Starting phenix.real_space_refine on Sun Jul 5 01:38:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28ke_56573/07_2026/28ke_56573.cif Found real_map, /net/cci-nas-00/data/ceres_data/28ke_56573/07_2026/28ke_56573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28ke_56573/07_2026/28ke_56573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28ke_56573/07_2026/28ke_56573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28ke_56573/07_2026/28ke_56573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28ke_56573/07_2026/28ke_56573.map" } resolution = 3.6 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= 0.002 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 40 5.49 5 S 146 5.16 5 C 15236 2.51 5 N 4173 2.21 5 O 4502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24107 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5052 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 25, 'TRANS': 599} Chain breaks: 3 Chain: "B" Number of atoms: 5600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5600 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 29, 'TRANS': 664} Chain breaks: 2 Chain: "C" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1221 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 145} Chain: "D" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3490 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2923 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 353} Chain breaks: 1 Chain: "F" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2045 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 1 Chain: "G" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 537 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "H" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 642 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "I" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 322 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain breaks: 1 Chain: "N" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 165} Chain: "L" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "M" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5995 SG CYS B 116 56.185 38.932 65.812 1.00222.50 S ATOM 6304 SG CYS B 155 52.473 35.094 61.863 1.00229.46 S ATOM 6135 SG CYS B 134 55.234 41.048 60.256 1.00213.53 S ATOM 6593 SG CYS B 190 50.256 40.375 64.368 1.00214.73 S ATOM 17955 SG CYS E 345 40.215 62.257 160.274 1.00 92.06 S ATOM 17977 SG CYS E 348 42.153 65.371 161.188 1.00 77.62 S ATOM 18134 SG CYS E 368 40.400 65.175 157.803 1.00 87.77 S ATOM 18155 SG CYS E 371 43.429 63.050 158.424 1.00 77.72 S ATOM 18075 SG CYS E 360 39.001 51.213 154.672 1.00111.21 S ATOM 18093 SG CYS E 363 39.920 49.805 158.136 1.00116.26 S ATOM 18242 SG CYS E 382 42.039 52.555 156.586 1.00 83.11 S ATOM 18259 SG CYS E 385 42.199 48.972 155.525 1.00 85.80 S ATOM 17519 SG CYS E 291 79.075 37.795 149.286 1.00 84.09 S ATOM 17541 SG CYS E 294 82.637 36.615 149.043 1.00 97.03 S ATOM 17630 SG CYS E 305 81.375 39.048 146.446 1.00 89.45 S ATOM 17653 SG CYS E 308 80.078 35.559 146.363 1.00 97.68 S ATOM 20175 SG CYS F 268 59.201 37.535 139.361 1.00 65.93 S ATOM 20194 SG CYS F 271 57.048 39.695 141.628 1.00 70.18 S ATOM 20279 SG CYS F 282 56.013 36.250 141.119 1.00 96.59 S ATOM 20299 SG CYS F 285 55.595 38.535 138.250 1.00103.44 S ATOM 20067 SG CYS F 255 60.075 34.986 154.006 1.00 74.47 S ATOM 20084 SG CYS F 257 58.337 32.297 151.873 1.00 78.65 S ATOM 20233 SG CYS F 276 62.073 32.046 152.440 1.00 77.35 S ATOM 21865 SG CYS N 105 48.702 102.565 47.799 1.00196.17 S ATOM 21889 SG CYS N 108 48.720 103.387 44.068 1.00204.58 S ATOM 22037 SG CYS N 126 50.685 100.460 45.433 1.00196.02 S ATOM 22059 SG CYS N 129 51.888 103.910 46.220 1.00200.61 S Time building chain proxies: 4.77, per 1000 atoms: 0.20 Number of scatterers: 24107 At special positions: 0 Unit cell: (120.6, 154.1, 207.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 146 16.00 P 40 15.00 O 4502 8.00 N 4173 7.00 C 15236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 126 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 129 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 108 " Number of angles added : 33 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 25 sheets defined 53.0% alpha, 10.8% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.551A pdb=" N MET A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.805A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.836A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.935A pdb=" N LEU A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 3.925A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.530A pdb=" N ARG A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 515 through 525 removed outlier: 4.199A pdb=" N ALA A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 removed outlier: 4.122A pdb=" N LEU A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 564 through 576 Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 667 through 676 removed outlier: 4.365A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.569A pdb=" N VAL A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 774 through 780 removed outlier: 3.991A pdb=" N ARG A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 46 through 63 Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.536A pdb=" N ARG B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.983A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.830A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 325 through 344 Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 369 through 387 removed outlier: 5.100A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.724A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.709A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.501A pdb=" N ARG B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.787A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 573 through 590 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.597A pdb=" N PHE B 651 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 685 Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 701 No H-bonds generated for 'chain 'B' and resid 700 through 701' Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.637A pdb=" N LEU B 706 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 725 Processing helix chain 'C' and resid 398 through 413 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 478 removed outlier: 3.576A pdb=" N CYS C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 516 removed outlier: 4.672A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 522 through 548 Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.517A pdb=" N PHE D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.582A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 75 No H-bonds generated for 'chain 'D' and resid 74 through 75' Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.757A pdb=" N LEU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.530A pdb=" N GLY D 227 " --> pdb=" O GLN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 removed outlier: 3.515A pdb=" N PHE D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 321 through 331 removed outlier: 4.198A pdb=" N PHE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.654A pdb=" N LYS D 378 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 397 removed outlier: 3.551A pdb=" N THR D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 400 No H-bonds generated for 'chain 'D' and resid 398 through 400' Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.601A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 removed outlier: 3.924A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 removed outlier: 3.826A pdb=" N GLU E 12 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 13 " --> pdb=" O ARG E 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 9 through 13' Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.677A pdb=" N LEU E 22 " --> pdb=" O TRP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 134 removed outlier: 4.627A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 157 removed outlier: 3.713A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.855A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.774A pdb=" N THR E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 removed outlier: 3.681A pdb=" N HIS E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 314 through 319 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 388 removed outlier: 3.520A pdb=" N LYS E 388 " --> pdb=" O GLY E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.110A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 removed outlier: 3.556A pdb=" N LYS F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 148 removed outlier: 3.536A pdb=" N SER F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'G' and resid 13 through 26 Processing helix chain 'G' and resid 50 through 64 removed outlier: 3.569A pdb=" N ASN G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 4.213A pdb=" N ILE H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.833A pdb=" N TYR H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN H 111 " --> pdb=" O PHE H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.746A pdb=" N THR H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 140 Processing helix chain 'I' and resid 890 through 902 removed outlier: 4.661A pdb=" N ALA I 894 " --> pdb=" O THR I 890 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU I 895 " --> pdb=" O SER I 891 " (cutoff:3.500A) Processing helix chain 'I' and resid 903 through 916 removed outlier: 4.017A pdb=" N ARG I 908 " --> pdb=" O TRP I 904 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) Processing helix chain 'I' and resid 935 through 939 removed outlier: 3.579A pdb=" N GLN I 939 " --> pdb=" O PRO I 936 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 120 removed outlier: 3.998A pdb=" N HIS N 120 " --> pdb=" O TYR N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 149 removed outlier: 3.619A pdb=" N LEU N 149 " --> pdb=" O LYS N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 156 Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 199 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.030A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 5.530A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 removed outlier: 4.533A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.030A pdb=" N GLY A 436 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 336 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 467 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL A 339 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.584A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 559 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN A 506 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N SER A 661 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA A 508 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 663 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 510 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS A 507 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ILE A 690 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 509 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.554A pdb=" N VAL B 206 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR B 207 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR B 72 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 231 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 494 removed outlier: 6.388A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 535 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.638A pdb=" N LEU D 66 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB5, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.556A pdb=" N VAL D 432 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 406 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY G 7 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.285A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE E 104 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU E 120 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.985A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 220 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.340A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 257 through 258 removed outlier: 3.579A pdb=" N VAL F 249 " --> pdb=" O HIS E 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC3, first strand: chain 'F' and resid 67 through 69 removed outlier: 8.213A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 8 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG F 160 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N LEU F 190 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU F 215 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 193 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AC5, first strand: chain 'N' and resid 103 through 104 Processing sheet with id=AC6, first strand: chain 'N' and resid 138 through 140 Processing sheet with id=AC7, first strand: chain 'N' and resid 246 through 251 removed outlier: 4.499A pdb=" N THR N 260 " --> pdb=" O PRO N 248 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10335 1.43 - 1.64: 14121 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24682 Sorted by residual: bond pdb=" C3' DT M 46 " pdb=" C2' DT M 46 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.42e+00 bond pdb=" C3' DG M 31 " pdb=" C2' DG M 31 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 bond pdb=" C3' DG M 42 " pdb=" C2' DG M 42 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.37e+00 bond pdb=" C1' DT L 20 " pdb=" N1 DT L 20 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.98e+00 bond pdb=" C3' DG M 38 " pdb=" C2' DG M 38 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.19e+00 ... (remaining 24677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 33265 2.58 - 5.17: 223 5.17 - 7.75: 30 7.75 - 10.34: 3 10.34 - 12.92: 2 Bond angle restraints: 33523 Sorted by residual: angle pdb=" CA MET H 122 " pdb=" CB MET H 122 " pdb=" CG MET H 122 " ideal model delta sigma weight residual 114.10 124.04 -9.94 2.00e+00 2.50e-01 2.47e+01 angle pdb=" N3 DT M 40 " pdb=" C4 DT M 40 " pdb=" O4 DT M 40 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT L 20 " pdb=" C4 DT L 20 " pdb=" O4 DT L 20 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT M 46 " pdb=" C4 DT M 46 " pdb=" O4 DT M 46 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT M 32 " pdb=" C4 DT M 32 " pdb=" O4 DT M 32 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 33518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 14144 33.95 - 67.90: 694 67.90 - 101.85: 42 101.85 - 135.80: 1 135.80 - 169.75: 3 Dihedral angle restraints: 14884 sinusoidal: 6394 harmonic: 8490 Sorted by residual: dihedral pdb=" C4' DG M 31 " pdb=" C3' DG M 31 " pdb=" O3' DG M 31 " pdb=" P DT M 32 " ideal model delta sinusoidal sigma weight residual -140.00 29.75 -169.75 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PRO B 532 " pdb=" C PRO B 532 " pdb=" N ASP B 533 " pdb=" CA ASP B 533 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C4' DT L 5 " pdb=" C3' DT L 5 " pdb=" O3' DT L 5 " pdb=" P DT L 6 " ideal model delta sinusoidal sigma weight residual 220.00 69.77 150.23 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 14881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3068 0.053 - 0.105: 577 0.105 - 0.158: 103 0.158 - 0.211: 4 0.211 - 0.264: 1 Chirality restraints: 3753 Sorted by residual: chirality pdb=" CB ILE B 418 " pdb=" CA ILE B 418 " pdb=" CG1 ILE B 418 " pdb=" CG2 ILE B 418 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO B 532 " pdb=" N PRO B 532 " pdb=" C PRO B 532 " pdb=" CB PRO B 532 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB VAL C 490 " pdb=" CA VAL C 490 " pdb=" CG1 VAL C 490 " pdb=" CG2 VAL C 490 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 3750 not shown) Planarity restraints: 4137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 501 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C GLN C 501 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN C 501 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL C 502 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 133 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ILE H 133 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE H 133 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN H 134 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 444 " -0.055 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO D 445 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 445 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 445 " -0.046 5.00e-02 4.00e+02 ... (remaining 4134 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 808 2.71 - 3.26: 23615 3.26 - 3.81: 38236 3.81 - 4.35: 45651 4.35 - 4.90: 77846 Nonbonded interactions: 186156 Sorted by model distance: nonbonded pdb=" O THR B 405 " pdb=" OG1 THR B 409 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASP H 114 " pdb=" ND2 ASN H 117 " model vdw 2.186 3.120 nonbonded pdb=" O LYS F 116 " pdb=" OG1 THR F 120 " model vdw 2.198 3.040 nonbonded pdb=" O PRO A 66 " pdb=" OG1 THR A 146 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B 72 " pdb=" OD2 ASP B 234 " model vdw 2.209 3.040 ... (remaining 186151 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 30.180 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.003 0.047 24710 Z= 0.191 Angle : 0.603 12.921 33568 Z= 0.342 Chirality : 0.042 0.264 3753 Planarity : 0.004 0.085 4137 Dihedral : 18.297 169.749 9376 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.26 % Allowed : 24.76 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2855 helix: 2.06 (0.14), residues: 1385 sheet: -0.31 (0.28), residues: 363 loop : -1.67 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 514 TYR 0.021 0.001 TYR C 516 PHE 0.027 0.001 PHE H 107 TRP 0.014 0.001 TRP I 904 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.19 (24682) covalent geometry : angle 0.58517 / 0.34 (33523) hydrogen bonds : bond 0.14986 / 9.73 ( 1154) hydrogen bonds : angle 5.30013 / 3.80 ( 3298) metal coordination : bond 0.00611 / 0.36 ( 28) metal coordination : angle 4.05628 / 2.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: A 412 MET cc_start: 0.8432 (tpp) cc_final: 0.7966 (tpp) REVERT: B 453 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7299 (p) REVERT: C 449 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6679 (tp) REVERT: C 452 MET cc_start: 0.6828 (tpp) cc_final: 0.6552 (tpp) REVERT: C 453 VAL cc_start: 0.6580 (t) cc_final: 0.6319 (p) REVERT: C 457 ILE cc_start: 0.5528 (mt) cc_final: 0.5237 (mt) REVERT: C 492 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8836 (mttt) REVERT: C 533 TYR cc_start: 0.8630 (m-10) cc_final: 0.8428 (m-10) REVERT: C 535 LYS cc_start: 0.8618 (tptp) cc_final: 0.8290 (tttp) REVERT: C 537 HIS cc_start: 0.8763 (t-170) cc_final: 0.8545 (t-170) REVERT: D 254 MET cc_start: 0.7499 (mtm) cc_final: 0.7249 (mtt) REVERT: D 315 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8906 (mt) REVERT: E 62 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.6859 (t80) REVERT: E 265 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: E 339 TYR cc_start: 0.6480 (t80) cc_final: 0.6017 (t80) REVERT: F 42 MET cc_start: 0.8974 (mtp) cc_final: 0.8738 (mtp) REVERT: F 215 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8659 (tp) REVERT: I 912 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6037 (mt-10) REVERT: I 928 LYS cc_start: 0.6512 (mmtt) cc_final: 0.5815 (tppt) REVERT: N 113 MET cc_start: 0.6004 (tpp) cc_final: 0.5765 (tpp) REVERT: N 118 MET cc_start: 0.8781 (tpp) cc_final: 0.8482 (mmm) REVERT: N 263 MET cc_start: 0.6487 (mmm) cc_final: 0.6192 (ptt) outliers start: 58 outliers final: 43 residues processed: 232 average time/residue: 0.1469 time to fit residues: 54.6647 Evaluate side-chains 219 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 97 GLN A 154 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 564 ASN A 598 HIS A 603 ASN A 665 GLN B 21 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 201 HIS B 241 ASN B 279 GLN B 629 GLN B 707 ASN C 474 HIS C 509 GLN C 537 HIS D 20 GLN D 83 GLN D 289 ASN D 312 ASN E 147 ASN F 63 HIS F 128 HIS F 145 HIS H 129 ASN I 914 GLN N 120 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.091210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063634 restraints weight = 71861.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062388 restraints weight = 48982.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.062847 restraints weight = 41097.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063164 restraints weight = 34605.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063262 restraints weight = 31866.259| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24710 Z= 0.150 Angle : 0.558 9.649 33568 Z= 0.290 Chirality : 0.041 0.233 3753 Planarity : 0.004 0.042 4137 Dihedral : 13.202 164.707 3668 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.62 % Allowed : 22.85 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2855 helix: 2.01 (0.14), residues: 1412 sheet: -0.22 (0.29), residues: 360 loop : -1.56 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 272 TYR 0.019 0.001 TYR A 534 PHE 0.011 0.001 PHE G 33 TRP 0.013 0.001 TRP I 904 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (24682) covalent geometry : angle 0.53867 / 0.29 (33523) hydrogen bonds : bond 0.04893 / 3.20 ( 1154) hydrogen bonds : angle 4.44692 / 3.20 ( 3298) metal coordination : bond 0.00680 / 0.39 ( 28) metal coordination : angle 4.02144 / 2.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 175 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8775 (tpp) cc_final: 0.8284 (tpp) REVERT: A 496 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 568 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 584 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7449 (p) REVERT: C 449 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6697 (tp) REVERT: C 453 VAL cc_start: 0.6681 (t) cc_final: 0.6436 (p) REVERT: C 492 LYS cc_start: 0.9157 (mmtp) cc_final: 0.8838 (mttt) REVERT: C 526 GLU cc_start: 0.7785 (mp0) cc_final: 0.7547 (mp0) REVERT: C 533 TYR cc_start: 0.8739 (m-10) cc_final: 0.8483 (m-10) REVERT: C 535 LYS cc_start: 0.8618 (tptp) cc_final: 0.8296 (tptm) REVERT: C 537 HIS cc_start: 0.8775 (t-90) cc_final: 0.8544 (t-170) REVERT: D 46 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8284 (mtm180) REVERT: D 62 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8581 (mp) REVERT: D 254 MET cc_start: 0.7460 (mtm) cc_final: 0.7117 (mtm) REVERT: D 258 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7657 (tt) REVERT: D 315 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8857 (mt) REVERT: E 62 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.6846 (t80) REVERT: E 339 TYR cc_start: 0.6360 (t80) cc_final: 0.5784 (t80) REVERT: F 42 MET cc_start: 0.9027 (mtp) cc_final: 0.8779 (mtp) REVERT: F 147 MET cc_start: 0.9128 (tpp) cc_final: 0.8809 (tpp) REVERT: G 32 LYS cc_start: 0.7960 (tptm) cc_final: 0.7265 (tppp) REVERT: I 912 GLU cc_start: 0.6431 (mm-30) cc_final: 0.5954 (mt-10) REVERT: I 928 LYS cc_start: 0.6515 (mmtt) cc_final: 0.5814 (tppt) REVERT: N 118 MET cc_start: 0.8861 (tpp) cc_final: 0.8578 (mmm) REVERT: N 258 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6953 (ttp80) REVERT: N 263 MET cc_start: 0.6533 (mmm) cc_final: 0.6317 (ptt) outliers start: 93 outliers final: 48 residues processed: 257 average time/residue: 0.1464 time to fit residues: 61.0050 Evaluate side-chains 229 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 265 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 198 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 363 GLN B 560 ASN D 460 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.063799 restraints weight = 71840.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062372 restraints weight = 50399.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063096 restraints weight = 40293.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063211 restraints weight = 35364.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.063639 restraints weight = 31235.755| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24710 Z= 0.136 Angle : 0.534 9.557 33568 Z= 0.274 Chirality : 0.040 0.217 3753 Planarity : 0.003 0.037 4137 Dihedral : 12.943 164.644 3614 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.97 % Allowed : 22.54 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2855 helix: 2.02 (0.14), residues: 1412 sheet: -0.19 (0.29), residues: 367 loop : -1.54 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.019 0.001 TYR A 534 PHE 0.010 0.001 PHE D 418 TRP 0.013 0.001 TRP I 904 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (24682) covalent geometry : angle 0.51329 / 0.27 (33523) hydrogen bonds : bond 0.04193 / 2.77 ( 1154) hydrogen bonds : angle 4.19640 / 3.02 ( 3298) metal coordination : bond 0.00592 / 0.34 ( 28) metal coordination : angle 4.03086 / 2.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 177 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8811 (tpp) cc_final: 0.8434 (tpp) REVERT: A 568 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8367 (tp) REVERT: A 584 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7401 (p) REVERT: B 42 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8249 (ttt) REVERT: B 365 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7532 (p) REVERT: B 438 MET cc_start: 0.8463 (mmt) cc_final: 0.8068 (mmm) REVERT: C 449 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6696 (tp) REVERT: C 457 ILE cc_start: 0.5654 (mt) cc_final: 0.5452 (mt) REVERT: C 470 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8143 (mm-30) REVERT: C 526 GLU cc_start: 0.7964 (mp0) cc_final: 0.7697 (mp0) REVERT: C 535 LYS cc_start: 0.8631 (tptp) cc_final: 0.8330 (tptm) REVERT: D 46 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8285 (mtm180) REVERT: D 62 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8549 (mp) REVERT: D 254 MET cc_start: 0.7442 (mtm) cc_final: 0.6961 (mtm) REVERT: D 258 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7619 (tt) REVERT: D 422 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8056 (pp) REVERT: E 62 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.6774 (t80) REVERT: F 42 MET cc_start: 0.9018 (mtp) cc_final: 0.8762 (mtp) REVERT: G 32 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7435 (tppp) REVERT: H 75 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7799 (mpp80) REVERT: I 911 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: I 912 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5930 (mt-10) REVERT: I 928 LYS cc_start: 0.6508 (mmtt) cc_final: 0.5818 (tppt) REVERT: N 118 MET cc_start: 0.8841 (tpp) cc_final: 0.8554 (mmm) REVERT: N 258 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7299 (ttp80) REVERT: N 263 MET cc_start: 0.6883 (mmm) cc_final: 0.6285 (ptt) outliers start: 102 outliers final: 61 residues processed: 269 average time/residue: 0.1672 time to fit residues: 72.0764 Evaluate side-chains 244 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 170 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 562 GLN Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 3 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 363 GLN C 537 HIS D 458 GLN G 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.091638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064571 restraints weight = 71469.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063278 restraints weight = 48269.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063828 restraints weight = 39559.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064074 restraints weight = 33001.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064239 restraints weight = 30840.958| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24710 Z= 0.166 Angle : 0.550 10.074 33568 Z= 0.280 Chirality : 0.041 0.306 3753 Planarity : 0.004 0.037 4137 Dihedral : 12.933 165.278 3605 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.32 % Allowed : 22.54 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 2855 helix: 1.99 (0.14), residues: 1414 sheet: -0.26 (0.29), residues: 369 loop : -1.55 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.019 0.001 TYR A 534 PHE 0.014 0.001 PHE C 500 TRP 0.014 0.001 TRP I 904 HIS 0.006 0.001 HIS N 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (24682) covalent geometry : angle 0.52894 / 0.28 (33523) hydrogen bonds : bond 0.04196 / 2.76 ( 1154) hydrogen bonds : angle 4.15814 / 2.99 ( 3298) metal coordination : bond 0.00716 / 0.42 ( 28) metal coordination : angle 4.16964 / 2.29 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 168 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8853 (tpp) cc_final: 0.8617 (tpt) REVERT: A 568 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8412 (tp) REVERT: B 42 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8252 (ttt) REVERT: B 365 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7529 (p) REVERT: B 438 MET cc_start: 0.8557 (mmt) cc_final: 0.8160 (mmm) REVERT: C 449 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6634 (tp) REVERT: C 526 GLU cc_start: 0.7965 (mp0) cc_final: 0.7641 (mp0) REVERT: D 46 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8303 (mtm180) REVERT: D 62 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8593 (mp) REVERT: D 254 MET cc_start: 0.7445 (mtm) cc_final: 0.6974 (mtm) REVERT: D 315 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8884 (mt) REVERT: D 422 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8123 (pp) REVERT: E 62 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.6982 (t80) REVERT: F 42 MET cc_start: 0.9002 (mtp) cc_final: 0.8733 (mtp) REVERT: G 32 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7501 (tppp) REVERT: H 75 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7788 (mpp80) REVERT: I 911 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: I 912 GLU cc_start: 0.6463 (mm-30) cc_final: 0.5958 (mt-10) REVERT: I 928 LYS cc_start: 0.6558 (mmtt) cc_final: 0.5867 (tppt) REVERT: N 118 MET cc_start: 0.8857 (tpp) cc_final: 0.8587 (mmm) REVERT: N 263 MET cc_start: 0.6942 (mmm) cc_final: 0.6408 (ptt) outliers start: 111 outliers final: 76 residues processed: 264 average time/residue: 0.1501 time to fit residues: 64.4216 Evaluate side-chains 251 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 163 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 125 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 15 optimal weight: 0.0980 chunk 237 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN C 537 HIS I 906 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065641 restraints weight = 70833.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064441 restraints weight = 46664.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064955 restraints weight = 38941.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065257 restraints weight = 32791.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065391 restraints weight = 30445.455| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24710 Z= 0.105 Angle : 0.514 9.898 33568 Z= 0.261 Chirality : 0.040 0.186 3753 Planarity : 0.003 0.037 4137 Dihedral : 12.883 164.380 3605 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.19 % Allowed : 23.86 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2855 helix: 2.06 (0.14), residues: 1415 sheet: -0.13 (0.29), residues: 366 loop : -1.50 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 473 TYR 0.024 0.001 TYR N 246 PHE 0.009 0.001 PHE C 500 TRP 0.013 0.001 TRP I 904 HIS 0.006 0.001 HIS N 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (24682) covalent geometry : angle 0.49398 / 0.26 (33523) hydrogen bonds : bond 0.03631 / 2.41 ( 1154) hydrogen bonds : angle 3.98310 / 2.87 ( 3298) metal coordination : bond 0.00456 / 0.25 ( 28) metal coordination : angle 3.90859 / 2.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 180 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8786 (tpp) cc_final: 0.8574 (tpt) REVERT: A 568 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8391 (tp) REVERT: A 584 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 42 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (ttt) REVERT: B 365 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7500 (p) REVERT: C 449 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6642 (tp) REVERT: C 526 GLU cc_start: 0.7979 (mp0) cc_final: 0.7610 (mp0) REVERT: D 46 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8247 (mtm180) REVERT: D 62 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8506 (mp) REVERT: D 254 MET cc_start: 0.7422 (mtm) cc_final: 0.7015 (mtm) REVERT: D 315 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8899 (mt) REVERT: E 62 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7051 (t80) REVERT: F 42 MET cc_start: 0.9007 (mtp) cc_final: 0.8716 (mtp) REVERT: G 32 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7865 (tppp) REVERT: H 75 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7701 (mpp80) REVERT: I 911 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: I 912 GLU cc_start: 0.6440 (mm-30) cc_final: 0.5937 (mt-10) REVERT: I 928 LYS cc_start: 0.6550 (mmtt) cc_final: 0.5823 (tppt) REVERT: N 118 MET cc_start: 0.8869 (tpp) cc_final: 0.8559 (mmm) REVERT: N 263 MET cc_start: 0.6942 (mmm) cc_final: 0.6634 (ptt) outliers start: 82 outliers final: 51 residues processed: 248 average time/residue: 0.1595 time to fit residues: 63.3841 Evaluate side-chains 231 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 58 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 189 optimal weight: 0.0870 chunk 284 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065177 restraints weight = 71638.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063551 restraints weight = 47204.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064106 restraints weight = 40434.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064451 restraints weight = 33820.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064541 restraints weight = 31110.513| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24710 Z= 0.165 Angle : 0.546 10.116 33568 Z= 0.276 Chirality : 0.040 0.204 3753 Planarity : 0.004 0.039 4137 Dihedral : 12.924 165.087 3602 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.13 % Allowed : 23.32 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2855 helix: 2.04 (0.14), residues: 1423 sheet: -0.27 (0.29), residues: 369 loop : -1.52 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 325 TYR 0.018 0.001 TYR A 534 PHE 0.016 0.001 PHE C 500 TRP 0.013 0.001 TRP I 904 HIS 0.008 0.001 HIS N 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (24682) covalent geometry : angle 0.52574 / 0.27 (33523) hydrogen bonds : bond 0.03917 / 2.58 ( 1154) hydrogen bonds : angle 4.02167 / 2.90 ( 3298) metal coordination : bond 0.00692 / 0.40 ( 28) metal coordination : angle 4.09399 / 2.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 170 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8876 (tpp) cc_final: 0.8672 (tpt) REVERT: A 568 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8407 (tp) REVERT: B 42 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (ttt) REVERT: C 498 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7268 (mt-10) REVERT: C 535 LYS cc_start: 0.8750 (tppt) cc_final: 0.8455 (tppp) REVERT: C 537 HIS cc_start: 0.8700 (t70) cc_final: 0.8474 (t70) REVERT: D 46 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8327 (mtm180) REVERT: D 62 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8551 (mp) REVERT: D 254 MET cc_start: 0.7524 (mtm) cc_final: 0.7142 (mtm) REVERT: D 258 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7771 (tt) REVERT: D 315 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8888 (mt) REVERT: E 62 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7012 (t80) REVERT: F 42 MET cc_start: 0.8990 (mtp) cc_final: 0.8710 (mtp) REVERT: G 32 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (tppp) REVERT: I 911 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: I 912 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5922 (mt-10) REVERT: I 928 LYS cc_start: 0.6573 (mmtt) cc_final: 0.5846 (tppt) REVERT: N 118 MET cc_start: 0.8877 (tpp) cc_final: 0.8570 (mmm) REVERT: N 263 MET cc_start: 0.6950 (mmm) cc_final: 0.6460 (ptt) outliers start: 106 outliers final: 84 residues processed: 262 average time/residue: 0.1501 time to fit residues: 63.9377 Evaluate side-chains 258 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 165 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 658 ARG Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 167 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 211 optimal weight: 0.0470 chunk 256 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.092741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065565 restraints weight = 71076.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064364 restraints weight = 47583.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064937 restraints weight = 38449.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065264 restraints weight = 32501.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065362 restraints weight = 30095.091| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24710 Z= 0.110 Angle : 0.521 10.515 33568 Z= 0.262 Chirality : 0.040 0.186 3753 Planarity : 0.003 0.036 4137 Dihedral : 12.893 164.467 3600 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.62 % Allowed : 24.33 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2855 helix: 2.08 (0.14), residues: 1422 sheet: -0.18 (0.29), residues: 369 loop : -1.46 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.018 0.001 TYR A 534 PHE 0.010 0.001 PHE B 720 TRP 0.012 0.001 TRP I 904 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (24682) covalent geometry : angle 0.50103 / 0.26 (33523) hydrogen bonds : bond 0.03520 / 2.33 ( 1154) hydrogen bonds : angle 3.90201 / 2.81 ( 3298) metal coordination : bond 0.00480 / 0.26 ( 28) metal coordination : angle 3.90805 / 2.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 179 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8845 (tpp) cc_final: 0.8612 (tpt) REVERT: A 568 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8397 (tp) REVERT: A 584 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7529 (p) REVERT: B 42 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8136 (ttt) REVERT: C 441 MET cc_start: 0.8526 (mmt) cc_final: 0.7945 (mmm) REVERT: C 449 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6684 (tp) REVERT: C 452 MET cc_start: 0.6675 (tpp) cc_final: 0.6278 (tpp) REVERT: C 535 LYS cc_start: 0.8710 (tppt) cc_final: 0.8366 (tptm) REVERT: D 46 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8245 (mtm180) REVERT: D 62 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8501 (mp) REVERT: D 254 MET cc_start: 0.7483 (mtm) cc_final: 0.7117 (mtm) REVERT: D 258 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7701 (tt) REVERT: D 315 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8898 (mt) REVERT: E 62 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.7013 (t80) REVERT: E 339 TYR cc_start: 0.6226 (t80) cc_final: 0.5699 (t80) REVERT: E 342 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6644 (tp30) REVERT: F 42 MET cc_start: 0.8973 (mtp) cc_final: 0.8684 (mtp) REVERT: G 32 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7864 (tppp) REVERT: H 75 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7723 (mpp80) REVERT: I 911 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: I 912 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5918 (mt-10) REVERT: I 928 LYS cc_start: 0.6538 (mmtt) cc_final: 0.5816 (tppt) REVERT: N 118 MET cc_start: 0.8860 (tpp) cc_final: 0.8547 (mmm) REVERT: N 263 MET cc_start: 0.7030 (mmm) cc_final: 0.6458 (ptt) outliers start: 93 outliers final: 70 residues processed: 259 average time/residue: 0.1544 time to fit residues: 64.5936 Evaluate side-chains 251 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 168 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS C 458 GLN C 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063810 restraints weight = 71346.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062802 restraints weight = 48768.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063416 restraints weight = 38793.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063670 restraints weight = 32988.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063769 restraints weight = 30402.267| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24710 Z= 0.195 Angle : 0.571 11.562 33568 Z= 0.288 Chirality : 0.041 0.210 3753 Planarity : 0.004 0.036 4137 Dihedral : 13.006 165.631 3600 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 4.05 % Allowed : 23.90 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2855 helix: 2.02 (0.14), residues: 1422 sheet: -0.36 (0.29), residues: 367 loop : -1.52 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 227 TYR 0.024 0.001 TYR G 22 PHE 0.012 0.001 PHE F 182 TRP 0.013 0.001 TRP I 904 HIS 0.012 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (24682) covalent geometry : angle 0.54925 / 0.29 (33523) hydrogen bonds : bond 0.04144 / 2.73 ( 1154) hydrogen bonds : angle 4.04898 / 2.91 ( 3298) metal coordination : bond 0.00817 / 0.47 ( 28) metal coordination : angle 4.28709 / 2.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 167 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.8394 (ttm) cc_final: 0.8123 (ttm) REVERT: A 568 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8341 (tp) REVERT: B 42 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8232 (ttt) REVERT: C 449 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6698 (tp) REVERT: C 452 MET cc_start: 0.6595 (tpp) cc_final: 0.6094 (tpp) REVERT: C 535 LYS cc_start: 0.8788 (tppt) cc_final: 0.8565 (tppp) REVERT: D 46 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8376 (mtm180) REVERT: D 62 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8589 (mp) REVERT: D 254 MET cc_start: 0.7529 (mtm) cc_final: 0.7072 (mtm) REVERT: D 315 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8890 (mt) REVERT: E 62 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.7034 (t80) REVERT: E 342 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: F 42 MET cc_start: 0.8965 (mtp) cc_final: 0.8714 (mtp) REVERT: G 32 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7879 (tppp) REVERT: I 911 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: I 912 GLU cc_start: 0.6405 (mm-30) cc_final: 0.5912 (mt-10) REVERT: I 928 LYS cc_start: 0.6577 (mmtt) cc_final: 0.5850 (tppt) REVERT: N 118 MET cc_start: 0.8852 (tpp) cc_final: 0.8547 (mmm) outliers start: 104 outliers final: 80 residues processed: 259 average time/residue: 0.1564 time to fit residues: 66.4226 Evaluate side-chains 252 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 162 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 658 ARG Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 260 optimal weight: 0.5980 chunk 263 optimal weight: 8.9990 chunk 215 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065682 restraints weight = 71603.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064756 restraints weight = 48549.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065253 restraints weight = 39071.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.065561 restraints weight = 33430.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.065666 restraints weight = 30998.991| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24710 Z= 0.102 Angle : 0.529 12.525 33568 Z= 0.266 Chirality : 0.040 0.224 3753 Planarity : 0.003 0.036 4137 Dihedral : 12.943 164.574 3600 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.39 % Allowed : 24.76 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2855 helix: 2.10 (0.14), residues: 1422 sheet: -0.23 (0.29), residues: 369 loop : -1.45 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 75 TYR 0.025 0.001 TYR G 22 PHE 0.010 0.001 PHE G 33 TRP 0.012 0.001 TRP I 904 HIS 0.012 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (24682) covalent geometry : angle 0.50963 / 0.27 (33523) hydrogen bonds : bond 0.03544 / 2.34 ( 1154) hydrogen bonds : angle 3.89288 / 2.80 ( 3298) metal coordination : bond 0.00432 / 0.23 ( 28) metal coordination : angle 3.93638 / 2.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 176 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 42 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8125 (ttt) REVERT: C 441 MET cc_start: 0.8431 (mmt) cc_final: 0.8059 (mmm) REVERT: C 449 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6688 (tp) REVERT: C 452 MET cc_start: 0.6835 (tpp) cc_final: 0.6460 (tpp) REVERT: C 535 LYS cc_start: 0.8796 (tppt) cc_final: 0.8446 (tptm) REVERT: D 46 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8273 (mtm180) REVERT: D 62 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 315 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8887 (mt) REVERT: E 62 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7026 (t80) REVERT: E 339 TYR cc_start: 0.6658 (t80) cc_final: 0.6140 (t80) REVERT: F 42 MET cc_start: 0.8964 (mtp) cc_final: 0.8680 (mtp) REVERT: I 911 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: I 912 GLU cc_start: 0.6398 (mm-30) cc_final: 0.5908 (mt-10) REVERT: I 928 LYS cc_start: 0.6533 (mmtt) cc_final: 0.5806 (tppt) REVERT: N 118 MET cc_start: 0.8857 (tpp) cc_final: 0.8523 (mmm) REVERT: N 246 TYR cc_start: 0.3982 (m-80) cc_final: 0.3777 (t80) outliers start: 87 outliers final: 71 residues processed: 249 average time/residue: 0.1518 time to fit residues: 61.9203 Evaluate side-chains 250 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 171 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 49 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN C 537 HIS D 161 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.090794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064432 restraints weight = 71786.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.062615 restraints weight = 48045.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063159 restraints weight = 42047.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063364 restraints weight = 34895.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063737 restraints weight = 32139.734| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24710 Z= 0.257 Angle : 0.631 15.694 33568 Z= 0.318 Chirality : 0.043 0.219 3753 Planarity : 0.004 0.065 4137 Dihedral : 13.071 165.832 3600 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.46 % Allowed : 24.56 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2855 helix: 1.95 (0.14), residues: 1423 sheet: -0.49 (0.29), residues: 362 loop : -1.53 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 419 TYR 0.024 0.002 TYR E 339 PHE 0.021 0.002 PHE N 219 TRP 0.012 0.001 TRP I 904 HIS 0.005 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (24682) covalent geometry : angle 0.60979 / 0.32 (33523) hydrogen bonds : bond 0.04363 / 2.87 ( 1154) hydrogen bonds : angle 4.13927 / 2.97 ( 3298) metal coordination : bond 0.01003 / 0.59 ( 28) metal coordination : angle 4.44238 / 2.52 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 165 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 42 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8223 (ttt) REVERT: C 441 MET cc_start: 0.8585 (mmt) cc_final: 0.8068 (mmm) REVERT: C 449 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6665 (tp) REVERT: C 452 MET cc_start: 0.6576 (tpp) cc_final: 0.6066 (tpp) REVERT: C 498 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 527 GLU cc_start: 0.8713 (pt0) cc_final: 0.7826 (pt0) REVERT: C 535 LYS cc_start: 0.8757 (tppt) cc_final: 0.8422 (tptm) REVERT: D 46 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8427 (mtm180) REVERT: D 62 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8620 (mp) REVERT: D 315 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8907 (mt) REVERT: E 62 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.7100 (t80) REVERT: E 339 TYR cc_start: 0.6831 (t80) cc_final: 0.6311 (t80) REVERT: F 42 MET cc_start: 0.8956 (mtp) cc_final: 0.8708 (mtp) REVERT: H 75 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7391 (mpp80) REVERT: I 911 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: I 912 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5920 (mt-10) REVERT: I 928 LYS cc_start: 0.6595 (mmtt) cc_final: 0.5862 (tppt) REVERT: N 118 MET cc_start: 0.8861 (tpp) cc_final: 0.8553 (mmm) outliers start: 89 outliers final: 77 residues processed: 242 average time/residue: 0.1474 time to fit residues: 58.8040 Evaluate side-chains 248 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 163 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 238 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 72 optimal weight: 0.0770 chunk 148 optimal weight: 0.6980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN D 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.092572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065234 restraints weight = 70833.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064253 restraints weight = 47784.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.064828 restraints weight = 37914.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065127 restraints weight = 32310.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065230 restraints weight = 29815.450| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24710 Z= 0.107 Angle : 0.555 14.445 33568 Z= 0.277 Chirality : 0.040 0.179 3753 Planarity : 0.003 0.048 4137 Dihedral : 12.996 164.468 3600 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.11 % Allowed : 25.07 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2855 helix: 2.08 (0.14), residues: 1422 sheet: -0.31 (0.29), residues: 361 loop : -1.46 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 419 TYR 0.019 0.001 TYR A 534 PHE 0.013 0.001 PHE G 33 TRP 0.013 0.001 TRP A 429 HIS 0.036 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (24682) covalent geometry : angle 0.53627 / 0.28 (33523) hydrogen bonds : bond 0.03569 / 2.36 ( 1154) hydrogen bonds : angle 3.91084 / 2.82 ( 3298) metal coordination : bond 0.00455 / 0.24 ( 28) metal coordination : angle 3.98524 / 2.08 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3575.64 seconds wall clock time: 62 minutes 57.61 seconds (3777.61 seconds total)