Starting phenix.real_space_refine on Fri Sep 27 20:56:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/09_2024/5zqz_6940.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/09_2024/5zqz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/09_2024/5zqz_6940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/09_2024/5zqz_6940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/09_2024/5zqz_6940.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zqz_6940/09_2024/5zqz_6940.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 9.85, per 1000 atoms: 0.57 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: 4.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.26 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: 5.81 Time building geometry restraints manager: 5.14 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: 0.00 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: 0.260 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: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 40.350 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- 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= 0.595 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.004 TRP C 80 HIS 0.012 0.003 HIS B 465 PHE 0.030 0.004 PHE C 545 TYR 0.030 0.004 TYR D 100 ARG 0.018 0.002 ARG B 436 *********************** 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 fitting. rotamer outliers: 71 poor density : 470 time to evaluate : 2.061 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: 0.3454 time to fit residues: 256.0182 Evaluate side-chains 320 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 297 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 142 ASN A 432 GLN A 532 GLN B 50 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17466 Z= 0.287 Angle : 0.832 8.803 23552 Z= 0.434 Chirality : 0.050 0.197 2704 Planarity : 0.006 0.077 3026 Dihedral : 7.363 38.969 2394 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 0.32 % Allowed : 6.49 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.16), residues: 2242 helix: -2.82 (0.15), residues: 810 sheet: -2.34 (0.31), residues: 240 loop : -2.87 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 397 HIS 0.005 0.001 HIS C 69 PHE 0.021 0.002 PHE A 277 TYR 0.019 0.003 TYR C 239 ARG 0.008 0.001 ARG D 436 *********************** 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 453 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 447 time to evaluate : 2.161 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9228 (mm) cc_final: 0.9000 (mm) REVERT: A 273 MET cc_start: 0.5084 (ptt) cc_final: 0.4752 (ptm) REVERT: A 321 LEU cc_start: 0.8768 (pp) cc_final: 0.8340 (tp) REVERT: A 330 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 383 LYS cc_start: 0.8309 (pttt) cc_final: 0.7569 (pttt) REVERT: A 490 ARG cc_start: 0.8142 (mpp-170) cc_final: 0.7893 (ptp-170) REVERT: A 722 ASP cc_start: 0.6958 (p0) cc_final: 0.6441 (p0) REVERT: A 724 TYR cc_start: 0.5873 (t80) cc_final: 0.5526 (t80) REVERT: A 728 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8556 (ttmm) REVERT: A 748 GLN cc_start: 0.8301 (mp-120) cc_final: 0.8072 (mm-40) REVERT: B 107 ILE cc_start: 0.8383 (mm) cc_final: 0.7755 (pt) REVERT: B 206 PHE cc_start: 0.6766 (p90) cc_final: 0.5884 (p90) REVERT: B 221 GLU cc_start: 0.7962 (pp20) cc_final: 0.7501 (pp20) REVERT: B 350 GLN cc_start: 0.8832 (mp10) cc_final: 0.8284 (mp10) REVERT: B 376 PHE cc_start: 0.8100 (m-10) cc_final: 0.7893 (m-10) REVERT: B 380 GLU cc_start: 0.8283 (pm20) cc_final: 0.7890 (pm20) REVERT: B 387 LEU cc_start: 0.9236 (pp) cc_final: 0.8658 (tp) REVERT: B 451 GLN cc_start: 0.7712 (pt0) cc_final: 0.7059 (pt0) REVERT: C 200 MET cc_start: 0.8723 (ttt) cc_final: 0.8082 (tmm) REVERT: C 201 MET cc_start: 0.9034 (pmm) cc_final: 0.8826 (pmm) REVERT: C 219 ASP cc_start: 0.7300 (p0) cc_final: 0.6663 (p0) REVERT: C 273 MET cc_start: 0.4766 (ptt) cc_final: 0.4463 (ptm) REVERT: C 330 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.7867 (mp) REVERT: C 382 ASP cc_start: 0.8225 (p0) cc_final: 0.8023 (p0) REVERT: C 435 TYR cc_start: 0.7917 (m-80) cc_final: 0.7636 (m-80) REVERT: C 722 ASP cc_start: 0.6880 (p0) cc_final: 0.6353 (p0) REVERT: C 748 GLN cc_start: 0.8317 (mp-120) cc_final: 0.7951 (mm-40) REVERT: D 100 TYR cc_start: 0.8785 (t80) cc_final: 0.8375 (t80) REVERT: D 107 ILE cc_start: 0.8461 (mm) cc_final: 0.7693 (pt) REVERT: D 136 MET cc_start: 0.7340 (mtp) cc_final: 0.6903 (mtp) REVERT: D 206 PHE cc_start: 0.6387 (p90) cc_final: 0.5734 (p90) REVERT: D 221 GLU cc_start: 0.7963 (pp20) cc_final: 0.7547 (pp20) REVERT: D 241 GLN cc_start: 0.8705 (tt0) cc_final: 0.8484 (tt0) REVERT: D 350 GLN cc_start: 0.8781 (mp10) cc_final: 0.8250 (mp10) REVERT: D 360 PRO cc_start: 0.9539 (Cg_endo) cc_final: 0.9335 (Cg_exo) REVERT: D 380 GLU cc_start: 0.8346 (pm20) cc_final: 0.8027 (pm20) REVERT: D 387 LEU cc_start: 0.9202 (pp) cc_final: 0.8674 (tp) REVERT: D 451 GLN cc_start: 0.7776 (pt0) cc_final: 0.7105 (pt0) outliers start: 6 outliers final: 0 residues processed: 447 average time/residue: 0.3053 time to fit residues: 202.6569 Evaluate side-chains 297 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 363 HIS ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 17466 Z= 0.443 Angle : 0.883 12.410 23552 Z= 0.459 Chirality : 0.052 0.232 2704 Planarity : 0.006 0.074 3026 Dihedral : 7.211 35.914 2394 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 0.11 % Allowed : 9.09 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.16), residues: 2242 helix: -2.44 (0.16), residues: 808 sheet: -2.38 (0.29), residues: 272 loop : -2.69 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 80 HIS 0.008 0.002 HIS B 465 PHE 0.024 0.003 PHE C 718 TYR 0.023 0.003 TYR A 239 ARG 0.011 0.001 ARG D 81 *********************** 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 378 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 1.992 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 45 VAL cc_start: 0.7099 (p) cc_final: 0.6778 (m) REVERT: A 128 GLU cc_start: 0.8493 (mp0) cc_final: 0.7566 (mp0) REVERT: A 273 MET cc_start: 0.5104 (ptt) cc_final: 0.4339 (ptm) REVERT: A 321 LEU cc_start: 0.8816 (pp) cc_final: 0.8188 (tp) REVERT: A 383 LYS cc_start: 0.7964 (ptpp) cc_final: 0.7569 (pttt) REVERT: A 401 GLN cc_start: 0.8814 (mp-120) cc_final: 0.8242 (mp10) REVERT: A 507 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 536 ILE cc_start: 0.9175 (tp) cc_final: 0.8947 (tp) REVERT: A 722 ASP cc_start: 0.7257 (p0) cc_final: 0.6592 (p0) REVERT: B 100 TYR cc_start: 0.8843 (t80) cc_final: 0.8245 (t80) REVERT: B 107 ILE cc_start: 0.8563 (mm) cc_final: 0.7961 (pt) REVERT: B 206 PHE cc_start: 0.6776 (p90) cc_final: 0.5819 (p90) REVERT: B 263 ASP cc_start: 0.7459 (p0) cc_final: 0.6964 (p0) REVERT: B 268 LYS cc_start: 0.9144 (tmmt) cc_final: 0.8891 (tptt) REVERT: B 380 GLU cc_start: 0.8452 (pm20) cc_final: 0.8015 (pm20) REVERT: B 387 LEU cc_start: 0.9419 (pp) cc_final: 0.8864 (tp) REVERT: C 128 GLU cc_start: 0.8392 (mp0) cc_final: 0.7529 (mp0) REVERT: C 200 MET cc_start: 0.8728 (ttt) cc_final: 0.8185 (tmm) REVERT: C 273 MET cc_start: 0.5108 (ptt) cc_final: 0.4723 (ptm) REVERT: C 383 LYS cc_start: 0.8839 (pttt) cc_final: 0.8303 (pttm) REVERT: C 435 TYR cc_start: 0.8331 (m-80) cc_final: 0.7786 (m-80) REVERT: C 507 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7854 (tm-30) REVERT: C 536 ILE cc_start: 0.9172 (tp) cc_final: 0.8963 (tp) REVERT: C 722 ASP cc_start: 0.7105 (p0) cc_final: 0.6390 (p0) REVERT: D 73 ASP cc_start: 0.7403 (t70) cc_final: 0.7160 (t0) REVERT: D 107 ILE cc_start: 0.8550 (mm) cc_final: 0.7952 (pt) REVERT: D 136 MET cc_start: 0.7425 (mtp) cc_final: 0.6781 (mtp) REVERT: D 206 PHE cc_start: 0.6492 (p90) cc_final: 0.5758 (p90) REVERT: D 263 ASP cc_start: 0.7497 (p0) cc_final: 0.7228 (p0) REVERT: D 268 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8893 (ptmt) REVERT: D 380 GLU cc_start: 0.8441 (pm20) cc_final: 0.8090 (pm20) REVERT: D 387 LEU cc_start: 0.9420 (pp) cc_final: 0.8882 (tp) outliers start: 2 outliers final: 1 residues processed: 378 average time/residue: 0.2715 time to fit residues: 155.8816 Evaluate side-chains 287 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** A 615 ASN B 108 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 ASN D 175 HIS ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3405 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= 0.228 Angle : 0.780 10.636 23552 Z= 0.396 Chirality : 0.049 0.240 2704 Planarity : 0.005 0.086 3026 Dihedral : 6.607 33.006 2394 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.17), residues: 2242 helix: -2.15 (0.16), residues: 816 sheet: -2.22 (0.29), residues: 262 loop : -2.63 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.009 0.001 HIS C 69 PHE 0.024 0.002 PHE A 72 TYR 0.015 0.002 TYR A 239 ARG 0.007 0.000 ARG B 81 *********************** 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 423 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9289 (mm) cc_final: 0.8980 (mm) REVERT: A 198 LEU cc_start: 0.8484 (tp) cc_final: 0.8279 (tp) REVERT: A 200 MET cc_start: 0.8987 (ttt) cc_final: 0.8236 (tmm) REVERT: A 273 MET cc_start: 0.4871 (ptt) cc_final: 0.4524 (ptm) REVERT: A 305 ILE cc_start: 0.9282 (mm) cc_final: 0.8775 (mm) REVERT: A 309 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8213 (ptpt) REVERT: A 321 LEU cc_start: 0.8756 (pp) cc_final: 0.8283 (tp) REVERT: A 401 GLN cc_start: 0.8597 (mp-120) cc_final: 0.8312 (mp10) REVERT: A 497 MET cc_start: 0.9060 (mtt) cc_final: 0.8632 (mtp) REVERT: A 536 ILE cc_start: 0.9098 (tp) cc_final: 0.8837 (tp) REVERT: A 678 VAL cc_start: 0.8989 (t) cc_final: 0.8634 (p) REVERT: A 722 ASP cc_start: 0.6869 (p0) cc_final: 0.6274 (p0) REVERT: B 107 ILE cc_start: 0.8315 (mm) cc_final: 0.7744 (pt) REVERT: B 206 PHE cc_start: 0.6140 (p90) cc_final: 0.5787 (p90) REVERT: B 263 ASP cc_start: 0.7408 (p0) cc_final: 0.6990 (p0) REVERT: B 380 GLU cc_start: 0.8397 (pm20) cc_final: 0.8054 (pm20) REVERT: B 387 LEU cc_start: 0.9362 (pp) cc_final: 0.8732 (tp) REVERT: B 430 PHE cc_start: 0.7528 (t80) cc_final: 0.7231 (t80) REVERT: B 451 GLN cc_start: 0.7881 (pt0) cc_final: 0.7457 (pt0) REVERT: B 463 GLN cc_start: 0.8847 (mp10) cc_final: 0.8484 (mp10) REVERT: C 41 ILE cc_start: 0.9286 (mm) cc_final: 0.8999 (mm) REVERT: C 198 LEU cc_start: 0.8289 (tp) cc_final: 0.8072 (tp) REVERT: C 200 MET cc_start: 0.8735 (ttt) cc_final: 0.8242 (tmm) REVERT: C 219 ASP cc_start: 0.7310 (p0) cc_final: 0.7105 (p0) REVERT: C 273 MET cc_start: 0.4936 (ptt) cc_final: 0.4601 (ptm) REVERT: C 401 GLN cc_start: 0.8656 (mp-120) cc_final: 0.8139 (mp10) REVERT: C 435 TYR cc_start: 0.8323 (m-80) cc_final: 0.7715 (m-80) REVERT: C 497 MET cc_start: 0.9076 (mtt) cc_final: 0.8703 (mtp) REVERT: C 536 ILE cc_start: 0.9068 (tp) cc_final: 0.8833 (tp) REVERT: C 678 VAL cc_start: 0.8943 (t) cc_final: 0.8590 (p) REVERT: C 722 ASP cc_start: 0.6766 (p0) cc_final: 0.6175 (p0) REVERT: D 73 ASP cc_start: 0.7344 (t70) cc_final: 0.7084 (t0) REVERT: D 107 ILE cc_start: 0.8380 (mm) cc_final: 0.7796 (pt) REVERT: D 139 ILE cc_start: 0.9226 (pt) cc_final: 0.9000 (pt) REVERT: D 174 ARG cc_start: 0.7569 (ptp-110) cc_final: 0.7169 (mtm-85) REVERT: D 206 PHE cc_start: 0.6023 (p90) cc_final: 0.5664 (p90) REVERT: D 263 ASP cc_start: 0.7401 (p0) cc_final: 0.7010 (p0) REVERT: D 380 GLU cc_start: 0.8430 (pm20) cc_final: 0.8193 (pm20) REVERT: D 387 LEU cc_start: 0.9341 (pp) cc_final: 0.8731 (tp) REVERT: D 451 GLN cc_start: 0.7964 (pt0) cc_final: 0.7624 (pt0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2820 time to fit residues: 182.4648 Evaluate side-chains 307 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** 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 389 ASN D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17466 Z= 0.220 Angle : 0.756 9.621 23552 Z= 0.383 Chirality : 0.048 0.189 2704 Planarity : 0.005 0.071 3026 Dihedral : 6.274 30.571 2394 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.17), residues: 2242 helix: -1.93 (0.17), residues: 828 sheet: -1.93 (0.31), residues: 262 loop : -2.49 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 397 HIS 0.009 0.001 HIS A 69 PHE 0.026 0.002 PHE D 417 TYR 0.021 0.002 TYR A 283 ARG 0.004 0.000 ARG D 81 *********************** 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 405 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.096 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: 0.9275 (mm) cc_final: 0.9018 (mm) REVERT: A 200 MET cc_start: 0.8858 (ttt) cc_final: 0.8172 (tmm) REVERT: A 273 MET cc_start: 0.5219 (ptt) cc_final: 0.4820 (ptm) REVERT: A 305 ILE cc_start: 0.9298 (mm) cc_final: 0.8809 (mm) REVERT: A 309 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8287 (ptpt) REVERT: A 321 LEU cc_start: 0.8762 (pp) cc_final: 0.8190 (tp) REVERT: A 401 GLN cc_start: 0.8513 (mp-120) cc_final: 0.8245 (mp10) REVERT: A 423 ASP cc_start: 0.7839 (t70) cc_final: 0.7351 (t0) REVERT: A 497 MET cc_start: 0.9085 (mtt) cc_final: 0.8716 (mtp) REVERT: A 507 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 536 ILE cc_start: 0.9061 (tp) cc_final: 0.8795 (tp) REVERT: A 678 VAL cc_start: 0.8956 (t) cc_final: 0.8628 (p) REVERT: A 722 ASP cc_start: 0.7018 (p0) cc_final: 0.6422 (p0) REVERT: A 731 ASP cc_start: 0.8384 (m-30) cc_final: 0.8118 (m-30) REVERT: B 73 ASP cc_start: 0.7470 (t70) cc_final: 0.7218 (t0) REVERT: B 174 ARG cc_start: 0.7454 (ptp-110) cc_final: 0.7157 (ptp-110) REVERT: B 206 PHE cc_start: 0.6324 (p90) cc_final: 0.5764 (p90) REVERT: B 263 ASP cc_start: 0.7452 (p0) cc_final: 0.7068 (p0) REVERT: B 387 LEU cc_start: 0.9344 (pp) cc_final: 0.8710 (tp) REVERT: B 389 ASN cc_start: 0.9107 (m110) cc_final: 0.8755 (m-40) REVERT: C 41 ILE cc_start: 0.9268 (mm) cc_final: 0.8996 (mm) REVERT: C 128 GLU cc_start: 0.8119 (mp0) cc_final: 0.7422 (mp0) REVERT: C 151 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8240 (mm-30) REVERT: C 200 MET cc_start: 0.8914 (ttt) cc_final: 0.8348 (tmm) REVERT: C 273 MET cc_start: 0.5088 (ptt) cc_final: 0.4734 (ptm) REVERT: C 305 ILE cc_start: 0.9296 (mm) cc_final: 0.8794 (mm) REVERT: C 309 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8239 (ptpt) REVERT: C 372 MET cc_start: 0.7969 (mmp) cc_final: 0.7540 (mmp) REVERT: C 401 GLN cc_start: 0.8396 (mp-120) cc_final: 0.8117 (mp10) REVERT: C 435 TYR cc_start: 0.8307 (m-80) cc_final: 0.7613 (m-80) REVERT: C 497 MET cc_start: 0.9089 (mtt) cc_final: 0.8675 (mtp) REVERT: C 507 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7935 (tm-30) REVERT: C 536 ILE cc_start: 0.9032 (tp) cc_final: 0.8779 (tp) REVERT: C 722 ASP cc_start: 0.6941 (p0) cc_final: 0.6317 (p0) REVERT: D 73 ASP cc_start: 0.7404 (t70) cc_final: 0.7153 (t0) REVERT: D 100 TYR cc_start: 0.8796 (t80) cc_final: 0.8290 (t80) REVERT: D 174 ARG cc_start: 0.7486 (ptp-110) cc_final: 0.7105 (mtm-85) REVERT: D 206 PHE cc_start: 0.6358 (p90) cc_final: 0.5869 (p90) REVERT: D 263 ASP cc_start: 0.7469 (p0) cc_final: 0.7082 (p0) REVERT: D 352 LEU cc_start: 0.9193 (mp) cc_final: 0.8971 (mp) REVERT: D 387 LEU cc_start: 0.9399 (pp) cc_final: 0.8718 (tp) REVERT: D 417 PHE cc_start: 0.6569 (t80) cc_final: 0.6360 (t80) REVERT: D 418 ASN cc_start: 0.7364 (t0) cc_final: 0.7134 (t0) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2761 time to fit residues: 168.8771 Evaluate side-chains 304 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 463 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 456 HIS ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 443 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17466 Z= 0.256 Angle : 0.766 9.993 23552 Z= 0.387 Chirality : 0.049 0.211 2704 Planarity : 0.005 0.069 3026 Dihedral : 6.212 30.187 2394 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.17), residues: 2242 helix: -1.79 (0.17), residues: 820 sheet: -1.89 (0.31), residues: 260 loop : -2.42 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 397 HIS 0.008 0.001 HIS C 69 PHE 0.021 0.002 PHE D 125 TYR 0.016 0.002 TYR A 239 ARG 0.012 0.001 ARG A 676 *********************** 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 382 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8787 (ttt) cc_final: 0.8142 (tmm) REVERT: A 273 MET cc_start: 0.5319 (ptt) cc_final: 0.4890 (ptm) REVERT: A 305 ILE cc_start: 0.9217 (mm) cc_final: 0.8661 (mm) REVERT: A 309 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8254 (ptpt) REVERT: A 321 LEU cc_start: 0.8744 (pp) cc_final: 0.8177 (tp) REVERT: A 372 MET cc_start: 0.7920 (mmp) cc_final: 0.7556 (mmp) REVERT: A 401 GLN cc_start: 0.8420 (mp-120) cc_final: 0.8211 (mp10) REVERT: A 497 MET cc_start: 0.9090 (mtt) cc_final: 0.8718 (mtp) REVERT: A 536 ILE cc_start: 0.9042 (tp) cc_final: 0.8803 (tp) REVERT: A 722 ASP cc_start: 0.7012 (p0) cc_final: 0.6430 (p0) REVERT: B 73 ASP cc_start: 0.7498 (t70) cc_final: 0.7267 (t0) REVERT: B 136 MET cc_start: 0.7566 (mtp) cc_final: 0.7299 (mtp) REVERT: B 174 ARG cc_start: 0.7300 (ptp-110) cc_final: 0.6727 (mtm-85) REVERT: B 206 PHE cc_start: 0.6308 (p90) cc_final: 0.5827 (p90) REVERT: B 263 ASP cc_start: 0.7367 (p0) cc_final: 0.6953 (p0) REVERT: B 387 LEU cc_start: 0.9387 (pp) cc_final: 0.8722 (tp) REVERT: C 41 ILE cc_start: 0.9272 (mm) cc_final: 0.9021 (mm) REVERT: C 45 VAL cc_start: 0.7575 (p) cc_final: 0.7136 (m) REVERT: C 200 MET cc_start: 0.8809 (ttt) cc_final: 0.8274 (tmm) REVERT: C 273 MET cc_start: 0.5133 (ptt) cc_final: 0.4765 (ptm) REVERT: C 305 ILE cc_start: 0.9293 (mm) cc_final: 0.8670 (mm) REVERT: C 309 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8198 (ptpt) REVERT: C 372 MET cc_start: 0.7919 (mmp) cc_final: 0.7563 (mmp) REVERT: C 435 TYR cc_start: 0.8159 (m-80) cc_final: 0.7598 (m-80) REVERT: C 536 ILE cc_start: 0.9050 (tp) cc_final: 0.8810 (tp) REVERT: C 722 ASP cc_start: 0.6916 (p0) cc_final: 0.6333 (p0) REVERT: D 73 ASP cc_start: 0.7408 (t70) cc_final: 0.7144 (t0) REVERT: D 174 ARG cc_start: 0.7607 (ptp-110) cc_final: 0.6878 (mtm-85) REVERT: D 179 MET cc_start: 0.7883 (mtt) cc_final: 0.7537 (mtt) REVERT: D 206 PHE cc_start: 0.6135 (p90) cc_final: 0.5648 (p90) REVERT: D 263 ASP cc_start: 0.7415 (p0) cc_final: 0.7078 (p0) REVERT: D 387 LEU cc_start: 0.9405 (pp) cc_final: 0.8724 (tp) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2661 time to fit residues: 155.6745 Evaluate side-chains 297 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 288 GLN ** 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 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17466 Z= 0.231 Angle : 0.775 10.668 23552 Z= 0.389 Chirality : 0.048 0.191 2704 Planarity : 0.005 0.068 3026 Dihedral : 6.086 31.123 2394 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.17), residues: 2242 helix: -1.67 (0.17), residues: 814 sheet: -1.79 (0.32), residues: 260 loop : -2.37 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 397 HIS 0.009 0.001 HIS A 69 PHE 0.030 0.002 PHE D 417 TYR 0.022 0.002 TYR A 283 ARG 0.009 0.000 ARG C 260 *********************** 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 386 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9157 (mm) cc_final: 0.8829 (mm) REVERT: A 200 MET cc_start: 0.8710 (ttt) cc_final: 0.8187 (tmm) REVERT: A 273 MET cc_start: 0.5276 (ptt) cc_final: 0.4892 (ptm) REVERT: A 305 ILE cc_start: 0.9209 (mm) cc_final: 0.8627 (mm) REVERT: A 309 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8257 (ptpt) REVERT: A 321 LEU cc_start: 0.8731 (pp) cc_final: 0.8156 (tp) REVERT: A 372 MET cc_start: 0.7921 (mmp) cc_final: 0.7553 (mmp) REVERT: A 497 MET cc_start: 0.9079 (mtt) cc_final: 0.8699 (mtp) REVERT: A 536 ILE cc_start: 0.9020 (tp) cc_final: 0.8806 (tp) REVERT: A 722 ASP cc_start: 0.6923 (p0) cc_final: 0.6375 (p0) REVERT: B 73 ASP cc_start: 0.7448 (t70) cc_final: 0.7193 (t0) REVERT: B 174 ARG cc_start: 0.7464 (ptp-110) cc_final: 0.6669 (mtm-85) REVERT: B 179 MET cc_start: 0.8167 (mtt) cc_final: 0.7593 (mtt) REVERT: B 206 PHE cc_start: 0.6369 (p90) cc_final: 0.5830 (p90) REVERT: B 263 ASP cc_start: 0.7406 (p0) cc_final: 0.6996 (p0) REVERT: B 387 LEU cc_start: 0.9438 (pp) cc_final: 0.8721 (tp) REVERT: B 451 GLN cc_start: 0.7705 (pt0) cc_final: 0.7422 (pt0) REVERT: C 41 ILE cc_start: 0.9287 (mm) cc_final: 0.9034 (mm) REVERT: C 45 VAL cc_start: 0.7537 (p) cc_final: 0.7078 (m) REVERT: C 200 MET cc_start: 0.8687 (ttt) cc_final: 0.8154 (tmm) REVERT: C 273 MET cc_start: 0.5099 (ptt) cc_final: 0.4743 (ptm) REVERT: C 305 ILE cc_start: 0.9259 (mm) cc_final: 0.8650 (mm) REVERT: C 309 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8164 (ptpt) REVERT: C 340 MET cc_start: 0.6674 (mmp) cc_final: 0.5850 (tpt) REVERT: C 372 MET cc_start: 0.7843 (mmp) cc_final: 0.7520 (mmp) REVERT: C 722 ASP cc_start: 0.6778 (p0) cc_final: 0.6177 (p0) REVERT: D 73 ASP cc_start: 0.7458 (t70) cc_final: 0.7119 (t0) REVERT: D 174 ARG cc_start: 0.7454 (ptp-110) cc_final: 0.6677 (mtm-85) REVERT: D 179 MET cc_start: 0.8253 (mtt) cc_final: 0.7452 (mtt) REVERT: D 206 PHE cc_start: 0.6153 (p90) cc_final: 0.5692 (p90) REVERT: D 263 ASP cc_start: 0.7277 (p0) cc_final: 0.6907 (p0) REVERT: D 387 LEU cc_start: 0.9355 (pp) cc_final: 0.8757 (tp) REVERT: D 389 ASN cc_start: 0.9172 (m-40) cc_final: 0.8770 (m-40) REVERT: D 417 PHE cc_start: 0.6268 (t80) cc_final: 0.5698 (t80) REVERT: D 423 SER cc_start: 0.8421 (t) cc_final: 0.8058 (t) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.2693 time to fit residues: 159.7075 Evaluate side-chains 295 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 138 optimal weight: 0.0770 chunk 148 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 B 156 GLN B 288 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 401 GLN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4340 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= 0.204 Angle : 0.777 11.158 23552 Z= 0.388 Chirality : 0.048 0.167 2704 Planarity : 0.005 0.067 3026 Dihedral : 5.873 28.271 2394 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.17), residues: 2242 helix: -1.66 (0.17), residues: 826 sheet: -1.50 (0.33), residues: 262 loop : -2.32 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 420 HIS 0.010 0.001 HIS C 69 PHE 0.024 0.002 PHE B 417 TYR 0.019 0.001 TYR C 283 ARG 0.006 0.000 ARG C 260 *********************** 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 407 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.371 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: 0.9111 (mm) cc_final: 0.8797 (mm) REVERT: A 200 MET cc_start: 0.8661 (ttt) cc_final: 0.7958 (tmm) REVERT: A 201 MET cc_start: 0.8892 (pmm) cc_final: 0.8552 (pmm) REVERT: A 273 MET cc_start: 0.5210 (ptt) cc_final: 0.4810 (ptm) REVERT: A 305 ILE cc_start: 0.9190 (mm) cc_final: 0.8619 (mm) REVERT: A 309 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8284 (ptpt) REVERT: A 321 LEU cc_start: 0.8696 (pp) cc_final: 0.8154 (tp) REVERT: A 372 MET cc_start: 0.7828 (mmp) cc_final: 0.7537 (mmp) REVERT: A 497 MET cc_start: 0.9019 (mtt) cc_final: 0.8533 (mtp) REVERT: A 554 MET cc_start: 0.8243 (tmm) cc_final: 0.7964 (tmm) REVERT: A 701 ASP cc_start: 0.8429 (p0) cc_final: 0.8183 (t0) REVERT: A 722 ASP cc_start: 0.6844 (p0) cc_final: 0.6343 (p0) REVERT: B 73 ASP cc_start: 0.7428 (t70) cc_final: 0.7169 (t0) REVERT: B 174 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.6696 (mtm-85) REVERT: B 179 MET cc_start: 0.8069 (mtt) cc_final: 0.7537 (mtt) REVERT: B 206 PHE cc_start: 0.6327 (p90) cc_final: 0.5863 (p90) REVERT: B 263 ASP cc_start: 0.7067 (p0) cc_final: 0.6674 (p0) REVERT: B 387 LEU cc_start: 0.9424 (pp) cc_final: 0.8760 (tp) REVERT: B 389 ASN cc_start: 0.9242 (m-40) cc_final: 0.8748 (m-40) REVERT: B 451 GLN cc_start: 0.7576 (pt0) cc_final: 0.7354 (pt0) REVERT: C 41 ILE cc_start: 0.9247 (mm) cc_final: 0.9005 (mm) REVERT: C 200 MET cc_start: 0.8630 (ttt) cc_final: 0.7956 (tmm) REVERT: C 201 MET cc_start: 0.8905 (pmm) cc_final: 0.8645 (pmm) REVERT: C 273 MET cc_start: 0.5301 (ptt) cc_final: 0.4882 (ptm) REVERT: C 305 ILE cc_start: 0.9182 (mm) cc_final: 0.8649 (mm) REVERT: C 309 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8218 (ptpt) REVERT: C 340 MET cc_start: 0.6758 (mmp) cc_final: 0.5845 (tpt) REVERT: C 372 MET cc_start: 0.7820 (mmp) cc_final: 0.7566 (mmp) REVERT: C 554 MET cc_start: 0.8243 (tmm) cc_final: 0.7990 (tmm) REVERT: C 555 MET cc_start: 0.8425 (tpt) cc_final: 0.7878 (mmm) REVERT: C 687 MET cc_start: 0.7571 (ttt) cc_final: 0.7371 (ttm) REVERT: C 701 ASP cc_start: 0.8386 (p0) cc_final: 0.8141 (t0) REVERT: C 708 LEU cc_start: 0.8443 (tt) cc_final: 0.8169 (mt) REVERT: C 722 ASP cc_start: 0.6935 (p0) cc_final: 0.6315 (p0) REVERT: D 73 ASP cc_start: 0.7147 (t70) cc_final: 0.6925 (t0) REVERT: D 174 ARG cc_start: 0.7488 (ptp-110) cc_final: 0.6786 (mtm-85) REVERT: D 179 MET cc_start: 0.8203 (mtt) cc_final: 0.7499 (mtt) REVERT: D 206 PHE cc_start: 0.6210 (p90) cc_final: 0.5767 (p90) REVERT: D 223 MET cc_start: 0.7127 (tpt) cc_final: 0.6884 (tpt) REVERT: D 263 ASP cc_start: 0.7066 (p0) cc_final: 0.6618 (p0) REVERT: D 318 MET cc_start: 0.9064 (ptp) cc_final: 0.8792 (ptp) REVERT: D 387 LEU cc_start: 0.9405 (pp) cc_final: 0.8666 (tp) REVERT: D 417 PHE cc_start: 0.6115 (t80) cc_final: 0.5795 (t80) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2604 time to fit residues: 162.5726 Evaluate side-chains 308 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.0370 chunk 190 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** 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 389 ASN D 418 ASN D 443 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17466 Z= 0.217 Angle : 0.774 10.968 23552 Z= 0.390 Chirality : 0.048 0.200 2704 Planarity : 0.005 0.068 3026 Dihedral : 5.796 27.301 2394 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.17), residues: 2242 helix: -1.55 (0.17), residues: 824 sheet: -1.55 (0.33), residues: 262 loop : -2.27 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 420 HIS 0.010 0.001 HIS A 69 PHE 0.027 0.002 PHE A 681 TYR 0.023 0.002 TYR A 283 ARG 0.008 0.001 ARG B 444 *********************** 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 379 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.097 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: 0.9082 (mm) cc_final: 0.8780 (mm) REVERT: A 200 MET cc_start: 0.8582 (ttt) cc_final: 0.8138 (tmm) REVERT: A 273 MET cc_start: 0.5119 (ptt) cc_final: 0.4786 (ptm) REVERT: A 295 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7965 (mmmm) REVERT: A 305 ILE cc_start: 0.9196 (mm) cc_final: 0.8627 (mm) REVERT: A 321 LEU cc_start: 0.8686 (pp) cc_final: 0.8126 (tp) REVERT: A 372 MET cc_start: 0.7918 (mmp) cc_final: 0.7672 (mmp) REVERT: A 507 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 722 ASP cc_start: 0.6779 (p0) cc_final: 0.6387 (p0) REVERT: B 73 ASP cc_start: 0.7516 (t70) cc_final: 0.7205 (t0) REVERT: B 174 ARG cc_start: 0.7498 (ptp-110) cc_final: 0.6876 (mtm-85) REVERT: B 206 PHE cc_start: 0.6359 (p90) cc_final: 0.5888 (p90) REVERT: B 263 ASP cc_start: 0.6932 (p0) cc_final: 0.6638 (p0) REVERT: B 387 LEU cc_start: 0.9409 (pp) cc_final: 0.8761 (tp) REVERT: B 451 GLN cc_start: 0.7669 (pt0) cc_final: 0.7333 (pt0) REVERT: C 41 ILE cc_start: 0.9220 (mm) cc_final: 0.8990 (mm) REVERT: C 200 MET cc_start: 0.8574 (ttt) cc_final: 0.8086 (tmm) REVERT: C 273 MET cc_start: 0.5246 (ptt) cc_final: 0.4887 (ptm) REVERT: C 305 ILE cc_start: 0.9214 (mm) cc_final: 0.8645 (mm) REVERT: C 309 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8207 (ptpt) REVERT: C 340 MET cc_start: 0.6674 (mmp) cc_final: 0.5671 (tpt) REVERT: C 372 MET cc_start: 0.7830 (mmp) cc_final: 0.7562 (mmp) REVERT: C 507 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 536 ILE cc_start: 0.9026 (tp) cc_final: 0.8768 (tp) REVERT: C 722 ASP cc_start: 0.6860 (p0) cc_final: 0.6277 (p0) REVERT: D 174 ARG cc_start: 0.7481 (ptp-110) cc_final: 0.7236 (ptp-110) REVERT: D 179 MET cc_start: 0.8006 (mtt) cc_final: 0.7319 (mtt) REVERT: D 206 PHE cc_start: 0.6034 (p90) cc_final: 0.5710 (p90) REVERT: D 263 ASP cc_start: 0.6881 (p0) cc_final: 0.6572 (p0) REVERT: D 387 LEU cc_start: 0.9381 (pp) cc_final: 0.8777 (tp) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.2664 time to fit residues: 155.4533 Evaluate side-chains 299 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 186 GLN A 456 HIS A 753 HIS B 156 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** 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 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 443 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17466 Z= 0.272 Angle : 0.808 10.688 23552 Z= 0.407 Chirality : 0.049 0.203 2704 Planarity : 0.005 0.065 3026 Dihedral : 5.855 27.351 2394 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.53 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.17), residues: 2242 helix: -1.49 (0.17), residues: 838 sheet: -1.86 (0.32), residues: 250 loop : -2.22 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 420 HIS 0.010 0.001 HIS C 69 PHE 0.025 0.002 PHE D 125 TYR 0.023 0.002 TYR C 283 ARG 0.006 0.001 ARG C 279 ********************** 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 363 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9104 (mm) cc_final: 0.8801 (mm) REVERT: A 76 MET cc_start: 0.7498 (mpp) cc_final: 0.6825 (mpp) REVERT: A 200 MET cc_start: 0.8783 (ttt) cc_final: 0.8197 (tmm) REVERT: A 273 MET cc_start: 0.5259 (ptt) cc_final: 0.4915 (ptm) REVERT: A 321 LEU cc_start: 0.8613 (pp) cc_final: 0.8035 (tp) REVERT: A 340 MET cc_start: 0.6807 (mmp) cc_final: 0.5986 (tpt) REVERT: A 372 MET cc_start: 0.7885 (mmp) cc_final: 0.7666 (mmp) REVERT: A 507 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 536 ILE cc_start: 0.8894 (tp) cc_final: 0.8633 (tp) REVERT: A 555 MET cc_start: 0.8392 (mmm) cc_final: 0.8031 (mmm) REVERT: A 722 ASP cc_start: 0.6851 (p0) cc_final: 0.6457 (p0) REVERT: B 73 ASP cc_start: 0.7605 (t70) cc_final: 0.7313 (t0) REVERT: B 174 ARG cc_start: 0.7303 (ptp-110) cc_final: 0.6654 (mtm-85) REVERT: B 179 MET cc_start: 0.8244 (mtt) cc_final: 0.7636 (mtt) REVERT: B 206 PHE cc_start: 0.6356 (p90) cc_final: 0.5865 (p90) REVERT: B 223 MET cc_start: 0.7070 (tpt) cc_final: 0.6797 (tpt) REVERT: B 263 ASP cc_start: 0.7293 (p0) cc_final: 0.6885 (p0) REVERT: B 387 LEU cc_start: 0.9433 (pp) cc_final: 0.8810 (tp) REVERT: C 41 ILE cc_start: 0.9242 (mm) cc_final: 0.9025 (mm) REVERT: C 130 LEU cc_start: 0.8440 (pt) cc_final: 0.8181 (pp) REVERT: C 200 MET cc_start: 0.8572 (ttt) cc_final: 0.7914 (tmm) REVERT: C 273 MET cc_start: 0.5372 (ptt) cc_final: 0.5012 (ptm) REVERT: C 295 LYS cc_start: 0.8242 (mmmt) cc_final: 0.8005 (mmmm) REVERT: C 305 ILE cc_start: 0.9222 (mm) cc_final: 0.8832 (mm) REVERT: C 309 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8230 (ptpt) REVERT: C 340 MET cc_start: 0.6788 (mmp) cc_final: 0.5867 (tpt) REVERT: C 372 MET cc_start: 0.7881 (mmp) cc_final: 0.7617 (mmp) REVERT: C 507 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 536 ILE cc_start: 0.9100 (tp) cc_final: 0.8844 (tp) REVERT: C 687 MET cc_start: 0.7601 (ttt) cc_final: 0.7276 (ttm) REVERT: C 722 ASP cc_start: 0.6846 (p0) cc_final: 0.6389 (p0) REVERT: D 73 ASP cc_start: 0.7439 (t70) cc_final: 0.7211 (t0) REVERT: D 174 ARG cc_start: 0.7548 (ptp-110) cc_final: 0.6929 (mtm-85) REVERT: D 179 MET cc_start: 0.8187 (mtt) cc_final: 0.7469 (mtt) REVERT: D 206 PHE cc_start: 0.6188 (p90) cc_final: 0.5752 (p90) REVERT: D 223 MET cc_start: 0.7216 (tpt) cc_final: 0.6970 (tpt) REVERT: D 263 ASP cc_start: 0.7080 (p0) cc_final: 0.6644 (p0) REVERT: D 288 GLN cc_start: 0.8298 (mm110) cc_final: 0.8095 (pt0) REVERT: D 387 LEU cc_start: 0.9437 (pp) cc_final: 0.8796 (tp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2604 time to fit residues: 146.7132 Evaluate side-chains 292 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.0370 chunk 165 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 456 HIS B 156 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106739 restraints weight = 35771.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107900 restraints weight = 27566.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109038 restraints weight = 21530.766| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17466 Z= 0.226 Angle : 0.799 11.164 23552 Z= 0.399 Chirality : 0.049 0.192 2704 Planarity : 0.005 0.067 3026 Dihedral : 5.752 26.288 2394 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 2242 helix: -1.42 (0.17), residues: 842 sheet: -1.74 (0.32), residues: 250 loop : -2.20 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 420 HIS 0.011 0.001 HIS A 69 PHE 0.028 0.002 PHE C 718 TYR 0.019 0.002 TYR C 283 ARG 0.006 0.000 ARG C 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3738.85 seconds wall clock time: 67 minutes 42.87 seconds (4062.87 seconds total)