Starting phenix.real_space_refine on Fri Mar 6 00:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btq_30182/03_2026/7btq_30182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btq_30182/03_2026/7btq_30182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7btq_30182/03_2026/7btq_30182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btq_30182/03_2026/7btq_30182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7btq_30182/03_2026/7btq_30182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btq_30182/03_2026/7btq_30182.map" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8103 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 37 5.16 5 C 12762 2.51 5 N 3439 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20419 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3740 Classifications: {'peptide': 474} Link IDs: {'CIS': 21, 'PTRANS': 13, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 906 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain: "C" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 892 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain: "D" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3740 Classifications: {'peptide': 474} Link IDs: {'CIS': 21, 'PTRANS': 13, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "F" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8042 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 955} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 3.89, per 1000 atoms: 0.19 Number of scatterers: 20419 At special positions: 0 Unit cell: (147.15, 166.05, 128.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 86 15.00 O 4095 8.00 N 3439 7.00 C 12762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 851.2 milliseconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 45.3% alpha, 6.5% beta 42 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 28 through 54 removed outlier: 3.891A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.818A pdb=" N SER A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.677A pdb=" N SER A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 256 through 270 removed outlier: 4.035A pdb=" N HIS A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.878A pdb=" N ASP A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 4.083A pdb=" N VAL A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.140A pdb=" N GLU A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.921A pdb=" N SER A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 482 through 507 removed outlier: 4.230A pdb=" N ILE A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 28 through 54 removed outlier: 3.891A pdb=" N PHE D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR D 35 " --> pdb=" O ASP D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 86 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 115 through 121 removed outlier: 3.817A pdb=" N SER D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 163 Processing helix chain 'D' and resid 178 through 187 Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.677A pdb=" N SER D 206 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 241 Processing helix chain 'D' and resid 256 through 270 removed outlier: 4.034A pdb=" N HIS D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.878A pdb=" N ASP D 320 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 removed outlier: 4.084A pdb=" N VAL D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR D 346 " --> pdb=" O HIS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 376 removed outlier: 4.141A pdb=" N GLU D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.921A pdb=" N SER D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 482 through 507 removed outlier: 4.229A pdb=" N ILE D 499 " --> pdb=" O THR D 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.725A pdb=" N ASN E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 4.345A pdb=" N LYS E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 191 removed outlier: 3.996A pdb=" N ILE E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.791A pdb=" N VAL E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 326 removed outlier: 3.551A pdb=" N ILE E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER E 320 " --> pdb=" O GLY E 316 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP E 321 " --> pdb=" O SER E 317 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.672A pdb=" N LEU E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.747A pdb=" N ARG E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 394 removed outlier: 4.163A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 48 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.507A pdb=" N MET F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 61 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 95 through 105 removed outlier: 3.519A pdb=" N LYS F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 218 through 226 removed outlier: 4.059A pdb=" N SER F 222 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE F 223 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP F 224 " --> pdb=" O ASN F 221 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR F 226 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 Processing helix chain 'F' and resid 249 through 260 removed outlier: 3.739A pdb=" N ASN F 255 " --> pdb=" O HIS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 293 removed outlier: 3.903A pdb=" N ILE F 277 " --> pdb=" O ARG F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.969A pdb=" N THR F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 4.600A pdb=" N TYR F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 373 Processing helix chain 'F' and resid 383 through 393 Processing helix chain 'F' and resid 396 through 401 removed outlier: 3.619A pdb=" N TYR F 399 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN F 400 " --> pdb=" O PRO F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 425 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 462 through 469 removed outlier: 4.028A pdb=" N ALA F 466 " --> pdb=" O VAL F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 491 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'F' and resid 509 through 528 removed outlier: 5.214A pdb=" N ARG F 525 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN F 526 " --> pdb=" O ASN F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 569 removed outlier: 3.572A pdb=" N ALA F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA F 555 " --> pdb=" O LYS F 551 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER F 568 " --> pdb=" O ALA F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 624 removed outlier: 4.434A pdb=" N PHE F 611 " --> pdb=" O SER F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 647 removed outlier: 3.550A pdb=" N ASN F 636 " --> pdb=" O ASN F 632 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS F 646 " --> pdb=" O ALA F 642 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN F 647 " --> pdb=" O GLN F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 687 Processing helix chain 'F' and resid 708 through 720 Processing helix chain 'F' and resid 721 through 729 removed outlier: 4.080A pdb=" N LYS F 725 " --> pdb=" O ASP F 721 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 738 Processing helix chain 'F' and resid 751 through 763 removed outlier: 3.614A pdb=" N PHE F 763 " --> pdb=" O LEU F 759 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 793 Processing helix chain 'F' and resid 795 through 804 Processing helix chain 'F' and resid 811 through 822 Processing helix chain 'F' and resid 825 through 835 removed outlier: 3.999A pdb=" N GLU F 831 " --> pdb=" O GLU F 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 857 Processing helix chain 'F' and resid 879 through 885 removed outlier: 3.545A pdb=" N LEU F 883 " --> pdb=" O GLU F 879 " (cutoff:3.500A) Processing helix chain 'F' and resid 890 through 900 Processing helix chain 'F' and resid 911 through 921 removed outlier: 3.758A pdb=" N LYS F 915 " --> pdb=" O ILE F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 926 No H-bonds generated for 'chain 'F' and resid 924 through 926' Processing helix chain 'F' and resid 927 through 936 removed outlier: 3.953A pdb=" N VAL F 931 " --> pdb=" O LYS F 927 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 932 " --> pdb=" O GLU F 928 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 972 removed outlier: 3.516A pdb=" N ALA F 967 " --> pdb=" O ARG F 963 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU F 972 " --> pdb=" O LEU F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 975 through 990 Processing helix chain 'F' and resid 998 through 1002 Processing helix chain 'F' and resid 1016 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254 removed outlier: 3.636A pdb=" N GLU A 254 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 357 Processing sheet with id=AA3, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.636A pdb=" N GLU D 254 " --> pdb=" O LYS D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AA5, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AA6, first strand: chain 'E' and resid 26 through 28 removed outlier: 4.113A pdb=" N LYS E 99 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 202 through 205 removed outlier: 3.960A pdb=" N GLU E 202 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 250 through 251 Processing sheet with id=AA9, first strand: chain 'E' and resid 284 through 287 removed outlier: 3.650A pdb=" N ALA E 285 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 270 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 50 through 51 removed outlier: 6.047A pdb=" N GLU F 50 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLN F 138 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 162 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL F 156 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 109 through 113 Processing sheet with id=AB3, first strand: chain 'F' and resid 261 through 262 Processing sheet with id=AB4, first strand: chain 'F' and resid 379 through 382 removed outlier: 3.999A pdb=" N VAL F 337 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 435 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS F 307 " --> pdb=" O THR F 435 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR F 304 " --> pdb=" O LEU F 458 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER F 460 " --> pdb=" O TYR F 304 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP F 306 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 474 through 479 removed outlier: 6.735A pdb=" N LYS F 474 " --> pdb=" O GLY F 700 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE F 702 " --> pdb=" O LYS F 474 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS F 476 " --> pdb=" O ILE F 702 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR F 704 " --> pdb=" O LYS F 476 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP F 478 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN F 669 " --> pdb=" O ASN F 701 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL F 703 " --> pdb=" O ASN F 669 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU F 671 " --> pdb=" O VAL F 703 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN F 539 " --> pdb=" O THR F 670 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE F 672 " --> pdb=" O ASN F 539 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET F 541 " --> pdb=" O PHE F 672 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASP F 674 " --> pdb=" O MET F 541 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA F 543 " --> pdb=" O ASP F 674 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA F 540 " --> pdb=" O LEU F 653 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL F 655 " --> pdb=" O ALA F 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 542 " --> pdb=" O VAL F 655 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA F 577 " --> pdb=" O ILE F 654 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 740 through 741 732 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5953 1.34 - 1.46: 5030 1.46 - 1.58: 9793 1.58 - 1.70: 171 1.70 - 1.82: 65 Bond restraints: 21012 Sorted by residual: bond pdb=" O3' DT C -6 " pdb=" P DC C -5 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.85e+00 bond pdb=" CA ASN A 429 " pdb=" C ASN A 429 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.10e-02 2.27e+03 5.49e+00 bond pdb=" CA ASN D 429 " pdb=" C ASN D 429 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.10e-02 2.27e+03 5.34e+00 bond pdb=" CA LEU F 809 " pdb=" CB LEU F 809 " ideal model delta sigma weight residual 1.526 1.564 -0.038 1.70e-02 3.46e+03 4.97e+00 bond pdb=" C1' DC B 27 " pdb=" N1 DC B 27 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.87e+00 ... (remaining 21007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 27880 3.08 - 6.16: 758 6.16 - 9.23: 119 9.23 - 12.31: 26 12.31 - 15.39: 9 Bond angle restraints: 28792 Sorted by residual: angle pdb=" O3' DT C 12 " pdb=" C3' DT C 12 " pdb=" C2' DT C 12 " ideal model delta sigma weight residual 111.50 100.23 11.27 1.50e+00 4.44e-01 5.64e+01 angle pdb=" C ASN D 427 " pdb=" N ASN D 428 " pdb=" CA ASN D 428 " ideal model delta sigma weight residual 121.70 134.39 -12.69 1.80e+00 3.09e-01 4.97e+01 angle pdb=" C ASN A 427 " pdb=" N ASN A 428 " pdb=" CA ASN A 428 " ideal model delta sigma weight residual 121.70 134.36 -12.66 1.80e+00 3.09e-01 4.95e+01 angle pdb=" C4' DT B 4 " pdb=" C3' DT B 4 " pdb=" O3' DT B 4 " ideal model delta sigma weight residual 110.00 100.25 9.75 1.50e+00 4.44e-01 4.22e+01 angle pdb=" C THR D 395 " pdb=" N THR D 396 " pdb=" CA THR D 396 " ideal model delta sigma weight residual 121.70 133.18 -11.48 1.80e+00 3.09e-01 4.06e+01 ... (remaining 28787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 11773 34.72 - 69.43: 598 69.43 - 104.15: 26 104.15 - 138.86: 1 138.86 - 173.58: 3 Dihedral angle restraints: 12401 sinusoidal: 5560 harmonic: 6841 Sorted by residual: dihedral pdb=" CA ASP F 28 " pdb=" C ASP F 28 " pdb=" N SER F 29 " pdb=" CA SER F 29 " ideal model delta harmonic sigma weight residual 180.00 -137.21 -42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA LEU F 729 " pdb=" C LEU F 729 " pdb=" N GLU F 730 " pdb=" CA GLU F 730 " ideal model delta harmonic sigma weight residual -180.00 -141.99 -38.01 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA HIS E 303 " pdb=" C HIS E 303 " pdb=" N GLU E 304 " pdb=" CA GLU E 304 " ideal model delta harmonic sigma weight residual 180.00 145.60 34.40 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 12398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2544 0.070 - 0.139: 558 0.139 - 0.209: 84 0.209 - 0.278: 10 0.278 - 0.348: 4 Chirality restraints: 3200 Sorted by residual: chirality pdb=" CB ILE E 277 " pdb=" CA ILE E 277 " pdb=" CG1 ILE E 277 " pdb=" CG2 ILE E 277 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE D 361 " pdb=" CA ILE D 361 " pdb=" CG1 ILE D 361 " pdb=" CG2 ILE D 361 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3197 not shown) Planarity restraints: 3412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 117 " 0.026 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP E 117 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP E 117 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP E 117 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 117 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 117 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP E 117 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 117 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 117 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 117 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F1007 " 0.058 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO F1008 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO F1008 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F1008 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 46 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO E 47 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " -0.045 5.00e-02 4.00e+02 ... (remaining 3409 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 1 1.98 - 2.71: 1028 2.71 - 3.44: 29154 3.44 - 4.17: 49655 4.17 - 4.90: 81308 Nonbonded interactions: 161146 Sorted by model distance: nonbonded pdb=" O THR A 395 " pdb=" OP2 DT B 3 " model vdw 1.250 3.040 nonbonded pdb=" O GLY A 131 " pdb=" OH TYR A 274 " model vdw 2.234 3.040 nonbonded pdb=" O GLY D 131 " pdb=" OH TYR D 274 " model vdw 2.234 3.040 nonbonded pdb=" O LYS D 493 " pdb=" OG SER D 497 " model vdw 2.275 3.040 nonbonded pdb=" O LYS A 493 " pdb=" OG SER A 497 " model vdw 2.276 3.040 ... (remaining 161141 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 '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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.006 0.082 21012 Z= 0.283 Angle : 1.226 15.389 28792 Z= 0.690 Chirality : 0.059 0.348 3200 Planarity : 0.007 0.086 3412 Dihedral : 17.584 173.577 7967 Min Nonbonded Distance : 1.250 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 0.85 % Allowed : 4.69 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 2.99 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.13), residues: 2296 helix: -2.33 (0.12), residues: 979 sheet: -1.60 (0.35), residues: 190 loop : -4.11 (0.14), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 377 TYR 0.047 0.003 TYR F 553 PHE 0.033 0.003 PHE A 422 TRP 0.059 0.004 TRP E 117 HIS 0.016 0.002 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00590 (21012) covalent geometry : angle 1.22602 (28792) hydrogen bonds : bond 0.11694 ( 831) hydrogen bonds : angle 6.96709 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 416 time to evaluate : 0.720 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8907 (t0) cc_final: 0.8692 (t0) REVERT: A 267 MET cc_start: 0.7991 (ptt) cc_final: 0.7613 (ptt) REVERT: A 341 LEU cc_start: 0.9480 (mt) cc_final: 0.9194 (mt) REVERT: A 371 ILE cc_start: 0.9360 (mm) cc_final: 0.9092 (mm) REVERT: A 397 ILE cc_start: 0.8951 (pt) cc_final: 0.8731 (tt) REVERT: A 488 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8434 (pt) REVERT: A 498 LYS cc_start: 0.8833 (mptp) cc_final: 0.8271 (tptt) REVERT: D 117 GLU cc_start: 0.7822 (pp20) cc_final: 0.7381 (tt0) REVERT: D 150 LYS cc_start: 0.9201 (mttt) cc_final: 0.8888 (pttt) REVERT: D 222 LYS cc_start: 0.7908 (mttt) cc_final: 0.7369 (mttt) REVERT: D 277 PHE cc_start: 0.7133 (t80) cc_final: 0.6855 (t80) REVERT: D 385 ILE cc_start: 0.9368 (mp) cc_final: 0.9074 (mm) REVERT: D 412 ASN cc_start: 0.8965 (m-40) cc_final: 0.8653 (t0) REVERT: D 413 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7861 (m) REVERT: D 493 LYS cc_start: 0.9241 (mptt) cc_final: 0.8975 (mmtp) REVERT: D 504 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8886 (tptt) REVERT: E 84 ASN cc_start: 0.7835 (t0) cc_final: 0.6971 (t0) REVERT: E 86 TRP cc_start: 0.6971 (m100) cc_final: 0.6609 (m100) REVERT: E 132 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7727 (mmm160) REVERT: E 175 LEU cc_start: 0.9695 (mt) cc_final: 0.9155 (mt) REVERT: E 297 MET cc_start: 0.9215 (ptm) cc_final: 0.7616 (ptt) REVERT: E 314 MET cc_start: 0.8993 (tpt) cc_final: 0.8688 (tpp) REVERT: E 346 ILE cc_start: 0.9563 (pt) cc_final: 0.9296 (mp) REVERT: E 380 GLU cc_start: 0.8992 (pm20) cc_final: 0.8785 (pm20) REVERT: F 225 PHE cc_start: 0.8271 (m-10) cc_final: 0.7920 (m-10) REVERT: F 261 SER cc_start: 0.9116 (m) cc_final: 0.8512 (p) REVERT: F 298 LYS cc_start: 0.9161 (mttt) cc_final: 0.8780 (mttp) REVERT: F 332 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8004 (mmtp) REVERT: F 390 MET cc_start: 0.8589 (mmp) cc_final: 0.8265 (tpp) REVERT: F 391 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8177 (mmmt) REVERT: F 511 MET cc_start: 0.8666 (mmm) cc_final: 0.8303 (mmm) REVERT: F 636 ASN cc_start: 0.8945 (m-40) cc_final: 0.8438 (p0) REVERT: F 668 LEU cc_start: 0.9319 (tt) cc_final: 0.9058 (tt) REVERT: F 792 LEU cc_start: 0.9591 (mt) cc_final: 0.9328 (mt) REVERT: F 797 GLU cc_start: 0.9513 (mp0) cc_final: 0.9052 (mp0) outliers start: 17 outliers final: 4 residues processed: 430 average time/residue: 0.1682 time to fit residues: 105.5586 Evaluate side-chains 216 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.0010 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.0170 overall best weight: 2.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 435 HIS D 102 ASN D 204 HIS D 435 HIS ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS E 313 HIS E 385 GLN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 72 ASN F 91 ASN F 104 HIS F 178 ASN F 179 GLN F 251 HIS F 522 ASN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 GLN F 622 HIS F 626 ASN F 648 GLN ** F 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 805 GLN F 822 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056460 restraints weight = 115081.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.057981 restraints weight = 73796.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059080 restraints weight = 53514.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059804 restraints weight = 42166.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060386 restraints weight = 35504.221| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 21012 Z= 0.161 Angle : 0.779 11.904 28792 Z= 0.418 Chirality : 0.046 0.366 3200 Planarity : 0.005 0.089 3412 Dihedral : 20.874 172.667 3488 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.25 % Allowed : 3.19 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.16), residues: 2296 helix: -0.50 (0.15), residues: 963 sheet: -1.09 (0.37), residues: 189 loop : -3.68 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 854 TYR 0.024 0.002 TYR A 188 PHE 0.027 0.002 PHE D 422 TRP 0.023 0.002 TRP D 17 HIS 0.008 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00342 (21012) covalent geometry : angle 0.77878 (28792) hydrogen bonds : bond 0.04016 ( 831) hydrogen bonds : angle 5.15792 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 285 time to evaluate : 0.801 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8865 (t0) cc_final: 0.8426 (t0) REVERT: A 260 TYR cc_start: 0.8316 (t80) cc_final: 0.7887 (t80) REVERT: A 268 PHE cc_start: 0.8682 (t80) cc_final: 0.8380 (t80) REVERT: A 337 PHE cc_start: 0.9013 (m-80) cc_final: 0.8752 (m-80) REVERT: A 397 ILE cc_start: 0.9054 (pt) cc_final: 0.8787 (tt) REVERT: A 480 ARG cc_start: 0.8406 (tpp80) cc_final: 0.8042 (tpp80) REVERT: A 488 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8527 (pt) REVERT: A 498 LYS cc_start: 0.8913 (mptt) cc_final: 0.8692 (mmmt) REVERT: D 116 ILE cc_start: 0.8604 (mp) cc_final: 0.8163 (tp) REVERT: D 150 LYS cc_start: 0.9201 (mttt) cc_final: 0.8853 (pttt) REVERT: D 222 LYS cc_start: 0.7986 (mttt) cc_final: 0.7423 (mttt) REVERT: D 362 PHE cc_start: 0.4251 (t80) cc_final: 0.4047 (t80) REVERT: D 412 ASN cc_start: 0.9123 (m-40) cc_final: 0.8796 (t0) REVERT: D 459 GLU cc_start: 0.8721 (mp0) cc_final: 0.8510 (mp0) REVERT: D 493 LYS cc_start: 0.9366 (mptt) cc_final: 0.9143 (mmtm) REVERT: D 504 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8997 (tptt) REVERT: E 84 ASN cc_start: 0.7499 (t0) cc_final: 0.6504 (t0) REVERT: E 86 TRP cc_start: 0.6949 (m100) cc_final: 0.6405 (m100) REVERT: E 100 MET cc_start: 0.7538 (mpp) cc_final: 0.7070 (mpp) REVERT: E 130 HIS cc_start: 0.8403 (p90) cc_final: 0.8151 (p90) REVERT: E 295 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.9000 (mp10) REVERT: E 297 MET cc_start: 0.8839 (ptm) cc_final: 0.7755 (ptp) REVERT: E 314 MET cc_start: 0.9060 (tpt) cc_final: 0.8749 (tpp) REVERT: F 78 ASP cc_start: 0.8283 (m-30) cc_final: 0.8069 (t70) REVERT: F 225 PHE cc_start: 0.8442 (m-10) cc_final: 0.8124 (m-80) REVERT: F 261 SER cc_start: 0.9087 (m) cc_final: 0.8664 (p) REVERT: F 267 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7845 (tm-30) REVERT: F 332 LYS cc_start: 0.8224 (mmmt) cc_final: 0.8022 (mmtp) REVERT: F 390 MET cc_start: 0.8506 (mmp) cc_final: 0.8244 (ptp) REVERT: F 391 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8579 (mmmt) REVERT: F 469 ASP cc_start: 0.9235 (t0) cc_final: 0.8812 (m-30) REVERT: F 511 MET cc_start: 0.8749 (mmm) cc_final: 0.8490 (tpp) REVERT: F 668 LEU cc_start: 0.9372 (tt) cc_final: 0.9145 (tp) REVERT: F 688 ARG cc_start: 0.8804 (mmp80) cc_final: 0.8452 (tpp80) REVERT: F 1020 VAL cc_start: 0.9500 (p) cc_final: 0.9199 (m) REVERT: F 1029 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8926 (mt-10) outliers start: 5 outliers final: 1 residues processed: 290 average time/residue: 0.1699 time to fit residues: 74.3396 Evaluate side-chains 172 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 133 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 chunk 149 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN E 84 ASN E 385 GLN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN ** F 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.071079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057417 restraints weight = 112883.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058972 restraints weight = 72809.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060061 restraints weight = 52819.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060820 restraints weight = 41651.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061378 restraints weight = 34873.595| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21012 Z= 0.136 Angle : 0.730 10.878 28792 Z= 0.390 Chirality : 0.044 0.311 3200 Planarity : 0.005 0.094 3412 Dihedral : 20.628 175.659 3488 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.17), residues: 2296 helix: 0.06 (0.16), residues: 982 sheet: -0.91 (0.37), residues: 196 loop : -3.45 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 352 TYR 0.018 0.002 TYR A 188 PHE 0.037 0.001 PHE D 422 TRP 0.017 0.001 TRP A 17 HIS 0.009 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00293 (21012) covalent geometry : angle 0.73047 (28792) hydrogen bonds : bond 0.03338 ( 831) hydrogen bonds : angle 4.81711 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.786 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6568 (tm-30) REVERT: A 256 ASN cc_start: 0.8916 (t0) cc_final: 0.8446 (t0) REVERT: A 267 MET cc_start: 0.8343 (ppp) cc_final: 0.7588 (ppp) REVERT: A 269 LEU cc_start: 0.9435 (mt) cc_final: 0.9155 (mp) REVERT: A 287 GLU cc_start: 0.7999 (mp0) cc_final: 0.7488 (mp0) REVERT: A 309 TRP cc_start: 0.6979 (p-90) cc_final: 0.5803 (p-90) REVERT: A 337 PHE cc_start: 0.8989 (m-80) cc_final: 0.8702 (m-80) REVERT: A 397 ILE cc_start: 0.8852 (pt) cc_final: 0.8537 (tt) REVERT: A 480 ARG cc_start: 0.8355 (tpp80) cc_final: 0.8005 (tpp80) REVERT: A 498 LYS cc_start: 0.8932 (mptt) cc_final: 0.8648 (mmmt) REVERT: D 43 ARG cc_start: 0.8959 (ttt180) cc_final: 0.8327 (ttt180) REVERT: D 116 ILE cc_start: 0.8575 (mp) cc_final: 0.8146 (tp) REVERT: D 141 ASN cc_start: 0.7808 (t0) cc_final: 0.7555 (t0) REVERT: D 150 LYS cc_start: 0.9183 (mttt) cc_final: 0.8799 (pttt) REVERT: D 222 LYS cc_start: 0.8013 (mttt) cc_final: 0.7483 (mttt) REVERT: D 412 ASN cc_start: 0.9084 (m-40) cc_final: 0.8771 (t0) REVERT: D 459 GLU cc_start: 0.8768 (mp0) cc_final: 0.8547 (mp0) REVERT: D 493 LYS cc_start: 0.9302 (mptt) cc_final: 0.9087 (mmtm) REVERT: D 504 LYS cc_start: 0.9270 (ttmt) cc_final: 0.8998 (tptt) REVERT: E 70 SER cc_start: 0.7258 (m) cc_final: 0.6920 (t) REVERT: E 84 ASN cc_start: 0.7715 (t0) cc_final: 0.6457 (t0) REVERT: E 86 TRP cc_start: 0.6790 (m100) cc_final: 0.6209 (m100) REVERT: E 100 MET cc_start: 0.7487 (mpp) cc_final: 0.6978 (mpp) REVERT: E 132 ARG cc_start: 0.8398 (tpt170) cc_final: 0.7491 (tpt-90) REVERT: E 175 LEU cc_start: 0.9619 (mt) cc_final: 0.9253 (mt) REVERT: E 239 MET cc_start: 0.9286 (mmm) cc_final: 0.9039 (tmm) REVERT: E 297 MET cc_start: 0.8643 (ptm) cc_final: 0.7496 (ptp) REVERT: F 78 ASP cc_start: 0.8392 (m-30) cc_final: 0.8150 (t70) REVERT: F 225 PHE cc_start: 0.8318 (m-10) cc_final: 0.7854 (m-10) REVERT: F 267 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7732 (tm-30) REVERT: F 332 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8045 (mmtp) REVERT: F 347 MET cc_start: 0.8913 (tmm) cc_final: 0.8612 (mmp) REVERT: F 469 ASP cc_start: 0.9151 (t0) cc_final: 0.8727 (m-30) REVERT: F 470 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 668 LEU cc_start: 0.9322 (tt) cc_final: 0.9121 (tp) REVERT: F 683 MET cc_start: 0.8867 (tmm) cc_final: 0.8625 (tmm) REVERT: F 688 ARG cc_start: 0.8749 (mmp80) cc_final: 0.8394 (tpp80) REVERT: F 708 LEU cc_start: 0.8847 (mt) cc_final: 0.8643 (mm) REVERT: F 714 ASP cc_start: 0.9005 (m-30) cc_final: 0.8768 (t0) REVERT: F 753 MET cc_start: 0.9189 (mmt) cc_final: 0.8882 (mmm) REVERT: F 879 GLU cc_start: 0.8035 (tp30) cc_final: 0.7354 (tm-30) REVERT: F 1029 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8985 (mp0) outliers start: 3 outliers final: 2 residues processed: 270 average time/residue: 0.1570 time to fit residues: 65.3284 Evaluate side-chains 176 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 88 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 230 optimal weight: 0.4980 chunk 120 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 270 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 479 ASN E 385 GLN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN F 643 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.065897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052489 restraints weight = 118501.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053904 restraints weight = 76368.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054921 restraints weight = 55831.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055644 restraints weight = 44310.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056140 restraints weight = 37300.635| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21012 Z= 0.219 Angle : 0.800 12.076 28792 Z= 0.431 Chirality : 0.046 0.255 3200 Planarity : 0.005 0.087 3412 Dihedral : 20.812 177.648 3488 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.17), residues: 2296 helix: 0.18 (0.16), residues: 986 sheet: -1.06 (0.36), residues: 190 loop : -3.48 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 274 TYR 0.040 0.002 TYR E 113 PHE 0.039 0.002 PHE D 422 TRP 0.014 0.002 TRP A 17 HIS 0.010 0.002 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00463 (21012) covalent geometry : angle 0.79987 (28792) hydrogen bonds : bond 0.04543 ( 831) hydrogen bonds : angle 4.95973 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.283 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8303 (mmpt) cc_final: 0.8062 (mmmt) REVERT: A 254 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6506 (tm-30) REVERT: A 256 ASN cc_start: 0.9142 (t0) cc_final: 0.8522 (t0) REVERT: A 267 MET cc_start: 0.8509 (ppp) cc_final: 0.8001 (ppp) REVERT: A 278 ASP cc_start: 0.8024 (p0) cc_final: 0.7596 (p0) REVERT: A 287 GLU cc_start: 0.8442 (mp0) cc_final: 0.8205 (mp0) REVERT: A 397 ILE cc_start: 0.9200 (pt) cc_final: 0.8983 (tt) REVERT: A 480 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8153 (tpp80) REVERT: A 484 ASP cc_start: 0.8844 (m-30) cc_final: 0.8207 (p0) REVERT: D 116 ILE cc_start: 0.8687 (mp) cc_final: 0.8376 (tp) REVERT: D 150 LYS cc_start: 0.9263 (mttt) cc_final: 0.8874 (pttt) REVERT: D 222 LYS cc_start: 0.7835 (mttt) cc_final: 0.7323 (mttt) REVERT: D 412 ASN cc_start: 0.9218 (m-40) cc_final: 0.8774 (t0) REVERT: D 459 GLU cc_start: 0.8719 (mp0) cc_final: 0.8488 (mp0) REVERT: D 493 LYS cc_start: 0.9357 (mptt) cc_final: 0.9093 (mmtm) REVERT: E 77 PHE cc_start: 0.8086 (m-10) cc_final: 0.7691 (m-10) REVERT: E 84 ASN cc_start: 0.7607 (t0) cc_final: 0.6477 (t0) REVERT: E 86 TRP cc_start: 0.7053 (m100) cc_final: 0.6395 (m100) REVERT: E 100 MET cc_start: 0.7823 (mpp) cc_final: 0.7311 (mpp) REVERT: E 134 TRP cc_start: 0.6041 (m100) cc_final: 0.5806 (m100) REVERT: E 239 MET cc_start: 0.9335 (mmm) cc_final: 0.9105 (tpt) REVERT: E 297 MET cc_start: 0.8683 (ptm) cc_final: 0.7372 (ptt) REVERT: E 298 LYS cc_start: 0.8510 (mmpt) cc_final: 0.8279 (mmmt) REVERT: E 364 PHE cc_start: 0.8946 (m-80) cc_final: 0.8737 (m-80) REVERT: F 60 MET cc_start: 0.8859 (mtm) cc_final: 0.8656 (mtt) REVERT: F 78 ASP cc_start: 0.8457 (m-30) cc_final: 0.8011 (t0) REVERT: F 225 PHE cc_start: 0.8409 (m-10) cc_final: 0.7796 (m-10) REVERT: F 267 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7855 (tm-30) REVERT: F 470 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8254 (tm-30) REVERT: F 676 ASN cc_start: 0.7932 (t0) cc_final: 0.7732 (t0) REVERT: F 683 MET cc_start: 0.9027 (tmm) cc_final: 0.8812 (tmm) REVERT: F 879 GLU cc_start: 0.8006 (tp30) cc_final: 0.7480 (tm-30) REVERT: F 966 GLU cc_start: 0.8693 (mp0) cc_final: 0.8216 (mp0) REVERT: F 1001 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8258 (pt0) REVERT: F 1029 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9011 (mt-10) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.1628 time to fit residues: 56.3395 Evaluate side-chains 150 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 149 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 204 HIS ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.052837 restraints weight = 117473.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054290 restraints weight = 75571.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055324 restraints weight = 54981.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056032 restraints weight = 43357.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056569 restraints weight = 36494.626| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21012 Z= 0.178 Angle : 0.754 10.379 28792 Z= 0.404 Chirality : 0.045 0.221 3200 Planarity : 0.005 0.091 3412 Dihedral : 20.701 175.185 3488 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2296 helix: 0.39 (0.16), residues: 985 sheet: -0.99 (0.35), residues: 202 loop : -3.44 (0.16), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 132 TYR 0.022 0.002 TYR E 113 PHE 0.029 0.002 PHE D 277 TRP 0.015 0.002 TRP E 18 HIS 0.007 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00383 (21012) covalent geometry : angle 0.75440 (28792) hydrogen bonds : bond 0.03877 ( 831) hydrogen bonds : angle 4.82467 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.810 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6493 (tm-30) REVERT: A 256 ASN cc_start: 0.9121 (t0) cc_final: 0.8556 (t0) REVERT: A 267 MET cc_start: 0.8228 (ppp) cc_final: 0.7860 (ppp) REVERT: A 287 GLU cc_start: 0.8502 (mp0) cc_final: 0.8272 (mp0) REVERT: A 484 ASP cc_start: 0.8817 (m-30) cc_final: 0.8212 (p0) REVERT: A 504 LYS cc_start: 0.9147 (tptp) cc_final: 0.8910 (mmmm) REVERT: D 116 ILE cc_start: 0.8648 (mp) cc_final: 0.8328 (tp) REVERT: D 150 LYS cc_start: 0.9308 (mttt) cc_final: 0.8839 (pttt) REVERT: D 222 LYS cc_start: 0.7824 (mttt) cc_final: 0.7317 (mttt) REVERT: D 412 ASN cc_start: 0.9163 (m-40) cc_final: 0.8663 (t0) REVERT: D 459 GLU cc_start: 0.8701 (mp0) cc_final: 0.8474 (mp0) REVERT: D 493 LYS cc_start: 0.9348 (mptt) cc_final: 0.9069 (mmtm) REVERT: D 504 LYS cc_start: 0.9247 (tttm) cc_final: 0.8962 (tptp) REVERT: E 77 PHE cc_start: 0.8195 (m-10) cc_final: 0.7491 (m-10) REVERT: E 84 ASN cc_start: 0.7651 (t0) cc_final: 0.6510 (t0) REVERT: E 86 TRP cc_start: 0.6957 (m100) cc_final: 0.6375 (m100) REVERT: E 100 MET cc_start: 0.7814 (mpp) cc_final: 0.7195 (mpp) REVERT: E 132 ARG cc_start: 0.8252 (tpt170) cc_final: 0.7311 (tpt90) REVERT: E 239 MET cc_start: 0.9273 (mmm) cc_final: 0.9001 (tpt) REVERT: E 297 MET cc_start: 0.8683 (ptm) cc_final: 0.7914 (ptt) REVERT: F 78 ASP cc_start: 0.8398 (m-30) cc_final: 0.8000 (t0) REVERT: F 225 PHE cc_start: 0.8429 (m-10) cc_final: 0.7873 (m-80) REVERT: F 267 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7846 (tm-30) REVERT: F 347 MET cc_start: 0.8965 (tmm) cc_final: 0.8574 (tpp) REVERT: F 470 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8255 (tm-30) REVERT: F 676 ASN cc_start: 0.7795 (t0) cc_final: 0.7595 (t0) REVERT: F 683 MET cc_start: 0.9016 (tmm) cc_final: 0.8774 (tmm) REVERT: F 879 GLU cc_start: 0.8047 (tp30) cc_final: 0.7672 (tp30) REVERT: F 883 LEU cc_start: 0.8952 (mm) cc_final: 0.8678 (pp) REVERT: F 1001 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8226 (pt0) REVERT: F 1029 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8979 (mt-10) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.1547 time to fit residues: 52.8095 Evaluate side-chains 147 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 63 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 224 optimal weight: 0.0020 chunk 29 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 0.0040 chunk 59 optimal weight: 10.0000 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 501 GLN ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055431 restraints weight = 114088.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.056916 restraints weight = 73674.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057968 restraints weight = 53759.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.058718 restraints weight = 42463.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059221 restraints weight = 35567.381| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21012 Z= 0.129 Angle : 0.715 11.174 28792 Z= 0.379 Chirality : 0.044 0.207 3200 Planarity : 0.004 0.093 3412 Dihedral : 20.446 174.481 3488 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2296 helix: 0.69 (0.17), residues: 980 sheet: -0.75 (0.36), residues: 196 loop : -3.33 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 132 TYR 0.019 0.001 TYR E 40 PHE 0.048 0.001 PHE D 422 TRP 0.032 0.002 TRP A 309 HIS 0.005 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00275 (21012) covalent geometry : angle 0.71463 (28792) hydrogen bonds : bond 0.03274 ( 831) hydrogen bonds : angle 4.56410 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8104 (mmpt) cc_final: 0.7767 (mmmt) REVERT: A 254 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6787 (tm-30) REVERT: A 256 ASN cc_start: 0.9131 (t0) cc_final: 0.8535 (t0) REVERT: A 267 MET cc_start: 0.8282 (ppp) cc_final: 0.8073 (ppp) REVERT: A 287 GLU cc_start: 0.8468 (mp0) cc_final: 0.8237 (mp0) REVERT: A 484 ASP cc_start: 0.8790 (m-30) cc_final: 0.8150 (p0) REVERT: A 504 LYS cc_start: 0.9122 (tptp) cc_final: 0.8901 (mmmm) REVERT: D 116 ILE cc_start: 0.8550 (mp) cc_final: 0.8095 (tp) REVERT: D 150 LYS cc_start: 0.9216 (mttt) cc_final: 0.8726 (pttt) REVERT: D 222 LYS cc_start: 0.7697 (mttt) cc_final: 0.7152 (mttp) REVERT: D 337 PHE cc_start: 0.8804 (m-10) cc_final: 0.8468 (m-10) REVERT: D 397 ILE cc_start: 0.8409 (mm) cc_final: 0.8163 (tt) REVERT: D 412 ASN cc_start: 0.9089 (m-40) cc_final: 0.8704 (t0) REVERT: D 459 GLU cc_start: 0.8728 (mp0) cc_final: 0.8488 (mp0) REVERT: D 493 LYS cc_start: 0.9347 (mptt) cc_final: 0.9144 (mmtm) REVERT: D 504 LYS cc_start: 0.9213 (tttm) cc_final: 0.8979 (tptp) REVERT: E 77 PHE cc_start: 0.7720 (m-10) cc_final: 0.6714 (m-10) REVERT: E 84 ASN cc_start: 0.7553 (t0) cc_final: 0.6749 (t0) REVERT: E 86 TRP cc_start: 0.6692 (m100) cc_final: 0.6442 (m100) REVERT: E 98 MET cc_start: 0.6954 (mpp) cc_final: 0.6223 (mpp) REVERT: E 100 MET cc_start: 0.7728 (mpp) cc_final: 0.7119 (mpp) REVERT: E 175 LEU cc_start: 0.9611 (mt) cc_final: 0.9391 (mt) REVERT: E 239 MET cc_start: 0.9253 (mmm) cc_final: 0.9004 (tpt) REVERT: E 297 MET cc_start: 0.8629 (ptm) cc_final: 0.7614 (ptp) REVERT: E 298 LYS cc_start: 0.8308 (mmpt) cc_final: 0.7979 (mmmt) REVERT: F 78 ASP cc_start: 0.8391 (m-30) cc_final: 0.8031 (t0) REVERT: F 129 LEU cc_start: 0.9437 (mt) cc_final: 0.8936 (mt) REVERT: F 225 PHE cc_start: 0.8483 (m-10) cc_final: 0.7883 (m-10) REVERT: F 267 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7744 (tm-30) REVERT: F 347 MET cc_start: 0.8980 (tmm) cc_final: 0.8571 (tpp) REVERT: F 469 ASP cc_start: 0.9064 (t0) cc_final: 0.8586 (m-30) REVERT: F 470 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8339 (tm-30) REVERT: F 683 MET cc_start: 0.9022 (tmm) cc_final: 0.8727 (tmm) REVERT: F 792 LEU cc_start: 0.9624 (mt) cc_final: 0.9422 (mt) REVERT: F 879 GLU cc_start: 0.8017 (tp30) cc_final: 0.7639 (tp30) REVERT: F 883 LEU cc_start: 0.9007 (mm) cc_final: 0.8763 (pp) REVERT: F 1001 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8218 (pt0) REVERT: F 1029 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8922 (mt-10) outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.1464 time to fit residues: 54.2416 Evaluate side-chains 167 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 221 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 106 optimal weight: 0.0870 chunk 154 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS D 270 HIS ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN F 857 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.066138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.053034 restraints weight = 117002.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054503 restraints weight = 75091.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055513 restraints weight = 54380.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056200 restraints weight = 42992.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056755 restraints weight = 36127.055| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21012 Z= 0.181 Angle : 0.749 10.940 28792 Z= 0.401 Chirality : 0.045 0.270 3200 Planarity : 0.005 0.089 3412 Dihedral : 20.506 177.849 3488 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2296 helix: 0.66 (0.17), residues: 989 sheet: -0.92 (0.36), residues: 192 loop : -3.33 (0.16), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 264 TYR 0.023 0.002 TYR E 113 PHE 0.043 0.002 PHE D 422 TRP 0.014 0.002 TRP E 18 HIS 0.009 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00387 (21012) covalent geometry : angle 0.74935 (28792) hydrogen bonds : bond 0.03928 ( 831) hydrogen bonds : angle 4.68067 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.710 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: A 130 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7867 (mmmt) REVERT: A 254 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6621 (tm-30) REVERT: A 256 ASN cc_start: 0.9323 (t0) cc_final: 0.8730 (t0) REVERT: A 265 MET cc_start: 0.8726 (mmt) cc_final: 0.8517 (mmt) REVERT: A 267 MET cc_start: 0.8237 (ppp) cc_final: 0.7577 (ppp) REVERT: A 268 PHE cc_start: 0.8562 (t80) cc_final: 0.8241 (t80) REVERT: A 287 GLU cc_start: 0.8509 (mp0) cc_final: 0.7921 (mp0) REVERT: A 484 ASP cc_start: 0.8970 (m-30) cc_final: 0.8311 (p0) REVERT: A 504 LYS cc_start: 0.9206 (tptp) cc_final: 0.8951 (mmmm) REVERT: D 116 ILE cc_start: 0.8644 (mp) cc_final: 0.8163 (tp) REVERT: D 150 LYS cc_start: 0.9332 (mttt) cc_final: 0.8824 (pttt) REVERT: D 222 LYS cc_start: 0.7950 (mttt) cc_final: 0.7422 (mttt) REVERT: D 412 ASN cc_start: 0.9113 (m-40) cc_final: 0.8673 (t0) REVERT: D 459 GLU cc_start: 0.8704 (mp0) cc_final: 0.8457 (mp0) REVERT: D 493 LYS cc_start: 0.9457 (mptt) cc_final: 0.9232 (mmtp) REVERT: E 84 ASN cc_start: 0.7546 (t0) cc_final: 0.6659 (t0) REVERT: E 86 TRP cc_start: 0.6912 (m100) cc_final: 0.6545 (m100) REVERT: E 100 MET cc_start: 0.7822 (mpp) cc_final: 0.7319 (mpp) REVERT: E 132 ARG cc_start: 0.8454 (tpt170) cc_final: 0.7361 (tpt170) REVERT: E 166 ASP cc_start: 0.8956 (m-30) cc_final: 0.8751 (m-30) REVERT: E 239 MET cc_start: 0.9265 (mmm) cc_final: 0.9016 (tmm) REVERT: E 297 MET cc_start: 0.8731 (ptm) cc_final: 0.7971 (ptt) REVERT: F 128 ASN cc_start: 0.8263 (t0) cc_final: 0.7922 (t0) REVERT: F 225 PHE cc_start: 0.8426 (m-10) cc_final: 0.7812 (m-10) REVERT: F 267 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7779 (tm-30) REVERT: F 347 MET cc_start: 0.8933 (tmm) cc_final: 0.8571 (tpp) REVERT: F 470 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8306 (tm-30) REVERT: F 683 MET cc_start: 0.9101 (tmm) cc_final: 0.8814 (tmm) REVERT: F 879 GLU cc_start: 0.8028 (tp30) cc_final: 0.7665 (tp30) REVERT: F 883 LEU cc_start: 0.8979 (mm) cc_final: 0.8772 (pp) REVERT: F 1001 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8240 (pt0) REVERT: F 1029 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8990 (mt-10) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.1467 time to fit residues: 47.5583 Evaluate side-chains 149 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 87 optimal weight: 4.9990 chunk 168 optimal weight: 0.0270 chunk 203 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054756 restraints weight = 115142.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056226 restraints weight = 74087.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057268 restraints weight = 53943.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057997 restraints weight = 42575.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058549 restraints weight = 35698.348| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21012 Z= 0.135 Angle : 0.719 12.098 28792 Z= 0.379 Chirality : 0.045 0.290 3200 Planarity : 0.004 0.094 3412 Dihedral : 20.340 178.167 3488 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 0.05 % Allowed : 1.40 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.17), residues: 2296 helix: 0.77 (0.17), residues: 988 sheet: -0.83 (0.37), residues: 186 loop : -3.17 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 142 TYR 0.017 0.001 TYR E 40 PHE 0.036 0.001 PHE D 422 TRP 0.016 0.001 TRP A 309 HIS 0.008 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00285 (21012) covalent geometry : angle 0.71854 (28792) hydrogen bonds : bond 0.03414 ( 831) hydrogen bonds : angle 4.54785 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.787 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: A 130 LYS cc_start: 0.8068 (mmpt) cc_final: 0.7695 (mmmt) REVERT: A 256 ASN cc_start: 0.9325 (t0) cc_final: 0.8681 (t0) REVERT: A 265 MET cc_start: 0.8819 (mmt) cc_final: 0.8517 (mmt) REVERT: A 267 MET cc_start: 0.8355 (ppp) cc_final: 0.7674 (ppp) REVERT: A 268 PHE cc_start: 0.8623 (t80) cc_final: 0.8393 (t80) REVERT: A 287 GLU cc_start: 0.8512 (mp0) cc_final: 0.7885 (mp0) REVERT: A 421 LEU cc_start: 0.7958 (mt) cc_final: 0.7424 (tt) REVERT: A 484 ASP cc_start: 0.8875 (m-30) cc_final: 0.8283 (p0) REVERT: A 504 LYS cc_start: 0.9211 (tptp) cc_final: 0.9000 (mmmm) REVERT: D 116 ILE cc_start: 0.8602 (mp) cc_final: 0.8145 (tp) REVERT: D 150 LYS cc_start: 0.9303 (mttt) cc_final: 0.8778 (pttt) REVERT: D 222 LYS cc_start: 0.7920 (mttt) cc_final: 0.7286 (mttp) REVERT: D 337 PHE cc_start: 0.8855 (m-10) cc_final: 0.8551 (m-10) REVERT: D 412 ASN cc_start: 0.9101 (m-40) cc_final: 0.8643 (t0) REVERT: D 459 GLU cc_start: 0.8739 (mp0) cc_final: 0.8486 (mp0) REVERT: D 493 LYS cc_start: 0.9540 (mptt) cc_final: 0.9336 (mmtm) REVERT: E 77 PHE cc_start: 0.7613 (m-10) cc_final: 0.7383 (m-10) REVERT: E 84 ASN cc_start: 0.7541 (t0) cc_final: 0.6823 (t0) REVERT: E 86 TRP cc_start: 0.6806 (m100) cc_final: 0.6548 (m100) REVERT: E 100 MET cc_start: 0.7646 (mpp) cc_final: 0.7104 (mpp) REVERT: E 132 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7301 (tpt-90) REVERT: E 239 MET cc_start: 0.9252 (mmm) cc_final: 0.8993 (tmm) REVERT: E 297 MET cc_start: 0.8573 (ptm) cc_final: 0.7767 (ptt) REVERT: F 128 ASN cc_start: 0.8295 (t0) cc_final: 0.7948 (t0) REVERT: F 225 PHE cc_start: 0.8597 (m-10) cc_final: 0.7980 (m-10) REVERT: F 267 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7495 (tm-30) REVERT: F 347 MET cc_start: 0.8970 (tmm) cc_final: 0.8627 (tpp) REVERT: F 469 ASP cc_start: 0.9163 (t0) cc_final: 0.8682 (m-30) REVERT: F 470 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8350 (tm-30) REVERT: F 683 MET cc_start: 0.9124 (tmm) cc_final: 0.8790 (tmm) REVERT: F 879 GLU cc_start: 0.8123 (tp30) cc_final: 0.7625 (tp30) REVERT: F 883 LEU cc_start: 0.8987 (mm) cc_final: 0.8689 (pp) REVERT: F 1001 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8215 (pt0) REVERT: F 1029 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8962 (mt-10) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.1399 time to fit residues: 48.4439 Evaluate side-chains 157 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 121 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053957 restraints weight = 115427.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055419 restraints weight = 74322.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056464 restraints weight = 54012.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057173 restraints weight = 42533.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.057707 restraints weight = 35729.817| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21012 Z= 0.149 Angle : 0.729 12.338 28792 Z= 0.387 Chirality : 0.045 0.267 3200 Planarity : 0.004 0.091 3412 Dihedral : 20.277 179.457 3488 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.05 % Allowed : 1.00 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2296 helix: 0.82 (0.17), residues: 973 sheet: -0.94 (0.36), residues: 196 loop : -3.20 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 274 TYR 0.026 0.002 TYR A 260 PHE 0.041 0.002 PHE D 277 TRP 0.015 0.001 TRP A 17 HIS 0.008 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00321 (21012) covalent geometry : angle 0.72905 (28792) hydrogen bonds : bond 0.03652 ( 831) hydrogen bonds : angle 4.60563 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.794 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: symmetry clash REVERT: A 130 LYS cc_start: 0.8107 (mmpt) cc_final: 0.7767 (mmmt) REVERT: A 256 ASN cc_start: 0.9104 (t0) cc_final: 0.8816 (t0) REVERT: A 265 MET cc_start: 0.8723 (mmt) cc_final: 0.8489 (mmt) REVERT: A 267 MET cc_start: 0.8459 (ppp) cc_final: 0.7844 (ppp) REVERT: A 268 PHE cc_start: 0.8714 (t80) cc_final: 0.8440 (t80) REVERT: A 278 ASP cc_start: 0.7977 (p0) cc_final: 0.7663 (p0) REVERT: A 287 GLU cc_start: 0.8494 (mp0) cc_final: 0.7870 (mp0) REVERT: A 421 LEU cc_start: 0.7996 (mt) cc_final: 0.7598 (tt) REVERT: A 484 ASP cc_start: 0.8871 (m-30) cc_final: 0.8289 (p0) REVERT: A 504 LYS cc_start: 0.9216 (tptp) cc_final: 0.8978 (mmmm) REVERT: D 116 ILE cc_start: 0.8682 (mp) cc_final: 0.8269 (tp) REVERT: D 150 LYS cc_start: 0.9333 (mttt) cc_final: 0.8783 (pttt) REVERT: D 222 LYS cc_start: 0.7961 (mttt) cc_final: 0.7348 (mttp) REVERT: D 337 PHE cc_start: 0.8847 (m-10) cc_final: 0.8562 (m-10) REVERT: D 402 LEU cc_start: 0.9303 (mp) cc_final: 0.8718 (tt) REVERT: D 412 ASN cc_start: 0.9108 (m-40) cc_final: 0.8622 (t0) REVERT: D 459 GLU cc_start: 0.8704 (mp0) cc_final: 0.8483 (mp0) REVERT: E 77 PHE cc_start: 0.7601 (m-10) cc_final: 0.7307 (m-10) REVERT: E 84 ASN cc_start: 0.7719 (t0) cc_final: 0.6796 (t0) REVERT: E 86 TRP cc_start: 0.6831 (m100) cc_final: 0.6571 (m100) REVERT: E 100 MET cc_start: 0.7717 (mpp) cc_final: 0.7220 (mpp) REVERT: E 239 MET cc_start: 0.9267 (mmm) cc_final: 0.9040 (tmm) REVERT: E 297 MET cc_start: 0.8870 (ptm) cc_final: 0.8044 (ptt) REVERT: F 128 ASN cc_start: 0.8336 (t0) cc_final: 0.8046 (t0) REVERT: F 225 PHE cc_start: 0.8599 (m-10) cc_final: 0.7957 (m-10) REVERT: F 267 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7486 (tm-30) REVERT: F 347 MET cc_start: 0.8944 (tmm) cc_final: 0.8626 (tpp) REVERT: F 470 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8324 (tm-30) REVERT: F 683 MET cc_start: 0.9122 (tmm) cc_final: 0.8794 (tmm) REVERT: F 879 GLU cc_start: 0.8067 (tp30) cc_final: 0.7324 (tp30) REVERT: F 883 LEU cc_start: 0.9013 (mm) cc_final: 0.8661 (pp) REVERT: F 1001 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8237 (pt0) REVERT: F 1029 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8984 (mt-10) outliers start: 1 outliers final: 1 residues processed: 215 average time/residue: 0.1427 time to fit residues: 49.1273 Evaluate side-chains 158 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 151 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 76 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.066786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053701 restraints weight = 115315.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055162 restraints weight = 74443.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056220 restraints weight = 54121.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056940 restraints weight = 42534.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057481 restraints weight = 35592.024| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21012 Z= 0.150 Angle : 0.731 12.433 28792 Z= 0.388 Chirality : 0.045 0.267 3200 Planarity : 0.004 0.093 3412 Dihedral : 20.200 179.112 3488 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2296 helix: 0.75 (0.17), residues: 973 sheet: -0.92 (0.39), residues: 172 loop : -3.09 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 483 TYR 0.018 0.002 TYR F 344 PHE 0.037 0.002 PHE D 277 TRP 0.016 0.001 TRP A 17 HIS 0.008 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00324 (21012) covalent geometry : angle 0.73114 (28792) hydrogen bonds : bond 0.03618 ( 831) hydrogen bonds : angle 4.63804 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.693 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: A 130 LYS cc_start: 0.8349 (mmpt) cc_final: 0.8042 (mmmt) REVERT: A 256 ASN cc_start: 0.9112 (t0) cc_final: 0.8773 (t0) REVERT: A 265 MET cc_start: 0.8825 (mmt) cc_final: 0.8569 (mmt) REVERT: A 267 MET cc_start: 0.8393 (ppp) cc_final: 0.7734 (ppp) REVERT: A 268 PHE cc_start: 0.8706 (t80) cc_final: 0.8494 (t80) REVERT: A 287 GLU cc_start: 0.8497 (mp0) cc_final: 0.7905 (mp0) REVERT: A 421 LEU cc_start: 0.7658 (mt) cc_final: 0.7151 (tt) REVERT: A 484 ASP cc_start: 0.8899 (m-30) cc_final: 0.8318 (p0) REVERT: A 504 LYS cc_start: 0.9229 (tptp) cc_final: 0.8988 (mmmm) REVERT: D 116 ILE cc_start: 0.8673 (mp) cc_final: 0.8244 (tp) REVERT: D 150 LYS cc_start: 0.9291 (mttt) cc_final: 0.8784 (pttt) REVERT: D 222 LYS cc_start: 0.7975 (mttt) cc_final: 0.7342 (mttp) REVERT: D 265 MET cc_start: 0.9317 (ptt) cc_final: 0.9060 (ptm) REVERT: D 337 PHE cc_start: 0.8854 (m-10) cc_final: 0.8549 (m-10) REVERT: D 339 PHE cc_start: 0.8963 (m-80) cc_final: 0.8740 (m-80) REVERT: D 402 LEU cc_start: 0.9279 (mp) cc_final: 0.8701 (tt) REVERT: D 412 ASN cc_start: 0.9116 (m-40) cc_final: 0.8621 (t0) REVERT: D 459 GLU cc_start: 0.8704 (mp0) cc_final: 0.8477 (mp0) REVERT: E 77 PHE cc_start: 0.7735 (m-10) cc_final: 0.7471 (m-10) REVERT: E 84 ASN cc_start: 0.7717 (t0) cc_final: 0.6868 (t0) REVERT: E 100 MET cc_start: 0.7712 (mpp) cc_final: 0.7149 (mpp) REVERT: E 239 MET cc_start: 0.9273 (mmm) cc_final: 0.9042 (tmm) REVERT: E 297 MET cc_start: 0.8813 (ptm) cc_final: 0.7978 (ptt) REVERT: F 128 ASN cc_start: 0.8305 (t0) cc_final: 0.8007 (t0) REVERT: F 225 PHE cc_start: 0.8599 (m-10) cc_final: 0.7941 (m-10) REVERT: F 347 MET cc_start: 0.8954 (tmm) cc_final: 0.8640 (tpp) REVERT: F 470 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8335 (tm-30) REVERT: F 683 MET cc_start: 0.9119 (tmm) cc_final: 0.8785 (tmm) REVERT: F 1001 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8220 (pt0) REVERT: F 1029 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8987 (mt-10) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.1372 time to fit residues: 46.2725 Evaluate side-chains 158 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 51 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN F 626 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054634 restraints weight = 115677.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056121 restraints weight = 74553.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057161 restraints weight = 54186.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.057920 restraints weight = 42764.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058457 restraints weight = 35702.526| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21012 Z= 0.135 Angle : 0.722 13.008 28792 Z= 0.379 Chirality : 0.045 0.277 3200 Planarity : 0.004 0.096 3412 Dihedral : 20.096 179.647 3488 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 0.05 % Allowed : 0.50 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2296 helix: 0.70 (0.17), residues: 985 sheet: -0.95 (0.36), residues: 195 loop : -3.10 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 132 TYR 0.018 0.001 TYR E 40 PHE 0.040 0.002 PHE D 277 TRP 0.047 0.002 TRP E 86 HIS 0.008 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00288 (21012) covalent geometry : angle 0.72165 (28792) hydrogen bonds : bond 0.03465 ( 831) hydrogen bonds : angle 4.59476 ( 2304) =============================================================================== Job complete usr+sys time: 2882.70 seconds wall clock time: 51 minutes 6.18 seconds (3066.18 seconds total)