Starting phenix.real_space_refine on Fri Feb 6 00:58:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khi_62343/02_2026/9khi_62343.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khi_62343/02_2026/9khi_62343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9khi_62343/02_2026/9khi_62343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khi_62343/02_2026/9khi_62343.map" model { file = "/net/cci-nas-00/data/ceres_data/9khi_62343/02_2026/9khi_62343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khi_62343/02_2026/9khi_62343.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 Zn 3 6.06 5 S 119 5.16 5 C 13838 2.51 5 N 3461 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21164 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5008 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 608} Chain breaks: 9 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 5295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5295 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 24, 'TRANS': 636} Chain breaks: 6 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 5322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5322 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 638} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 5302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5302 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 636} Chain breaks: 4 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6117 SG CYS D 178 79.280 22.090 92.970 1.00115.12 S ATOM 6139 SG CYS D 181 77.786 25.370 92.440 1.00109.74 S ATOM 11404 SG CYS C 176 27.379 59.348 97.286 1.00135.17 S ATOM 11418 SG CYS C 178 25.719 61.799 99.839 1.00133.48 S ATOM 11440 SG CYS C 181 28.943 63.078 98.996 1.00127.13 S ATOM 16706 SG CYS B 176 57.895 110.689 75.056 1.00107.62 S ATOM 16720 SG CYS B 178 60.425 113.878 75.585 1.00111.13 S ATOM 16742 SG CYS B 181 61.709 110.482 76.123 1.00104.36 S Time building chain proxies: 5.24, per 1000 atoms: 0.25 Number of scatterers: 21164 At special positions: 0 Unit cell: (126.352, 125.504, 150.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Ca 3 19.99 S 119 16.00 O 3740 8.00 N 3461 7.00 C 13838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.01 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: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5026 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 3 sheets defined 82.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 removed outlier: 4.023A pdb=" N LYS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.917A pdb=" N LEU A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 205 through 221 removed outlier: 3.511A pdb=" N HIS A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.574A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 274 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.947A pdb=" N MET A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.621A pdb=" N LEU A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.523A pdb=" N ILE A 379 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 380 " --> pdb=" O GLY A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 382 through 407 removed outlier: 4.355A pdb=" N SER A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.827A pdb=" N ASN A 414 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 446 Processing helix chain 'A' and resid 446 through 453 removed outlier: 4.312A pdb=" N GLU A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 480 removed outlier: 3.519A pdb=" N VAL A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.609A pdb=" N VAL A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.720A pdb=" N PHE A 515 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 533 through 561 removed outlier: 3.837A pdb=" N PHE A 537 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.842A pdb=" N THR A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.565A pdb=" N VAL A 608 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.676A pdb=" N GLN A 650 " --> pdb=" O HIS A 646 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.712A pdb=" N SER A 670 " --> pdb=" O LYS A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.989A pdb=" N ILE A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 751 removed outlier: 3.564A pdb=" N ASN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 775 removed outlier: 3.742A pdb=" N VAL A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 232 removed outlier: 4.042A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.549A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 327 through 340 removed outlier: 3.516A pdb=" N LEU D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 354 through 360 removed outlier: 3.750A pdb=" N ILE D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 387 removed outlier: 3.564A pdb=" N ALA D 384 " --> pdb=" O MET D 380 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 433 removed outlier: 3.563A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 460 removed outlier: 3.630A pdb=" N LEU D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 491 Processing helix chain 'D' and resid 492 through 500 removed outlier: 4.081A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 removed outlier: 4.352A pdb=" N LEU D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 540 removed outlier: 3.935A pdb=" N ILE D 517 " --> pdb=" O MET D 513 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 545 through 553 Proline residue: D 550 - end of helix removed outlier: 3.578A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 585 through 589 removed outlier: 3.648A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 removed outlier: 3.626A pdb=" N VAL D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 633 removed outlier: 3.511A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 removed outlier: 3.585A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 663 removed outlier: 4.144A pdb=" N ILE D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 732 removed outlier: 3.520A pdb=" N LYS D 722 " --> pdb=" O ARG D 718 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 729 " --> pdb=" O VAL D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 736 Processing helix chain 'D' and resid 738 through 755 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.501A pdb=" N HIS C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.513A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 removed outlier: 4.071A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.639A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 354 through 360 removed outlier: 4.124A pdb=" N ILE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 383 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.753A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 460 removed outlier: 3.885A pdb=" N LEU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 491 Processing helix chain 'C' and resid 492 through 500 removed outlier: 4.212A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 499 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 Processing helix chain 'C' and resid 513 through 540 removed outlier: 4.217A pdb=" N ILE C 517 " --> pdb=" O MET C 513 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.652A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 removed outlier: 3.645A pdb=" N VAL C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 633 removed outlier: 3.777A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 removed outlier: 3.569A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 664 removed outlier: 3.850A pdb=" N ILE C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 732 removed outlier: 4.031A pdb=" N ARG C 730 " --> pdb=" O ALA C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 753 removed outlier: 3.689A pdb=" N THR C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 741 " --> pdb=" O GLY C 737 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.959A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 removed outlier: 4.183A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.742A pdb=" N LEU B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.801A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.711A pdb=" N ALA B 384 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 433 removed outlier: 3.563A pdb=" N ILE B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 460 removed outlier: 3.860A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 491 Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.100A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 removed outlier: 4.540A pdb=" N LEU B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 540 removed outlier: 4.185A pdb=" N ILE B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.726A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 removed outlier: 3.725A pdb=" N VAL B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.785A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 removed outlier: 3.704A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.434A pdb=" N ILE B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 753 removed outlier: 3.734A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 734 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 748 " --> pdb=" O LYS B 744 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER B 751 " --> pdb=" O LYS B 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 19 1402 hydrogen bonds defined for protein. 4071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3376 1.32 - 1.44: 5816 1.44 - 1.57: 12255 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21639 Sorted by residual: bond pdb=" N GLU C 741 " pdb=" CA GLU C 741 " ideal model delta sigma weight residual 1.459 1.517 -0.058 1.25e-02 6.40e+03 2.16e+01 bond pdb=" N ILE B 556 " pdb=" CA ILE B 556 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.17e+01 bond pdb=" C ASN B 742 " pdb=" O ASN B 742 " ideal model delta sigma weight residual 1.235 1.278 -0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" N LEU B 408 " pdb=" CA LEU B 408 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.04e-02 9.25e+03 1.09e+01 bond pdb=" N LYS B 733 " pdb=" CA LYS B 733 " ideal model delta sigma weight residual 1.458 1.498 -0.041 1.28e-02 6.10e+03 1.02e+01 ... (remaining 21634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 28734 2.42 - 4.84: 543 4.84 - 7.26: 35 7.26 - 9.68: 4 9.68 - 12.10: 2 Bond angle restraints: 29318 Sorted by residual: angle pdb=" N PRO B 659 " pdb=" CA PRO B 659 " pdb=" C PRO B 659 " ideal model delta sigma weight residual 110.70 122.80 -12.10 1.22e+00 6.72e-01 9.84e+01 angle pdb=" N LYS B 733 " pdb=" CA LYS B 733 " pdb=" C LYS B 733 " ideal model delta sigma weight residual 112.45 122.67 -10.22 1.39e+00 5.18e-01 5.40e+01 angle pdb=" N PRO A 680 " pdb=" CA PRO A 680 " pdb=" C PRO A 680 " ideal model delta sigma weight residual 110.70 119.25 -8.55 1.22e+00 6.72e-01 4.92e+01 angle pdb=" N PRO D 659 " pdb=" CA PRO D 659 " pdb=" C PRO D 659 " ideal model delta sigma weight residual 110.70 119.21 -8.51 1.22e+00 6.72e-01 4.86e+01 angle pdb=" N PRO C 659 " pdb=" CA PRO C 659 " pdb=" C PRO C 659 " ideal model delta sigma weight residual 110.70 118.24 -7.54 1.22e+00 6.72e-01 3.82e+01 ... (remaining 29313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 12625 35.23 - 70.46: 405 70.46 - 105.70: 27 105.70 - 140.93: 13 140.93 - 176.16: 1 Dihedral angle restraints: 13071 sinusoidal: 5363 harmonic: 7708 Sorted by residual: dihedral pdb=" C5 YZY B 802 " pdb=" C3 YZY B 802 " pdb=" C4 YZY B 802 " pdb=" O2 YZY B 802 " ideal model delta sinusoidal sigma weight residual 177.74 1.58 176.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C ASN C 662 " pdb=" N ASN C 662 " pdb=" CA ASN C 662 " pdb=" CB ASN C 662 " ideal model delta harmonic sigma weight residual -122.60 -133.95 11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" CA CYS B 553 " pdb=" C CYS B 553 " pdb=" N LYS B 554 " pdb=" CA LYS B 554 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 13068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3025 0.074 - 0.148: 245 0.148 - 0.222: 64 0.222 - 0.297: 7 0.297 - 0.371: 3 Chirality restraints: 3344 Sorted by residual: chirality pdb=" CA PRO B 659 " pdb=" N PRO B 659 " pdb=" C PRO B 659 " pdb=" CB PRO B 659 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA ASN C 662 " pdb=" N ASN C 662 " pdb=" C ASN C 662 " pdb=" CB ASN C 662 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA ASN A 683 " pdb=" N ASN A 683 " pdb=" C ASN A 683 " pdb=" CB ASN A 683 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3341 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YZY D 802 " 0.077 2.00e-02 2.50e+03 7.85e-02 6.16e+01 pdb=" C28 YZY D 802 " -0.071 2.00e-02 2.50e+03 pdb=" C29 YZY D 802 " -0.085 2.00e-02 2.50e+03 pdb=" C30 YZY D 802 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY B 802 " -0.056 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C28 YZY B 802 " 0.056 2.00e-02 2.50e+03 pdb=" C29 YZY B 802 " 0.055 2.00e-02 2.50e+03 pdb=" C30 YZY B 802 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY C 802 " -0.035 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C28 YZY C 802 " 0.036 2.00e-02 2.50e+03 pdb=" C29 YZY C 802 " 0.033 2.00e-02 2.50e+03 pdb=" C30 YZY C 802 " -0.034 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 46 2.48 - 3.08: 14100 3.08 - 3.69: 30087 3.69 - 4.29: 44958 4.29 - 4.90: 74849 Nonbonded interactions: 164040 Sorted by model distance: nonbonded pdb=" OE2 GLU C 418 " pdb="CA CA C 801 " model vdw 1.871 2.510 nonbonded pdb=" OE1 GLU B 421 " pdb="CA CA B 801 " model vdw 2.098 2.510 nonbonded pdb=" OE1 GLU D 421 " pdb="CA CA D 801 " model vdw 2.225 2.510 nonbonded pdb=" O ASP B 44 " pdb=" OG1 THR B 47 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.270 3.040 ... (remaining 164035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 18 through 173 or resid 177 through 322 or resid 326 throu \ gh 804)) selection = (chain 'C' and (resid 18 through 58 or resid 63 through 173 or resid 177 through \ 322 or resid 326 through 804)) selection = (chain 'D' and (resid 18 through 58 or resid 63 through 753 or resid 801 through \ 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.330 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 0.495 21651 Z= 0.383 Angle : 0.696 12.100 29324 Z= 0.488 Chirality : 0.048 0.371 3344 Planarity : 0.004 0.078 3631 Dihedral : 16.917 176.162 8036 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.18 % Allowed : 18.07 % Favored : 81.75 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.16), residues: 2554 helix: 1.85 (0.12), residues: 1896 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 422 TYR 0.013 0.001 TYR B 524 PHE 0.019 0.001 PHE B 341 TRP 0.013 0.001 TRP D 315 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00495 (21639) covalent geometry : angle 0.69564 (29318) SS BOND : bond 0.01229 ( 3) SS BOND : angle 2.15999 ( 6) hydrogen bonds : bond 0.20751 ( 1402) hydrogen bonds : angle 5.23212 ( 4071) metal coordination : bond 0.20292 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 289 time to evaluate : 0.829 Fit side-chains REVERT: C 451 SER cc_start: 0.8238 (t) cc_final: 0.7990 (m) REVERT: C 551 ASN cc_start: 0.8280 (m-40) cc_final: 0.7702 (t0) REVERT: B 709 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7301 (tt0) REVERT: B 715 GLU cc_start: 0.7996 (tp30) cc_final: 0.7664 (tp30) outliers start: 4 outliers final: 2 residues processed: 292 average time/residue: 0.6372 time to fit residues: 210.8909 Evaluate side-chains 249 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain C residue 341 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 GLN A 581 ASN D 92 HIS D 177 ASN C 309 GLN C 563 ASN C 626 ASN C 634 HIS C 731 ASN B 551 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.162240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108102 restraints weight = 24228.474| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.17 r_work: 0.3163 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21651 Z= 0.169 Angle : 0.537 7.609 29324 Z= 0.286 Chirality : 0.038 0.170 3344 Planarity : 0.004 0.045 3631 Dihedral : 10.167 139.852 3116 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.05 % Allowed : 16.29 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.16), residues: 2554 helix: 2.24 (0.11), residues: 1937 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 557 TYR 0.016 0.001 TYR D 524 PHE 0.020 0.002 PHE C 341 TRP 0.018 0.001 TRP A 430 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00384 (21639) covalent geometry : angle 0.53724 (29318) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.27363 ( 6) hydrogen bonds : bond 0.06779 ( 1402) hydrogen bonds : angle 3.74219 ( 4071) metal coordination : bond 0.00906 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 258 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7249 (ttm110) REVERT: A 324 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.6248 (tm-30) REVERT: A 378 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7637 (ptp90) REVERT: A 467 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 485 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6912 (t0) REVERT: A 729 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: D 380 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: C 304 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: C 410 TRP cc_start: 0.8456 (OUTLIER) cc_final: 0.7264 (m-90) REVERT: C 551 ASN cc_start: 0.8747 (m-40) cc_final: 0.7943 (t0) REVERT: C 730 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.7120 (ttm110) REVERT: B 102 TYR cc_start: 0.7965 (t80) cc_final: 0.7758 (t80) REVERT: B 229 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: B 434 TRP cc_start: 0.6669 (m100) cc_final: 0.6304 (m-90) REVERT: B 709 GLN cc_start: 0.7683 (mm-40) cc_final: 0.6881 (pt0) REVERT: B 715 GLU cc_start: 0.8095 (tp30) cc_final: 0.7737 (tp30) outliers start: 91 outliers final: 28 residues processed: 311 average time/residue: 0.6112 time to fit residues: 216.1113 Evaluate side-chains 275 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 195 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 557 GLN D 38 ASN D 91 ASN D 177 ASN C 309 GLN C 533 ASN C 563 ASN B 173 GLN B 551 ASN B 710 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107574 restraints weight = 24369.217| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.14 r_work: 0.3156 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21651 Z= 0.160 Angle : 0.517 11.355 29324 Z= 0.273 Chirality : 0.038 0.167 3344 Planarity : 0.004 0.045 3631 Dihedral : 9.370 137.286 3115 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.14 % Allowed : 16.07 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.16), residues: 2554 helix: 2.38 (0.11), residues: 1938 sheet: None (None), residues: 0 loop : -0.11 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 196 TYR 0.016 0.001 TYR D 524 PHE 0.023 0.002 PHE C 341 TRP 0.018 0.001 TRP A 335 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00373 (21639) covalent geometry : angle 0.51683 (29318) SS BOND : bond 0.00092 ( 3) SS BOND : angle 1.22508 ( 6) hydrogen bonds : bond 0.06263 ( 1402) hydrogen bonds : angle 3.53896 ( 4071) metal coordination : bond 0.00382 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 240 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5954 (ptm) REVERT: A 62 MET cc_start: 0.5720 (ptp) cc_final: 0.5251 (pmm) REVERT: A 211 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7262 (ttm110) REVERT: A 339 MET cc_start: 0.6767 (ttm) cc_final: 0.6220 (ttm) REVERT: A 378 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7669 (ptp90) REVERT: A 439 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 747 ARG cc_start: 0.6152 (tmm-80) cc_final: 0.5950 (tmm-80) REVERT: D 34 LYS cc_start: 0.7933 (tmtm) cc_final: 0.7572 (tptp) REVERT: D 177 ASN cc_start: 0.5423 (OUTLIER) cc_final: 0.5190 (m-40) REVERT: D 230 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8072 (tt) REVERT: D 471 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7080 (ttm) REVERT: C 17 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7280 (mtp180) REVERT: C 186 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: C 304 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: C 410 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.7261 (m-90) REVERT: B 102 TYR cc_start: 0.7987 (t80) cc_final: 0.7783 (t80) REVERT: B 404 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: B 434 TRP cc_start: 0.6759 (m100) cc_final: 0.6447 (m-90) REVERT: B 709 GLN cc_start: 0.7585 (mm-40) cc_final: 0.6654 (pt0) REVERT: B 715 GLU cc_start: 0.7972 (tp30) cc_final: 0.7539 (tp30) outliers start: 93 outliers final: 32 residues processed: 299 average time/residue: 0.5740 time to fit residues: 195.0886 Evaluate side-chains 270 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 244 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 258 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 GLN D 91 ASN D 92 HIS D 177 ASN C 309 GLN B 53 GLN B 710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106292 restraints weight = 24297.163| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.16 r_work: 0.3137 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21651 Z= 0.186 Angle : 0.535 7.548 29324 Z= 0.282 Chirality : 0.038 0.170 3344 Planarity : 0.004 0.046 3631 Dihedral : 9.225 136.091 3115 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.45 % Allowed : 16.11 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.16), residues: 2554 helix: 2.33 (0.11), residues: 1938 sheet: None (None), residues: 0 loop : -0.24 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 557 TYR 0.016 0.001 TYR D 524 PHE 0.024 0.002 PHE C 341 TRP 0.020 0.001 TRP A 335 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00450 (21639) covalent geometry : angle 0.53509 (29318) SS BOND : bond 0.00082 ( 3) SS BOND : angle 1.26578 ( 6) hydrogen bonds : bond 0.06593 ( 1402) hydrogen bonds : angle 3.53781 ( 4071) metal coordination : bond 0.00433 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 234 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5788 (ptm) REVERT: A 62 MET cc_start: 0.5636 (ptp) cc_final: 0.5246 (pmm) REVERT: A 211 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7257 (ttm110) REVERT: A 378 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7639 (ptp90) REVERT: A 439 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 467 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7898 (mp) REVERT: D 471 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7247 (ttm) REVERT: C 17 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7255 (mtp180) REVERT: C 186 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: C 304 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: C 410 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7302 (m-90) REVERT: C 471 MET cc_start: 0.8356 (ttm) cc_final: 0.8137 (ttp) REVERT: B 102 TYR cc_start: 0.7998 (t80) cc_final: 0.7785 (t80) REVERT: B 229 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 404 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: B 434 TRP cc_start: 0.6785 (m100) cc_final: 0.6453 (m-90) REVERT: B 551 ASN cc_start: 0.8327 (t0) cc_final: 0.8107 (t160) REVERT: B 709 GLN cc_start: 0.7681 (mm-40) cc_final: 0.6650 (pt0) REVERT: B 715 GLU cc_start: 0.8013 (tp30) cc_final: 0.7559 (tp30) outliers start: 100 outliers final: 39 residues processed: 304 average time/residue: 0.5514 time to fit residues: 190.3113 Evaluate side-chains 277 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 248 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 GLN D 91 ASN D 92 HIS C 309 GLN C 533 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110341 restraints weight = 24267.546| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.15 r_work: 0.3194 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21651 Z= 0.111 Angle : 0.458 10.751 29324 Z= 0.242 Chirality : 0.035 0.165 3344 Planarity : 0.004 0.046 3631 Dihedral : 8.560 132.322 3115 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.34 % Allowed : 17.22 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.16), residues: 2554 helix: 2.58 (0.12), residues: 1939 sheet: None (None), residues: 0 loop : -0.12 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.013 0.001 TYR D 524 PHE 0.021 0.001 PHE C 341 TRP 0.012 0.001 TRP A 335 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00233 (21639) covalent geometry : angle 0.45747 (29318) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.71367 ( 6) hydrogen bonds : bond 0.04765 ( 1402) hydrogen bonds : angle 3.34930 ( 4071) metal coordination : bond 0.00069 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 241 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5768 (ptm) REVERT: A 62 MET cc_start: 0.5759 (ptp) cc_final: 0.5343 (pmm) REVERT: A 211 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7191 (ttm110) REVERT: A 378 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7577 (ptp90) REVERT: A 430 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.7868 (m-90) REVERT: A 439 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8101 (mp) REVERT: A 467 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7917 (mp) REVERT: D 230 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8156 (tt) REVERT: D 471 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7052 (ttm) REVERT: C 17 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: C 186 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: C 304 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: C 410 TRP cc_start: 0.8380 (OUTLIER) cc_final: 0.7270 (m-90) REVERT: C 471 MET cc_start: 0.8335 (ttm) cc_final: 0.8088 (ttp) REVERT: B 229 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: B 434 TRP cc_start: 0.6785 (m100) cc_final: 0.6441 (m-90) REVERT: B 551 ASN cc_start: 0.8191 (t0) cc_final: 0.7969 (t160) outliers start: 75 outliers final: 22 residues processed: 295 average time/residue: 0.5513 time to fit residues: 185.1218 Evaluate side-chains 258 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 86 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN C 309 GLN C 533 ASN B 326 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108949 restraints weight = 24339.782| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.15 r_work: 0.3174 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21651 Z= 0.129 Angle : 0.481 9.447 29324 Z= 0.253 Chirality : 0.036 0.177 3344 Planarity : 0.004 0.046 3631 Dihedral : 8.474 135.149 3115 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.16 % Allowed : 18.02 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.16), residues: 2554 helix: 2.61 (0.12), residues: 1938 sheet: None (None), residues: 0 loop : -0.12 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.014 0.001 TYR B 524 PHE 0.022 0.001 PHE C 341 TRP 0.016 0.001 TRP A 335 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00294 (21639) covalent geometry : angle 0.48128 (29318) SS BOND : bond 0.00082 ( 3) SS BOND : angle 0.85172 ( 6) hydrogen bonds : bond 0.05245 ( 1402) hydrogen bonds : angle 3.34755 ( 4071) metal coordination : bond 0.00135 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5776 (ptm) REVERT: A 62 MET cc_start: 0.5600 (ptp) cc_final: 0.5226 (pmm) REVERT: A 211 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7252 (ttm110) REVERT: A 324 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: A 339 MET cc_start: 0.6895 (ttm) cc_final: 0.6683 (ttm) REVERT: A 378 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7617 (ptp90) REVERT: A 439 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 467 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7886 (mp) REVERT: D 215 ASP cc_start: 0.7998 (p0) cc_final: 0.7716 (p0) REVERT: D 230 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8141 (tt) REVERT: D 524 TYR cc_start: 0.8265 (t80) cc_final: 0.8014 (t80) REVERT: D 629 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: D 728 MET cc_start: 0.5902 (ppp) cc_final: 0.5616 (pp-130) REVERT: C 17 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: C 186 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: C 304 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: C 410 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7270 (m-90) REVERT: C 718 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7551 (ttm170) REVERT: B 102 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7384 (t80) REVERT: B 229 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: B 434 TRP cc_start: 0.6794 (m100) cc_final: 0.6478 (m-90) REVERT: B 551 ASN cc_start: 0.8307 (t0) cc_final: 0.8096 (t160) outliers start: 71 outliers final: 33 residues processed: 280 average time/residue: 0.5702 time to fit residues: 181.3332 Evaluate side-chains 270 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN D 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105612 restraints weight = 24286.382| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.14 r_work: 0.3130 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21651 Z= 0.195 Angle : 0.560 13.144 29324 Z= 0.292 Chirality : 0.039 0.178 3344 Planarity : 0.004 0.046 3631 Dihedral : 8.742 141.861 3115 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.65 % Allowed : 17.62 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.66 (0.16), residues: 2554 helix: 2.39 (0.11), residues: 1938 sheet: None (None), residues: 0 loop : -0.27 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.017 0.001 TYR B 524 PHE 0.025 0.002 PHE C 341 TRP 0.019 0.002 TRP A 335 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00471 (21639) covalent geometry : angle 0.55962 (29318) SS BOND : bond 0.00116 ( 3) SS BOND : angle 1.29436 ( 6) hydrogen bonds : bond 0.06703 ( 1402) hydrogen bonds : angle 3.50036 ( 4071) metal coordination : bond 0.00233 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 240 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5918 (ptm) REVERT: A 62 MET cc_start: 0.5648 (ptp) cc_final: 0.5320 (pmm) REVERT: A 211 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7275 (ttm110) REVERT: A 339 MET cc_start: 0.7009 (ttm) cc_final: 0.6745 (ttm) REVERT: A 378 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7636 (ptp90) REVERT: A 439 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 467 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7919 (mp) REVERT: D 471 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7303 (ttp) REVERT: D 629 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8090 (tp40) REVERT: C 186 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: C 304 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: C 410 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7324 (m-90) REVERT: C 652 ASP cc_start: 0.7804 (m-30) cc_final: 0.7476 (p0) REVERT: C 718 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7518 (ttm110) REVERT: B 102 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 229 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: B 434 TRP cc_start: 0.6893 (m100) cc_final: 0.6625 (m-90) REVERT: B 709 GLN cc_start: 0.7746 (mm-40) cc_final: 0.6935 (tt0) outliers start: 82 outliers final: 39 residues processed: 298 average time/residue: 0.5702 time to fit residues: 192.9623 Evaluate side-chains 280 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 86 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 0.0000 chunk 230 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN D 91 ASN C 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108781 restraints weight = 24219.505| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.11 r_work: 0.3175 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21651 Z= 0.126 Angle : 0.489 13.207 29324 Z= 0.257 Chirality : 0.036 0.185 3344 Planarity : 0.004 0.047 3631 Dihedral : 8.384 139.536 3115 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.71 % Allowed : 18.56 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.86 (0.16), residues: 2554 helix: 2.53 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : -0.19 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.014 0.001 TYR B 524 PHE 0.022 0.001 PHE C 341 TRP 0.015 0.001 TRP A 335 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00280 (21639) covalent geometry : angle 0.48887 (29318) SS BOND : bond 0.00094 ( 3) SS BOND : angle 0.82883 ( 6) hydrogen bonds : bond 0.05183 ( 1402) hydrogen bonds : angle 3.36810 ( 4071) metal coordination : bond 0.00100 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.5923 (ptm) REVERT: A 62 MET cc_start: 0.5586 (ptp) cc_final: 0.5276 (pmm) REVERT: A 211 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7248 (ttm110) REVERT: A 378 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7643 (ptp90) REVERT: A 439 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 467 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 726 LYS cc_start: 0.6288 (pmtt) cc_final: 0.5775 (ptpp) REVERT: D 215 ASP cc_start: 0.8054 (p0) cc_final: 0.7723 (p0) REVERT: D 524 TYR cc_start: 0.8261 (t80) cc_final: 0.8025 (t80) REVERT: C 186 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: C 304 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 410 TRP cc_start: 0.8401 (OUTLIER) cc_final: 0.7297 (m-90) REVERT: C 652 ASP cc_start: 0.7736 (m-30) cc_final: 0.7471 (p0) REVERT: C 718 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7579 (ttm170) REVERT: B 102 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7306 (t80) REVERT: B 229 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: B 434 TRP cc_start: 0.6951 (m100) cc_final: 0.6655 (m-90) REVERT: B 709 GLN cc_start: 0.7642 (mm-40) cc_final: 0.6511 (pt0) outliers start: 61 outliers final: 36 residues processed: 274 average time/residue: 0.6117 time to fit residues: 190.9720 Evaluate side-chains 269 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 163 optimal weight: 0.0040 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 206 optimal weight: 0.0970 chunk 220 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN D 91 ASN D 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112744 restraints weight = 24130.317| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.14 r_work: 0.3233 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21651 Z= 0.098 Angle : 0.455 14.200 29324 Z= 0.239 Chirality : 0.035 0.199 3344 Planarity : 0.004 0.046 3631 Dihedral : 7.891 133.202 3115 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.96 % Allowed : 19.49 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.16), residues: 2554 helix: 2.68 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : -0.09 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.012 0.001 TYR B 524 PHE 0.020 0.001 PHE C 341 TRP 0.012 0.001 TRP A 335 HIS 0.004 0.000 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00200 (21639) covalent geometry : angle 0.45493 (29318) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.52043 ( 6) hydrogen bonds : bond 0.03871 ( 1402) hydrogen bonds : angle 3.24318 ( 4071) metal coordination : bond 0.00037 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.5821 (ptm) REVERT: A 62 MET cc_start: 0.5586 (ptp) cc_final: 0.5280 (pmm) REVERT: A 211 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7159 (ttm110) REVERT: A 378 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7586 (ptp90) REVERT: A 430 TRP cc_start: 0.8359 (OUTLIER) cc_final: 0.7790 (m-90) REVERT: A 439 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 467 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 726 LYS cc_start: 0.6279 (pmtt) cc_final: 0.5868 (ptpp) REVERT: D 81 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7514 (mm-30) REVERT: D 380 MET cc_start: 0.7969 (mtm) cc_final: 0.7580 (mmp) REVERT: D 471 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6949 (ttp) REVERT: C 147 MET cc_start: 0.8338 (mtt) cc_final: 0.8049 (mtp) REVERT: C 186 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 304 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: C 410 TRP cc_start: 0.8294 (OUTLIER) cc_final: 0.7243 (m-90) REVERT: C 652 ASP cc_start: 0.7801 (m-30) cc_final: 0.7524 (p0) REVERT: C 718 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7370 (ttm110) REVERT: B 102 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 434 TRP cc_start: 0.7021 (m100) cc_final: 0.6711 (m-90) outliers start: 44 outliers final: 20 residues processed: 272 average time/residue: 0.5699 time to fit residues: 176.6162 Evaluate side-chains 258 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 202 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN D 92 HIS D 629 GLN C 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110542 restraints weight = 24304.841| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.16 r_work: 0.3201 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21651 Z= 0.113 Angle : 0.476 14.504 29324 Z= 0.250 Chirality : 0.036 0.206 3344 Planarity : 0.004 0.046 3631 Dihedral : 7.944 134.698 3115 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 19.85 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.16), residues: 2554 helix: 2.71 (0.12), residues: 1938 sheet: None (None), residues: 0 loop : -0.08 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.023 0.001 TYR D 45 PHE 0.021 0.001 PHE C 341 TRP 0.015 0.001 TRP A 335 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00246 (21639) covalent geometry : angle 0.47614 (29318) SS BOND : bond 0.00046 ( 3) SS BOND : angle 0.73228 ( 6) hydrogen bonds : bond 0.04469 ( 1402) hydrogen bonds : angle 3.25005 ( 4071) metal coordination : bond 0.00082 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5108 Ramachandran restraints generated. 2554 Oldfield, 0 Emsley, 2554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.5819 (ptm) REVERT: A 62 MET cc_start: 0.5559 (ptp) cc_final: 0.5278 (pmm) REVERT: A 378 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7581 (ptp90) REVERT: A 430 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.7809 (m-90) REVERT: A 439 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 467 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 726 LYS cc_start: 0.6200 (pmtt) cc_final: 0.5756 (ptpp) REVERT: A 750 MET cc_start: 0.3651 (pp-130) cc_final: 0.3431 (ppp) REVERT: D 81 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7505 (mm-30) REVERT: D 215 ASP cc_start: 0.7923 (p0) cc_final: 0.7704 (p0) REVERT: D 380 MET cc_start: 0.7992 (mtm) cc_final: 0.7532 (mmp) REVERT: D 471 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6980 (ttp) REVERT: C 147 MET cc_start: 0.8410 (mtt) cc_final: 0.8102 (mtp) REVERT: C 186 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: C 304 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: C 383 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7636 (mp) REVERT: C 410 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.7348 (m-90) REVERT: C 652 ASP cc_start: 0.7815 (m-30) cc_final: 0.7540 (p0) REVERT: C 718 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7532 (ttm170) REVERT: B 102 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7321 (t80) REVERT: B 434 TRP cc_start: 0.7010 (m100) cc_final: 0.6678 (m-90) outliers start: 41 outliers final: 22 residues processed: 256 average time/residue: 0.6251 time to fit residues: 181.9124 Evaluate side-chains 257 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 729 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 40 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 217 optimal weight: 0.0030 chunk 124 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109641 restraints weight = 24271.898| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.15 r_work: 0.3186 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21651 Z= 0.122 Angle : 0.491 13.464 29324 Z= 0.257 Chirality : 0.036 0.212 3344 Planarity : 0.004 0.046 3631 Dihedral : 8.041 137.358 3115 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.05 % Allowed : 19.67 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.16), residues: 2554 helix: 2.68 (0.12), residues: 1937 sheet: None (None), residues: 0 loop : -0.15 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.016 0.001 TYR B 430 PHE 0.022 0.001 PHE C 341 TRP 0.014 0.001 TRP A 335 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00274 (21639) covalent geometry : angle 0.49087 (29318) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.77819 ( 6) hydrogen bonds : bond 0.04830 ( 1402) hydrogen bonds : angle 3.28041 ( 4071) metal coordination : bond 0.00106 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8795.67 seconds wall clock time: 149 minutes 50.90 seconds (8990.90 seconds total)