdb=" C ASN D 142 " pdb=" N GLN D 143 " pdb=" CA GLN D 143 " ideal model delta harmonic sigma weight residual 180.00 141.30 38.70 0 5.00e+00 4.00e-02 5.99e+01 ... (remaining 10697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2082 0.082 - 0.164: 543 0.164 - 0.246: 64 0.246 - 0.329: 13 0.329 - 0.411: 2 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CB ILE C 275 " pdb=" CA ILE C 275 " pdb=" CG1 ILE C 275 " pdb=" CG2 ILE C 275 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 275 " pdb=" CA ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CG2 ILE A 275 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2701 not shown) Planarity restraints: 3026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 662 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 663 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 663 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 663 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 662 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 663 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 663 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 663 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 298 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO D 299 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.043 5.00e-02 4.00e+02 ... (remaining 3023 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2427 2.74 - 3.28: 17004 3.28 - 3.82: 27674 3.82 - 4.36: 31707 4.36 - 4.90: 51028 Nonbonded interactions: 129840 Sorted by model distance: nonbonded pdb=" OH TYR D 357 " pdb=" O TYR D 402 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 357 " pdb=" O TYR B 402 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR D 244 " pdb=" OE2 GLU D 380 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 244 " pdb=" OE2 GLU B 380 " model vdw 2.232 3.040 nonbonded pdb=" O GLY D 422 " pdb=" OG SER D 425 " model vdw 2.272 3.040 ... (remaining 129835 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.009 0.104 17466 Z= 0.420 Angle : 1.415 18.869 23552 Z= 0.768 Chirality : 0.073 0.411 2704 Planarity : 0.009 0.081 3026 Dihedral : 14.223 89.604 6568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.22 % Favored : 87.29 % Rotamer: Outliers : 3.84 % Allowed : 13.74 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.96 (0.14), residues: 2242 helix: -3.83 (0.11), residues: 740 sheet: -2.73 (0.29), residues: 252 loop : -3.14 (0.15), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 436 TYR 0.030 0.004 TYR D 100 PHE 0.030 0.004 PHE C 545 TRP 0.021 0.004 TRP C 80 HIS 0.012 0.003 HIS B 465 Details of bonding type rmsd covalent geometry : bond 0.00915 (17466) covalent geometry : angle 1.41486 (23552) hydrogen bonds : bond 0.21948 ( 534) hydrogen bonds : angle 8.89789 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 470 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8381 (p0) cc_final: 0.8160 (p0) REVERT: A 166 LYS cc_start: 0.8327 (tptm) cc_final: 0.8112 (tptm) REVERT: A 198 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7947 (tm) REVERT: A 273 MET cc_start: 0.4865 (ptt) cc_final: 0.4542 (ptm) REVERT: A 321 LEU cc_start: 0.8666 (pp) cc_final: 0.8255 (tp) REVERT: A 330 LEU cc_start: 0.8684 (pt) cc_final: 0.7758 (mp) REVERT: A 382 ASP cc_start: 0.8123 (p0) cc_final: 0.7632 (p0) REVERT: A 497 MET cc_start: 0.8993 (mtt) cc_final: 0.8513 (mtp) REVERT: A 509 LEU cc_start: 0.9028 (mm) cc_final: 0.8781 (mm) REVERT: A 536 ILE cc_start: 0.9026 (tp) cc_final: 0.8761 (tp) REVERT: A 718 PHE cc_start: 0.7757 (t80) cc_final: 0.7375 (t80) REVERT: A 722 ASP cc_start: 0.7477 (p0) cc_final: 0.7016 (p0) REVERT: B 73 ASP cc_start: 0.7518 (t0) cc_final: 0.7299 (t0) REVERT: B 107 ILE cc_start: 0.8511 (mm) cc_final: 0.7636 (pt) REVERT: B 142 ASN cc_start: 0.8332 (t0) cc_final: 0.7925 (t0) REVERT: B 143 GLN cc_start: 0.9310 (tm130) cc_final: 0.9000 (tm-30) REVERT: B 206 PHE cc_start: 0.6925 (p90) cc_final: 0.6209 (p90) REVERT: B 258 GLU cc_start: 0.7649 (tp30) cc_final: 0.7203 (tp30) REVERT: B 318 MET cc_start: 0.9210 (ptp) cc_final: 0.8986 (ptp) REVERT: B 341 MET cc_start: 0.8396 (tpt) cc_final: 0.8129 (tpp) REVERT: B 371 ASN cc_start: 0.8408 (p0) cc_final: 0.8153 (t0) REVERT: B 387 LEU cc_start: 0.9380 (pp) cc_final: 0.8967 (tp) REVERT: B 390 PHE cc_start: 0.8083 (m-10) cc_final: 0.7863 (m-10) REVERT: B 418 ASN cc_start: 0.7817 (t0) cc_final: 0.7433 (t0) REVERT: B 423 SER cc_start: 0.8483 (t) cc_final: 0.7700 (t) REVERT: B 451 GLN cc_start: 0.7909 (pt0) cc_final: 0.7555 (pt0) REVERT: C 198 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7755 (tm) REVERT: C 200 MET cc_start: 0.8831 (ttt) cc_final: 0.8283 (tmm) REVERT: C 219 ASP cc_start: 0.7336 (p0) cc_final: 0.7104 (p0) REVERT: C 273 MET cc_start: 0.5151 (ptt) cc_final: 0.4777 (ptm) REVERT: C 330 LEU cc_start: 0.8670 (pt) cc_final: 0.7840 (mp) REVERT: C 382 ASP cc_start: 0.8337 (p0) cc_final: 0.7991 (p0) REVERT: C 383 LYS cc_start: 0.8074 (ptpp) cc_final: 0.7658 (pttt) REVERT: C 462 VAL cc_start: 0.8722 (t) cc_final: 0.8217 (p) REVERT: C 497 MET cc_start: 0.9077 (mtt) cc_final: 0.8837 (mtt) REVERT: C 536 ILE cc_start: 0.9036 (tp) cc_final: 0.8786 (tp) REVERT: C 718 PHE cc_start: 0.7755 (t80) cc_final: 0.7290 (t80) REVERT: C 722 ASP cc_start: 0.7284 (p0) cc_final: 0.6779 (p0) REVERT: D 107 ILE cc_start: 0.8630 (mm) cc_final: 0.7792 (pt) REVERT: D 136 MET cc_start: 0.7337 (mtp) cc_final: 0.7078 (mtp) REVERT: D 142 ASN cc_start: 0.8437 (t0) cc_final: 0.8020 (t0) REVERT: D 143 GLN cc_start: 0.9257 (tm130) cc_final: 0.8919 (tm-30) REVERT: D 206 PHE cc_start: 0.6389 (p90) cc_final: 0.5758 (p90) REVERT: D 221 GLU cc_start: 0.8085 (pp20) cc_final: 0.7528 (pp20) REVERT: D 341 MET cc_start: 0.8338 (tpt) cc_final: 0.8060 (tpp) REVERT: D 371 ASN cc_start: 0.8403 (p0) cc_final: 0.8140 (t0) REVERT: D 387 LEU cc_start: 0.9393 (pp) cc_final: 0.8946 (tp) REVERT: D 390 PHE cc_start: 0.8174 (m-10) cc_final: 0.7918 (m-10) REVERT: D 418 ASN cc_start: 0.7879 (t0) cc_final: 0.7370 (t0) REVERT: D 423 SER cc_start: 0.8579 (t) cc_final: 0.7808 (t) outliers start: 71 outliers final: 21 residues processed: 507 average time/residue: 0.1467 time to fit residues: 109.0690 Evaluate side-chains 320 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.3980 chunk 212 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 432 GLN A 532 GLN B 50 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107462 restraints weight = 35320.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107466 restraints weight = 26751.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109001 restraints weight = 21050.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109576 restraints weight = 16543.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109992 restraints weight = 15162.269| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17466 Z= 0.152 Angle : 0.805 9.183 23552 Z= 0.415 Chirality : 0.049 0.175 2704 Planarity : 0.006 0.080 3026 Dihedral : 7.160 37.256 2394 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.27 % Allowed : 6.39 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.25 (0.15), residues: 2242 helix: -2.86 (0.15), residues: 812 sheet: -2.13 (0.30), residues: 258 loop : -2.99 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 436 TYR 0.015 0.002 TYR C 239 PHE 0.022 0.002 PHE C 277 TRP 0.007 0.001 TRP C 80 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00329 (17466) covalent geometry : angle 0.80504 (23552) hydrogen bonds : bond 0.04887 ( 534) hydrogen bonds : angle 6.32230 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 479 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9093 (mm) cc_final: 0.8886 (mm) REVERT: A 205 ARG cc_start: 0.8306 (ttp-110) cc_final: 0.8091 (mmt-90) REVERT: A 273 MET cc_start: 0.5002 (ptt) cc_final: 0.4663 (ptm) REVERT: A 321 LEU cc_start: 0.8787 (pp) cc_final: 0.8411 (tp) REVERT: A 330 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.7805 (mp) REVERT: A 383 LYS cc_start: 0.7827 (pttt) cc_final: 0.7057 (pttt) REVERT: A 401 GLN cc_start: 0.8962 (mp-120) cc_final: 0.8532 (mp10) REVERT: A 536 ILE cc_start: 0.8774 (tp) cc_final: 0.8571 (tp) REVERT: A 678 VAL cc_start: 0.9014 (t) cc_final: 0.8647 (p) REVERT: A 722 ASP cc_start: 0.6628 (p0) cc_final: 0.6100 (p0) REVERT: A 724 TYR cc_start: 0.5620 (t80) cc_final: 0.5346 (t80) REVERT: A 728 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8505 (ttmm) REVERT: A 748 GLN cc_start: 0.8149 (mp-120) cc_final: 0.7888 (mm-40) REVERT: B 107 ILE cc_start: 0.8327 (mm) cc_final: 0.7644 (pt) REVERT: B 206 PHE cc_start: 0.6581 (p90) cc_final: 0.5973 (p90) REVERT: B 221 GLU cc_start: 0.7905 (pp20) cc_final: 0.7444 (pp20) REVERT: B 350 GLN cc_start: 0.8701 (mp10) cc_final: 0.8272 (mp10) REVERT: B 360 PRO cc_start: 0.9482 (Cg_endo) cc_final: 0.9254 (Cg_exo) REVERT: B 380 GLU cc_start: 0.8239 (pm20) cc_final: 0.7985 (pm20) REVERT: B 387 LEU cc_start: 0.9202 (pp) cc_final: 0.8605 (tp) REVERT: B 390 PHE cc_start: 0.8034 (m-10) cc_final: 0.7809 (m-10) REVERT: B 451 GLN cc_start: 0.7509 (pt0) cc_final: 0.6909 (pt0) REVERT: C 151 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 200 MET cc_start: 0.8584 (ttt) cc_final: 0.8003 (tmm) REVERT: C 273 MET cc_start: 0.4922 (ptt) cc_final: 0.4607 (ptm) REVERT: C 321 LEU cc_start: 0.8771 (pp) cc_final: 0.8307 (tp) REVERT: C 372 MET cc_start: 0.7921 (mmp) cc_final: 0.7681 (mmp) REVERT: C 435 TYR cc_start: 0.7860 (m-80) cc_final: 0.7618 (m-80) REVERT: C 722 ASP cc_start: 0.6585 (p0) cc_final: 0.6171 (p0) REVERT: C 724 TYR cc_start: 0.5612 (t80) cc_final: 0.5343 (t80) REVERT: C 728 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8588 (ttmm) REVERT: C 748 GLN cc_start: 0.8294 (mp-120) cc_final: 0.7937 (mm-40) REVERT: D 107 ILE cc_start: 0.8334 (mm) cc_final: 0.7593 (pt) REVERT: D 136 MET cc_start: 0.7051 (mtp) cc_final: 0.6674 (mtp) REVERT: D 206 PHE cc_start: 0.6195 (p90) cc_final: 0.5717 (p90) REVERT: D 221 GLU cc_start: 0.7986 (pp20) cc_final: 0.7498 (pp20) REVERT: D 312 THR cc_start: 0.9407 (t) cc_final: 0.9202 (t) REVERT: D 340 PHE cc_start: 0.8444 (p90) cc_final: 0.8017 (p90) REVERT: D 350 GLN cc_start: 0.8575 (mp10) cc_final: 0.8178 (mp10) REVERT: D 360 PRO cc_start: 0.9480 (Cg_endo) cc_final: 0.9266 (Cg_exo) REVERT: D 387 LEU cc_start: 0.9171 (pp) cc_final: 0.8581 (tp) REVERT: D 451 GLN cc_start: 0.7405 (pt0) cc_final: 0.6807 (pt0) outliers start: 5 outliers final: 0 residues processed: 479 average time/residue: 0.1383 time to fit residues: 99.6290 Evaluate side-chains 305 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 443 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 418 ASN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN D 463 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102624 restraints weight = 36328.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102847 restraints weight = 30215.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103933 restraints weight = 25140.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104491 restraints weight = 19511.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104858 restraints weight = 17713.508| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17466 Z= 0.217 Angle : 0.805 12.566 23552 Z= 0.417 Chirality : 0.050 0.217 2704 Planarity : 0.006 0.090 3026 Dihedral : 6.770 34.082 2394 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 0.16 % Allowed : 7.52 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.88 (0.16), residues: 2242 helix: -2.46 (0.16), residues: 816 sheet: -2.10 (0.30), residues: 262 loop : -2.78 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 159 TYR 0.020 0.002 TYR B 472 PHE 0.024 0.003 PHE C 718 TRP 0.007 0.001 TRP D 397 HIS 0.008 0.001 HIS B 465 Details of bonding type rmsd covalent geometry : bond 0.00487 (17466) covalent geometry : angle 0.80481 (23552) hydrogen bonds : bond 0.04726 ( 534) hydrogen bonds : angle 5.97657 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 404 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.4850 (ptt) cc_final: 0.4476 (ptm) REVERT: A 288 GLU cc_start: 0.8242 (tt0) cc_final: 0.8040 (tt0) REVERT: A 321 LEU cc_start: 0.8742 (pp) cc_final: 0.8298 (tp) REVERT: A 330 LEU cc_start: 0.8884 (pt) cc_final: 0.7835 (mp) REVERT: A 379 VAL cc_start: 0.9406 (t) cc_final: 0.9190 (t) REVERT: A 383 LYS cc_start: 0.7714 (ptpp) cc_final: 0.7313 (pttt) REVERT: A 401 GLN cc_start: 0.8787 (mp-120) cc_final: 0.8177 (mp10) REVERT: A 423 ASP cc_start: 0.7928 (t70) cc_final: 0.7119 (t0) REVERT: A 463 GLU cc_start: 0.6891 (pp20) cc_final: 0.6682 (pp20) REVERT: A 678 VAL cc_start: 0.8996 (t) cc_final: 0.8642 (p) REVERT: A 722 ASP cc_start: 0.6861 (p0) cc_final: 0.6252 (p0) REVERT: B 107 ILE cc_start: 0.8410 (mm) cc_final: 0.7855 (pt) REVERT: B 206 PHE cc_start: 0.6686 (p90) cc_final: 0.5997 (p90) REVERT: B 263 ASP cc_start: 0.7500 (p0) cc_final: 0.7070 (p0) REVERT: B 380 GLU cc_start: 0.8349 (pm20) cc_final: 0.8134 (pm20) REVERT: B 385 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8678 (tm130) REVERT: B 387 LEU cc_start: 0.9274 (pp) cc_final: 0.8731 (tp) REVERT: C 128 GLU cc_start: 0.8436 (mp0) cc_final: 0.7656 (mp0) REVERT: C 200 MET cc_start: 0.8793 (ttt) cc_final: 0.8264 (tmm) REVERT: C 273 MET cc_start: 0.4864 (ptt) cc_final: 0.4536 (ptm) REVERT: C 330 LEU cc_start: 0.8876 (pt) cc_final: 0.7818 (mp) REVERT: C 435 TYR cc_start: 0.8172 (m-80) cc_final: 0.6146 (m-80) REVERT: C 507 GLN cc_start: 0.7960 (pp30) cc_final: 0.6980 (pp30) REVERT: C 508 LEU cc_start: 0.8679 (pt) cc_final: 0.8420 (pt) REVERT: C 536 ILE cc_start: 0.9020 (tp) cc_final: 0.8798 (tp) REVERT: C 571 LEU cc_start: 0.8572 (pp) cc_final: 0.8310 (pp) REVERT: C 678 VAL cc_start: 0.8939 (t) cc_final: 0.8584 (p) REVERT: C 722 ASP cc_start: 0.6760 (p0) cc_final: 0.6054 (p0) REVERT: D 107 ILE cc_start: 0.8445 (mm) cc_final: 0.7829 (pt) REVERT: D 174 ARG cc_start: 0.7638 (ptp-110) cc_final: 0.7296 (mtm-85) REVERT: D 206 PHE cc_start: 0.6399 (p90) cc_final: 0.5791 (p90) REVERT: D 341 MET cc_start: 0.7883 (tpt) cc_final: 0.7537 (tpp) REVERT: D 385 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8722 (tm130) REVERT: D 387 LEU cc_start: 0.9394 (pp) cc_final: 0.8787 (tp) outliers start: 3 outliers final: 0 residues processed: 407 average time/residue: 0.1363 time to fit residues: 83.4030 Evaluate side-chains 305 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 67 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 206 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 443 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105884 restraints weight = 35953.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106274 restraints weight = 27975.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107561 restraints weight = 22136.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107936 restraints weight = 17505.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108232 restraints weight = 16630.065| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17466 Z= 0.148 Angle : 0.755 9.707 23552 Z= 0.384 Chirality : 0.048 0.191 2704 Planarity : 0.005 0.072 3026 Dihedral : 6.392 30.974 2394 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.60 (0.16), residues: 2242 helix: -2.22 (0.16), residues: 826 sheet: -1.92 (0.31), residues: 262 loop : -2.64 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 81 TYR 0.015 0.002 TYR A 239 PHE 0.024 0.002 PHE C 72 TRP 0.009 0.001 TRP B 397 HIS 0.009 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00332 (17466) covalent geometry : angle 0.75462 (23552) hydrogen bonds : bond 0.04256 ( 534) hydrogen bonds : angle 5.68647 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9225 (mm) cc_final: 0.8898 (mm) REVERT: A 200 MET cc_start: 0.8945 (ttt) cc_final: 0.8343 (tmm) REVERT: A 273 MET cc_start: 0.4819 (ptt) cc_final: 0.4496 (ptm) REVERT: A 305 ILE cc_start: 0.9269 (mm) cc_final: 0.8743 (mm) REVERT: A 321 LEU cc_start: 0.8715 (pp) cc_final: 0.8269 (tp) REVERT: A 372 MET cc_start: 0.8026 (mmp) cc_final: 0.7698 (mmp) REVERT: A 401 GLN cc_start: 0.8469 (mp-120) cc_final: 0.8259 (mp10) REVERT: A 536 ILE cc_start: 0.8963 (tp) cc_final: 0.8748 (tp) REVERT: A 678 VAL cc_start: 0.8945 (t) cc_final: 0.8603 (p) REVERT: A 722 ASP cc_start: 0.6674 (p0) cc_final: 0.6140 (p0) REVERT: B 107 ILE cc_start: 0.8137 (mm) cc_final: 0.7429 (pt) REVERT: B 206 PHE cc_start: 0.6076 (p90) cc_final: 0.5712 (p90) REVERT: B 263 ASP cc_start: 0.7375 (p0) cc_final: 0.6976 (p0) REVERT: B 380 GLU cc_start: 0.7977 (pm20) cc_final: 0.7681 (pm20) REVERT: B 387 LEU cc_start: 0.9356 (pp) cc_final: 0.8667 (tp) REVERT: C 41 ILE cc_start: 0.9248 (mm) cc_final: 0.8935 (mm) REVERT: C 151 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8266 (mm-30) REVERT: C 200 MET cc_start: 0.8717 (ttt) cc_final: 0.8126 (tmm) REVERT: C 273 MET cc_start: 0.4736 (ptt) cc_final: 0.4424 (ptm) REVERT: C 372 MET cc_start: 0.7949 (mmp) cc_final: 0.7603 (mmp) REVERT: C 382 ASP cc_start: 0.8221 (p0) cc_final: 0.7949 (p0) REVERT: C 497 MET cc_start: 0.9084 (mtt) cc_final: 0.8656 (mtp) REVERT: C 507 GLN cc_start: 0.8229 (pp30) cc_final: 0.7123 (pp30) REVERT: C 508 LEU cc_start: 0.8612 (pt) cc_final: 0.8312 (pt) REVERT: C 536 ILE cc_start: 0.9006 (tp) cc_final: 0.8772 (tp) REVERT: C 722 ASP cc_start: 0.6600 (p0) cc_final: 0.5988 (p0) REVERT: D 107 ILE cc_start: 0.8190 (mm) cc_final: 0.7567 (pt) REVERT: D 174 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.7060 (mtm-85) REVERT: D 206 PHE cc_start: 0.5859 (p90) cc_final: 0.5621 (p90) REVERT: D 263 ASP cc_start: 0.7433 (p0) cc_final: 0.7173 (p0) REVERT: D 387 LEU cc_start: 0.9354 (pp) cc_final: 0.8699 (tp) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1273 time to fit residues: 84.4939 Evaluate side-chains 302 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 133 optimal weight: 5.9990 chunk 169 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 194 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 451 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN C 432 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107176 restraints weight = 34979.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107399 restraints weight = 27151.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108723 restraints weight = 21195.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109264 restraints weight = 16966.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109808 restraints weight = 15994.846| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17466 Z= 0.135 Angle : 0.747 10.129 23552 Z= 0.375 Chirality : 0.047 0.179 2704 Planarity : 0.005 0.070 3026 Dihedral : 6.070 29.211 2394 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -3.40 (0.17), residues: 2242 helix: -2.06 (0.16), residues: 830 sheet: -1.74 (0.30), residues: 268 loop : -2.54 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 81 TYR 0.014 0.002 TYR A 283 PHE 0.029 0.002 PHE D 417 TRP 0.008 0.001 TRP D 397 HIS 0.009 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00308 (17466) covalent geometry : angle 0.74673 (23552) hydrogen bonds : bond 0.04060 ( 534) hydrogen bonds : angle 5.46423 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9196 (mm) cc_final: 0.8923 (mm) REVERT: A 200 MET cc_start: 0.8865 (ttt) cc_final: 0.8259 (tmm) REVERT: A 273 MET cc_start: 0.4827 (ptt) cc_final: 0.4535 (ptm) REVERT: A 321 LEU cc_start: 0.8677 (pp) cc_final: 0.8294 (tp) REVERT: A 372 MET cc_start: 0.7932 (mmp) cc_final: 0.7636 (mmp) REVERT: A 497 MET cc_start: 0.8998 (mtt) cc_final: 0.8542 (mtp) REVERT: A 536 ILE cc_start: 0.8965 (tp) cc_final: 0.8697 (tp) REVERT: A 722 ASP cc_start: 0.6578 (p0) cc_final: 0.6168 (p0) REVERT: B 206 PHE cc_start: 0.6176 (p90) cc_final: 0.5685 (p90) REVERT: B 211 LEU cc_start: 0.8292 (mt) cc_final: 0.7754 (pp) REVERT: B 263 ASP cc_start: 0.7274 (p0) cc_final: 0.6913 (p0) REVERT: B 341 MET cc_start: 0.7993 (tpt) cc_final: 0.7692 (tpp) REVERT: B 380 GLU cc_start: 0.8044 (pm20) cc_final: 0.7759 (pm20) REVERT: B 387 LEU cc_start: 0.9358 (pp) cc_final: 0.8669 (tp) REVERT: C 41 ILE cc_start: 0.9219 (mm) cc_final: 0.8928 (mm) REVERT: C 128 GLU cc_start: 0.8284 (mp0) cc_final: 0.7577 (mp0) REVERT: C 151 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8199 (mm-30) REVERT: C 200 MET cc_start: 0.8664 (ttt) cc_final: 0.8055 (tmm) REVERT: C 273 MET cc_start: 0.4867 (ptt) cc_final: 0.4526 (ptm) REVERT: C 305 ILE cc_start: 0.9203 (mm) cc_final: 0.8628 (mm) REVERT: C 321 LEU cc_start: 0.8693 (pp) cc_final: 0.8243 (tp) REVERT: C 372 MET cc_start: 0.7830 (mmp) cc_final: 0.7602 (mmp) REVERT: C 379 VAL cc_start: 0.9464 (t) cc_final: 0.9262 (t) REVERT: C 382 ASP cc_start: 0.8142 (p0) cc_final: 0.7833 (p0) REVERT: C 497 MET cc_start: 0.9034 (mtt) cc_final: 0.8646 (mtp) REVERT: C 507 GLN cc_start: 0.8145 (pp30) cc_final: 0.7252 (pp30) REVERT: C 536 ILE cc_start: 0.8954 (tp) cc_final: 0.8739 (tp) REVERT: C 722 ASP cc_start: 0.6685 (p0) cc_final: 0.6129 (p0) REVERT: D 73 ASP cc_start: 0.7255 (t70) cc_final: 0.7051 (t0) REVERT: D 174 ARG cc_start: 0.7502 (ptp-110) cc_final: 0.6919 (mtm-85) REVERT: D 206 PHE cc_start: 0.5991 (p90) cc_final: 0.5633 (p90) REVERT: D 263 ASP cc_start: 0.7345 (p0) cc_final: 0.7098 (p0) REVERT: D 387 LEU cc_start: 0.9364 (pp) cc_final: 0.8688 (tp) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1295 time to fit residues: 83.8631 Evaluate side-chains 326 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 222 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 35 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106327 restraints weight = 35334.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106149 restraints weight = 26985.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107435 restraints weight = 21920.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107916 restraints weight = 17320.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108222 restraints weight = 15883.960| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17466 Z= 0.153 Angle : 0.748 10.735 23552 Z= 0.375 Chirality : 0.048 0.202 2704 Planarity : 0.005 0.066 3026 Dihedral : 5.967 29.182 2394 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % 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: -3.20 (0.17), residues: 2242 helix: -1.89 (0.17), residues: 832 sheet: -1.73 (0.32), residues: 250 loop : -2.40 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 444 TYR 0.022 0.002 TYR C 283 PHE 0.023 0.002 PHE D 125 TRP 0.009 0.002 TRP D 397 HIS 0.008 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00357 (17466) covalent geometry : angle 0.74842 (23552) hydrogen bonds : bond 0.04014 ( 534) hydrogen bonds : angle 5.35920 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9226 (mm) cc_final: 0.8984 (mm) REVERT: A 200 MET cc_start: 0.8820 (ttt) cc_final: 0.8046 (tmm) REVERT: A 273 MET cc_start: 0.4893 (ptt) cc_final: 0.4310 (ptm) REVERT: A 321 LEU cc_start: 0.8699 (pp) cc_final: 0.8241 (tp) REVERT: A 372 MET cc_start: 0.7965 (mmp) cc_final: 0.7696 (mmp) REVERT: A 378 GLN cc_start: 0.8955 (tt0) cc_final: 0.7849 (tm-30) REVERT: A 379 VAL cc_start: 0.9542 (t) cc_final: 0.8879 (t) REVERT: A 383 LYS cc_start: 0.7659 (pttp) cc_final: 0.7200 (pttt) REVERT: A 497 MET cc_start: 0.8992 (mtt) cc_final: 0.8507 (mtp) REVERT: A 536 ILE cc_start: 0.8984 (tp) cc_final: 0.8719 (tp) REVERT: A 722 ASP cc_start: 0.6580 (p0) cc_final: 0.6291 (p0) REVERT: B 73 ASP cc_start: 0.7358 (t70) cc_final: 0.7067 (t0) REVERT: B 206 PHE cc_start: 0.6319 (p90) cc_final: 0.5728 (p90) REVERT: B 211 LEU cc_start: 0.8146 (mt) cc_final: 0.7834 (pp) REVERT: B 263 ASP cc_start: 0.7329 (p0) cc_final: 0.6974 (p0) REVERT: B 380 GLU cc_start: 0.8119 (pm20) cc_final: 0.7813 (pm20) REVERT: B 387 LEU cc_start: 0.9367 (pp) cc_final: 0.8731 (tp) REVERT: B 411 LEU cc_start: 0.8653 (tp) cc_final: 0.8439 (tp) REVERT: C 41 ILE cc_start: 0.9239 (mm) cc_final: 0.9013 (mm) REVERT: C 200 MET cc_start: 0.8720 (ttt) cc_final: 0.7928 (tmm) REVERT: C 273 MET cc_start: 0.4960 (ptt) cc_final: 0.4607 (ptm) REVERT: C 321 LEU cc_start: 0.8717 (pp) cc_final: 0.8276 (tp) REVERT: C 372 MET cc_start: 0.7882 (mmp) cc_final: 0.7612 (mmp) REVERT: C 379 VAL cc_start: 0.9343 (t) cc_final: 0.9134 (t) REVERT: C 382 ASP cc_start: 0.8179 (p0) cc_final: 0.7852 (p0) REVERT: C 497 MET cc_start: 0.9041 (mtt) cc_final: 0.8659 (mtp) REVERT: C 507 GLN cc_start: 0.8166 (pp30) cc_final: 0.7229 (pp30) REVERT: C 536 ILE cc_start: 0.9005 (tp) cc_final: 0.8789 (tp) REVERT: C 722 ASP cc_start: 0.6754 (p0) cc_final: 0.6285 (p0) REVERT: D 73 ASP cc_start: 0.7362 (t70) cc_final: 0.7138 (t0) REVERT: D 136 MET cc_start: 0.7549 (mtp) cc_final: 0.6963 (mtt) REVERT: D 143 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.9010 (tp40) REVERT: D 206 PHE cc_start: 0.6083 (p90) cc_final: 0.5776 (p90) REVERT: D 263 ASP cc_start: 0.7088 (p0) cc_final: 0.6772 (p0) REVERT: D 300 TYR cc_start: 0.7921 (p90) cc_final: 0.7685 (p90) REVERT: D 387 LEU cc_start: 0.9377 (pp) cc_final: 0.8732 (tp) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.1256 time to fit residues: 78.5275 Evaluate side-chains 302 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 173 optimal weight: 0.0980 chunk 194 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 451 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110171 restraints weight = 35188.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110522 restraints weight = 27140.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111907 restraints weight = 21356.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112382 restraints weight = 17078.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112699 restraints weight = 15515.390| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17466 Z= 0.129 Angle : 0.762 10.874 23552 Z= 0.376 Chirality : 0.047 0.176 2704 Planarity : 0.005 0.066 3026 Dihedral : 5.736 27.785 2394 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -3.01 (0.17), residues: 2242 helix: -1.75 (0.17), residues: 822 sheet: -1.41 (0.32), residues: 268 loop : -2.33 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 279 TYR 0.017 0.001 TYR C 283 PHE 0.052 0.002 PHE D 417 TRP 0.022 0.002 TRP B 420 HIS 0.009 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00280 (17466) covalent geometry : angle 0.76248 (23552) hydrogen bonds : bond 0.03851 ( 534) hydrogen bonds : angle 5.23712 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9202 (mm) cc_final: 0.8947 (mm) REVERT: A 200 MET cc_start: 0.8704 (ttt) cc_final: 0.8120 (tmm) REVERT: A 273 MET cc_start: 0.4642 (ptt) cc_final: 0.4088 (ptm) REVERT: A 305 ILE cc_start: 0.8771 (mm) cc_final: 0.8202 (tt) REVERT: A 321 LEU cc_start: 0.8680 (pp) cc_final: 0.8251 (tp) REVERT: A 340 MET cc_start: 0.6371 (mmp) cc_final: 0.5709 (tpt) REVERT: A 372 MET cc_start: 0.7918 (mmp) cc_final: 0.7683 (mmp) REVERT: A 378 GLN cc_start: 0.8952 (tt0) cc_final: 0.7775 (tm-30) REVERT: A 379 VAL cc_start: 0.9520 (t) cc_final: 0.9034 (t) REVERT: A 536 ILE cc_start: 0.8962 (tp) cc_final: 0.8678 (tp) REVERT: A 708 LEU cc_start: 0.8432 (tt) cc_final: 0.8168 (mt) REVERT: A 722 ASP cc_start: 0.6586 (p0) cc_final: 0.6277 (p0) REVERT: B 73 ASP cc_start: 0.7374 (t70) cc_final: 0.7104 (t0) REVERT: B 145 MET cc_start: 0.7932 (mtp) cc_final: 0.7720 (mtp) REVERT: B 206 PHE cc_start: 0.6130 (p90) cc_final: 0.5844 (p90) REVERT: B 263 ASP cc_start: 0.7355 (p0) cc_final: 0.6937 (p0) REVERT: B 380 GLU cc_start: 0.8099 (pm20) cc_final: 0.7848 (pm20) REVERT: B 387 LEU cc_start: 0.9359 (pp) cc_final: 0.8740 (tp) REVERT: C 41 ILE cc_start: 0.9227 (mm) cc_final: 0.8978 (mm) REVERT: C 200 MET cc_start: 0.8738 (ttt) cc_final: 0.8039 (tmm) REVERT: C 201 MET cc_start: 0.8953 (pmm) cc_final: 0.8689 (pmm) REVERT: C 273 MET cc_start: 0.4888 (ptt) cc_final: 0.4345 (ptm) REVERT: C 321 LEU cc_start: 0.8679 (pp) cc_final: 0.8288 (tp) REVERT: C 497 MET cc_start: 0.9013 (mtt) cc_final: 0.8569 (mtp) REVERT: C 507 GLN cc_start: 0.8264 (pp30) cc_final: 0.7364 (pp30) REVERT: C 536 ILE cc_start: 0.8969 (tp) cc_final: 0.8755 (tp) REVERT: C 722 ASP cc_start: 0.6710 (p0) cc_final: 0.6415 (p0) REVERT: D 174 ARG cc_start: 0.7466 (ptp-110) cc_final: 0.7012 (mtm-85) REVERT: D 179 MET cc_start: 0.8121 (mtt) cc_final: 0.7600 (mtt) REVERT: D 206 PHE cc_start: 0.6128 (p90) cc_final: 0.5821 (p90) REVERT: D 387 LEU cc_start: 0.9367 (pp) cc_final: 0.8719 (tp) REVERT: D 430 PHE cc_start: 0.6846 (t80) cc_final: 0.6636 (t80) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1245 time to fit residues: 82.9840 Evaluate side-chains 322 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 143 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 140 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 465 HIS C 456 HIS ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN D 451 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106321 restraints weight = 35274.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106675 restraints weight = 26547.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107978 restraints weight = 21334.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108373 restraints weight = 17438.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108635 restraints weight = 16190.395| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17466 Z= 0.172 Angle : 0.778 10.601 23552 Z= 0.391 Chirality : 0.048 0.198 2704 Planarity : 0.005 0.068 3026 Dihedral : 5.913 31.572 2394 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.70 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.95 (0.17), residues: 2242 helix: -1.66 (0.17), residues: 844 sheet: -1.56 (0.32), residues: 260 loop : -2.27 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 444 TYR 0.020 0.002 TYR A 283 PHE 0.068 0.002 PHE B 417 TRP 0.036 0.003 TRP D 420 HIS 0.009 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00397 (17466) covalent geometry : angle 0.77839 (23552) hydrogen bonds : bond 0.03958 ( 534) hydrogen bonds : angle 5.36869 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9216 (mm) cc_final: 0.8993 (mm) REVERT: A 200 MET cc_start: 0.8742 (ttt) cc_final: 0.8342 (tmm) REVERT: A 201 MET cc_start: 0.8890 (pmm) cc_final: 0.8558 (pmm) REVERT: A 273 MET cc_start: 0.4856 (ptt) cc_final: 0.4305 (ptm) REVERT: A 321 LEU cc_start: 0.8689 (pp) cc_final: 0.8223 (tp) REVERT: A 340 MET cc_start: 0.6458 (mmp) cc_final: 0.5714 (tpt) REVERT: A 378 GLN cc_start: 0.8912 (tt0) cc_final: 0.7844 (tm-30) REVERT: A 379 VAL cc_start: 0.9580 (t) cc_final: 0.9169 (t) REVERT: A 507 GLN cc_start: 0.7134 (pm20) cc_final: 0.6900 (pp30) REVERT: A 536 ILE cc_start: 0.9035 (tp) cc_final: 0.8789 (tp) REVERT: A 554 MET cc_start: 0.8326 (tmm) cc_final: 0.8120 (tmm) REVERT: A 555 MET cc_start: 0.8308 (tpt) cc_final: 0.7892 (mmm) REVERT: A 722 ASP cc_start: 0.6595 (p0) cc_final: 0.6299 (p0) REVERT: B 73 ASP cc_start: 0.7447 (t70) cc_final: 0.7218 (t0) REVERT: B 139 ILE cc_start: 0.9226 (pt) cc_final: 0.9011 (pt) REVERT: B 179 MET cc_start: 0.8168 (mtt) cc_final: 0.7863 (mtt) REVERT: B 206 PHE cc_start: 0.6294 (p90) cc_final: 0.5864 (p90) REVERT: B 263 ASP cc_start: 0.6996 (p0) cc_final: 0.6583 (p0) REVERT: B 318 MET cc_start: 0.9125 (ptp) cc_final: 0.8873 (ptp) REVERT: B 380 GLU cc_start: 0.8125 (pm20) cc_final: 0.7858 (pm20) REVERT: B 387 LEU cc_start: 0.9411 (pp) cc_final: 0.8849 (tp) REVERT: C 41 ILE cc_start: 0.9269 (mm) cc_final: 0.9029 (mm) REVERT: C 200 MET cc_start: 0.8654 (ttt) cc_final: 0.7903 (tmm) REVERT: C 273 MET cc_start: 0.4847 (ptt) cc_final: 0.4270 (ptm) REVERT: C 321 LEU cc_start: 0.8677 (pp) cc_final: 0.8274 (tp) REVERT: C 497 MET cc_start: 0.9003 (mtt) cc_final: 0.8604 (mtp) REVERT: C 507 GLN cc_start: 0.8296 (pp30) cc_final: 0.7307 (pp30) REVERT: C 536 ILE cc_start: 0.9093 (tp) cc_final: 0.8879 (tp) REVERT: C 687 MET cc_start: 0.7595 (ttt) cc_final: 0.7326 (ttm) REVERT: C 722 ASP cc_start: 0.6684 (p0) cc_final: 0.6343 (p0) REVERT: D 73 ASP cc_start: 0.7372 (t70) cc_final: 0.7168 (t0) REVERT: D 174 ARG cc_start: 0.7369 (ptp-110) cc_final: 0.6757 (mtm-85) REVERT: D 179 MET cc_start: 0.8117 (mtt) cc_final: 0.7502 (mtt) REVERT: D 206 PHE cc_start: 0.6138 (p90) cc_final: 0.5811 (p90) REVERT: D 263 ASP cc_start: 0.7545 (p0) cc_final: 0.7112 (p0) REVERT: D 300 TYR cc_start: 0.7935 (p90) cc_final: 0.7724 (p90) REVERT: D 318 MET cc_start: 0.9085 (ptp) cc_final: 0.8800 (ptp) REVERT: D 387 LEU cc_start: 0.9386 (pp) cc_final: 0.8794 (tp) REVERT: D 417 PHE cc_start: 0.6466 (t80) cc_final: 0.5767 (t80) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1273 time to fit residues: 77.4765 Evaluate side-chains 299 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 136 optimal weight: 0.0270 chunk 30 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 451 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN D 175 HIS ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109063 restraints weight = 35281.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109400 restraints weight = 27454.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110821 restraints weight = 21530.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111237 restraints weight = 17143.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111463 restraints weight = 16208.434| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17466 Z= 0.138 Angle : 0.776 11.173 23552 Z= 0.386 Chirality : 0.048 0.186 2704 Planarity : 0.005 0.071 3026 Dihedral : 5.723 32.292 2394 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.90 (0.17), residues: 2242 helix: -1.58 (0.17), residues: 848 sheet: -1.48 (0.31), residues: 266 loop : -2.31 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 279 TYR 0.019 0.002 TYR C 283 PHE 0.029 0.002 PHE B 417 TRP 0.026 0.003 TRP B 420 HIS 0.010 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00312 (17466) covalent geometry : angle 0.77557 (23552) hydrogen bonds : bond 0.03818 ( 534) hydrogen bonds : angle 5.29299 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9180 (mm) cc_final: 0.8968 (mm) REVERT: A 76 MET cc_start: 0.7121 (mpp) cc_final: 0.6570 (mpp) REVERT: A 200 MET cc_start: 0.8626 (ttt) cc_final: 0.8096 (tmm) REVERT: A 273 MET cc_start: 0.4901 (ptt) cc_final: 0.4350 (ptm) REVERT: A 321 LEU cc_start: 0.8663 (pp) cc_final: 0.8224 (tp) REVERT: A 340 MET cc_start: 0.6542 (mmp) cc_final: 0.5776 (tpt) REVERT: A 378 GLN cc_start: 0.8948 (tt0) cc_final: 0.7818 (tm-30) REVERT: A 379 VAL cc_start: 0.9560 (t) cc_final: 0.9158 (t) REVERT: A 536 ILE cc_start: 0.8939 (tp) cc_final: 0.8671 (tp) REVERT: A 554 MET cc_start: 0.8274 (tmm) cc_final: 0.8030 (tmm) REVERT: A 555 MET cc_start: 0.8273 (tpt) cc_final: 0.7807 (mmm) REVERT: A 708 LEU cc_start: 0.8433 (tt) cc_final: 0.8029 (mp) REVERT: A 722 ASP cc_start: 0.6908 (p0) cc_final: 0.6657 (p0) REVERT: B 73 ASP cc_start: 0.7488 (t70) cc_final: 0.7207 (t0) REVERT: B 179 MET cc_start: 0.8073 (mtt) cc_final: 0.7840 (mtt) REVERT: B 206 PHE cc_start: 0.6392 (p90) cc_final: 0.5983 (p90) REVERT: B 223 MET cc_start: 0.7154 (tpt) cc_final: 0.6918 (tpt) REVERT: B 242 ASP cc_start: 0.8356 (m-30) cc_final: 0.8132 (m-30) REVERT: B 263 ASP cc_start: 0.6937 (p0) cc_final: 0.6518 (p0) REVERT: B 380 GLU cc_start: 0.8045 (pm20) cc_final: 0.7798 (pm20) REVERT: B 387 LEU cc_start: 0.9413 (pp) cc_final: 0.8754 (tp) REVERT: C 41 ILE cc_start: 0.9208 (mm) cc_final: 0.8998 (mm) REVERT: C 200 MET cc_start: 0.8649 (ttt) cc_final: 0.8098 (tmm) REVERT: C 273 MET cc_start: 0.5097 (ptt) cc_final: 0.4531 (ptm) REVERT: C 321 LEU cc_start: 0.8671 (pp) cc_final: 0.8286 (tp) REVERT: C 340 MET cc_start: 0.6337 (mmp) cc_final: 0.5478 (tpp) REVERT: C 497 MET cc_start: 0.8965 (mtt) cc_final: 0.8510 (mtp) REVERT: C 507 GLN cc_start: 0.8217 (pp30) cc_final: 0.7495 (pp30) REVERT: C 536 ILE cc_start: 0.9065 (tp) cc_final: 0.8804 (tp) REVERT: C 554 MET cc_start: 0.8283 (tmm) cc_final: 0.7856 (tmm) REVERT: C 555 MET cc_start: 0.8276 (tpt) cc_final: 0.7825 (mmm) REVERT: C 687 MET cc_start: 0.7607 (ttt) cc_final: 0.7322 (ttm) REVERT: C 708 LEU cc_start: 0.8513 (tt) cc_final: 0.8184 (mp) REVERT: C 722 ASP cc_start: 0.7063 (p0) cc_final: 0.6847 (p0) REVERT: D 73 ASP cc_start: 0.7357 (t70) cc_final: 0.7148 (t0) REVERT: D 174 ARG cc_start: 0.7340 (ptp-110) cc_final: 0.6769 (mtm-85) REVERT: D 179 MET cc_start: 0.7971 (mtt) cc_final: 0.7507 (mtt) REVERT: D 206 PHE cc_start: 0.6011 (p90) cc_final: 0.5789 (p90) REVERT: D 223 MET cc_start: 0.7221 (tpt) cc_final: 0.6973 (tpt) REVERT: D 263 ASP cc_start: 0.7066 (p0) cc_final: 0.6561 (p0) REVERT: D 318 MET cc_start: 0.9011 (ptp) cc_final: 0.8803 (ptp) REVERT: D 387 LEU cc_start: 0.9364 (pp) cc_final: 0.8740 (tp) REVERT: D 417 PHE cc_start: 0.6082 (t80) cc_final: 0.5581 (t80) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1215 time to fit residues: 75.1988 Evaluate side-chains 310 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 158 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN D 288 GLN D 379 HIS D 428 HIS D 443 ASN D 451 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108385 restraints weight = 35171.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108811 restraints weight = 26679.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110054 restraints weight = 21089.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110536 restraints weight = 16669.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110851 restraints weight = 15708.210| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17466 Z= 0.146 Angle : 0.780 11.050 23552 Z= 0.390 Chirality : 0.049 0.200 2704 Planarity : 0.005 0.069 3026 Dihedral : 5.693 31.533 2394 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.86 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.77 (0.17), residues: 2242 helix: -1.45 (0.17), residues: 842 sheet: -1.49 (0.32), residues: 232 loop : -2.21 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 676 TYR 0.021 0.002 TYR A 736 PHE 0.025 0.002 PHE A 718 TRP 0.023 0.002 TRP D 420 HIS 0.010 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00336 (17466) covalent geometry : angle 0.78036 (23552) hydrogen bonds : bond 0.03853 ( 534) hydrogen bonds : angle 5.29444 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4484 Ramachandran restraints generated. 2242 Oldfield, 0 Emsley, 2242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9171 (mm) cc_final: 0.8959 (mm) REVERT: A 128 GLU cc_start: 0.7656 (mp0) cc_final: 0.7071 (mp0) REVERT: A 200 MET cc_start: 0.8817 (ttt) cc_final: 0.8307 (tmm) REVERT: A 201 MET cc_start: 0.8834 (pmm) cc_final: 0.8583 (pmm) REVERT: A 273 MET cc_start: 0.4877 (ptt) cc_final: 0.4284 (ptm) REVERT: A 321 LEU cc_start: 0.8660 (pp) cc_final: 0.8212 (tp) REVERT: A 330 LEU cc_start: 0.8506 (pt) cc_final: 0.8303 (pt) REVERT: A 340 MET cc_start: 0.6563 (mmp) cc_final: 0.5801 (tpt) REVERT: A 378 GLN cc_start: 0.9017 (tt0) cc_final: 0.7877 (tm-30) REVERT: A 379 VAL cc_start: 0.9540 (t) cc_final: 0.9166 (t) REVERT: A 423 ASP cc_start: 0.8099 (m-30) cc_final: 0.7704 (t70) REVERT: A 536 ILE cc_start: 0.8926 (tp) cc_final: 0.8689 (tp) REVERT: A 687 MET cc_start: 0.7593 (ttt) cc_final: 0.7341 (ttm) REVERT: A 708 LEU cc_start: 0.8502 (tt) cc_final: 0.8026 (mp) REVERT: A 722 ASP cc_start: 0.6978 (p0) cc_final: 0.6747 (p0) REVERT: B 73 ASP cc_start: 0.7562 (t70) cc_final: 0.7304 (t0) REVERT: B 179 MET cc_start: 0.8106 (mtt) cc_final: 0.7833 (mtt) REVERT: B 206 PHE cc_start: 0.6409 (p90) cc_final: 0.5965 (p90) REVERT: B 223 MET cc_start: 0.7028 (tpt) cc_final: 0.6822 (tpt) REVERT: B 263 ASP cc_start: 0.7051 (p0) cc_final: 0.6575 (p0) REVERT: B 318 MET cc_start: 0.9167 (ptp) cc_final: 0.8953 (ptp) REVERT: B 380 GLU cc_start: 0.8163 (pm20) cc_final: 0.7869 (pm20) REVERT: B 387 LEU cc_start: 0.9386 (pp) cc_final: 0.8743 (tp) REVERT: B 411 LEU cc_start: 0.8787 (tp) cc_final: 0.8583 (tp) REVERT: C 41 ILE cc_start: 0.9221 (mm) cc_final: 0.9014 (mm) REVERT: C 200 MET cc_start: 0.8634 (ttt) cc_final: 0.8048 (tmm) REVERT: C 201 MET cc_start: 0.8879 (pmm) cc_final: 0.8657 (pmm) REVERT: C 273 MET cc_start: 0.5094 (ptt) cc_final: 0.4525 (ptm) REVERT: C 321 LEU cc_start: 0.8677 (pp) cc_final: 0.8202 (tp) REVERT: C 340 MET cc_start: 0.6486 (mmp) cc_final: 0.5655 (tpp) REVERT: C 497 MET cc_start: 0.8953 (mtt) cc_final: 0.8720 (mmt) REVERT: C 507 GLN cc_start: 0.8288 (pp30) cc_final: 0.7456 (pp30) REVERT: C 511 ILE cc_start: 0.9689 (mm) cc_final: 0.9252 (mp) REVERT: C 536 ILE cc_start: 0.9054 (tp) cc_final: 0.8817 (tp) REVERT: C 708 LEU cc_start: 0.8543 (tt) cc_final: 0.8146 (mp) REVERT: C 722 ASP cc_start: 0.7060 (p0) cc_final: 0.6842 (p0) REVERT: C 727 GLN cc_start: 0.8336 (tp40) cc_final: 0.8121 (tp40) REVERT: D 174 ARG cc_start: 0.7409 (ptp-110) cc_final: 0.6761 (mtm-85) REVERT: D 179 MET cc_start: 0.8163 (mtt) cc_final: 0.7652 (mtt) REVERT: D 206 PHE cc_start: 0.6028 (p90) cc_final: 0.5801 (p90) REVERT: D 263 ASP cc_start: 0.7400 (p0) cc_final: 0.6925 (p0) REVERT: D 318 MET cc_start: 0.9062 (ptp) cc_final: 0.8859 (ptp) REVERT: D 387 LEU cc_start: 0.9368 (pp) cc_final: 0.8759 (tp) REVERT: D 417 PHE cc_start: 0.6100 (t80) cc_final: 0.5649 (t80) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1219 time to fit residues: 72.3331 Evaluate side-chains 301 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 70 optimal weight: 0.0470 chunk 108 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 451 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 HIS D 156 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111187 restraints weight = 35074.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111321 restraints weight = 28095.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112726 restraints weight = 21898.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113231 restraints weight = 16975.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113548 restraints weight = 15587.780| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17466 Z= 0.132 Angle : 0.775 11.476 23552 Z= 0.384 Chirality : 0.048 0.207 2704 Planarity : 0.005 0.070 3026 Dihedral : 5.522 25.142 2394 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.57 (0.17), residues: 2242 helix: -1.33 (0.18), residues: 826 sheet: -1.26 (0.34), residues: 234 loop : -2.08 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 676 TYR 0.019 0.002 TYR A 283 PHE 0.031 0.002 PHE B 417 TRP 0.011 0.002 TRP D 420 HIS 0.012 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00299 (17466) covalent geometry : angle 0.77491 (23552) hydrogen bonds : bond 0.03777 ( 534) hydrogen bonds : angle 5.24489 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.27 seconds wall clock time: 47 minutes 55.15 seconds (2875.15 seconds total)