Starting phenix.real_space_refine on Sat Aug 8 11:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oki_16929/08_2026/8oki_16929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oki_16929/08_2026/8oki_16929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oki_16929/08_2026/8oki_16929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oki_16929/08_2026/8oki_16929.map" model { file = "/net/cci-nas-00/data/ceres_data/8oki_16929/08_2026/8oki_16929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oki_16929/08_2026/8oki_16929.cif" } resolution = 3.45 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= 0.003 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 Zn 6 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 115 5.16 5 C 17992 2.51 5 N 4977 2.21 5 O 5413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28556 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7197 Classifications: {'peptide': 901} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 848} Chain: "B" Number of atoms: 8825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8825 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 61, 'TRANS': 1039} Chain breaks: 1 Chain: "C" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3057 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 16, 'TRANS': 373} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain: "G" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "H" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "I" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "K" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 6, 'TRANS': 47} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 777 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "N" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "P" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 393 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "X" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 537 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Y" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "Z" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1528 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} Chain: "P" 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 434 SG CYS A 57 49.398 75.659 72.807 1.00 0.73 S ATOM 456 SG CYS A 60 50.779 73.025 70.375 1.00 0.67 S ATOM 499 SG CYS A 67 52.874 74.139 73.409 1.00 0.77 S ATOM 736 SG CYS A 97 69.638 115.164 49.497 1.00 0.80 S ATOM 762 SG CYS A 100 68.180 113.138 47.037 1.00 0.73 S ATOM 1138 SG CYS A 144 71.514 114.945 46.201 1.00 0.72 S ATOM 1161 SG CYS A 147 68.177 116.813 46.195 1.00 0.78 S ATOM 15554 SG CYS B1059 56.821 76.522 54.477 1.00 0.85 S ATOM 15577 SG CYS B1062 57.993 79.965 55.428 1.00 30.00 S ATOM 15707 SG CYS B1077 54.957 78.426 57.137 1.00 0.84 S ATOM 15727 SG CYS B1080 54.678 79.520 53.509 1.00 0.68 S ATOM 22442 SG CYS I 6 28.316 124.163 97.178 1.00204.53 S ATOM 22469 SG CYS I 9 28.858 127.539 95.383 1.00190.06 S ATOM 22546 SG CYS I 18 30.715 126.584 98.670 1.00201.96 S ATOM 22566 SG CYS I 21 27.090 127.547 98.643 1.00203.74 S ATOM 24116 SG CYS N 7 100.574 45.559 119.323 1.00 0.59 S ATOM 24140 SG CYS N 10 101.983 42.016 119.431 1.00 0.59 S ATOM 24420 SG CYS N 44 104.280 45.056 118.641 1.00 0.60 S ATOM 24426 SG CYS N 45 102.978 44.330 122.104 1.00 0.60 S ATOM 24662 SG CYS P 8 63.388 69.175 130.153 1.00 86.83 S ATOM 24688 SG CYS P 11 63.317 67.111 133.080 1.00 84.70 S ATOM 24817 SG CYS P 27 60.075 69.096 132.078 1.00 79.74 S ATOM 24842 SG CYS P 30 63.150 70.776 133.697 1.00 82.76 S Time building chain proxies: 5.57, per 1000 atoms: 0.20 Number of scatterers: 28556 At special positions: 0 Unit cell: (151.976, 148.104, 151.008, 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 S 115 16.00 P 52 15.00 Mg 1 11.99 O 5413 8.00 N 4977 7.00 C 17992 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 57 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 60 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 67 " pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 100 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 144 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 147 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1059 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1077 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1062 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb=" ZN I 101 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 21 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 18 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 9 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 6 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 11 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 8 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 30 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 27 " Number of angles added : 33 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6370 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 43 sheets defined 41.4% alpha, 20.1% beta 23 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 106 through 119 removed outlier: 4.346A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.517A pdb=" N GLU A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.916A pdb=" N ASP A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 removed outlier: 6.154A pdb=" N LYS A 193 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 194 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 206 through 209 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 236 through 259 removed outlier: 3.636A pdb=" N HIS A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.715A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.643A pdb=" N LYS A 306 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.668A pdb=" N ASN A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 4.266A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.822A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.634A pdb=" N SER A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.874A pdb=" N LEU A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.171A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 663 removed outlier: 3.696A pdb=" N GLY A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.541A pdb=" N ASP A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 671 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A 672 " --> pdb=" O ASP A 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 667 through 672' Processing helix chain 'A' and resid 674 through 701 removed outlier: 3.809A pdb=" N VAL A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 695 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 738 removed outlier: 3.755A pdb=" N VAL A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.603A pdb=" N ILE A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 847 removed outlier: 4.355A pdb=" N GLU A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN A 835 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 880 Processing helix chain 'A' and resid 887 through 900 removed outlier: 3.593A pdb=" N ILE A 891 " --> pdb=" O ASP A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.678A pdb=" N LEU B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 51 removed outlier: 4.074A pdb=" N SER B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.697A pdb=" N LEU B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.607A pdb=" N ILE B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 4.069A pdb=" N GLU B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 283 through 299 removed outlier: 3.885A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 347 through 379 removed outlier: 3.663A pdb=" N LYS B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 3.971A pdb=" N ASN B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 Processing helix chain 'B' and resid 398 through 411 removed outlier: 3.612A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.827A pdb=" N ASP B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 460 Processing helix chain 'B' and resid 491 through 500 removed outlier: 4.018A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 removed outlier: 3.891A pdb=" N LEU B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 537 " --> pdb=" O LYS B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 597 Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 626 through 630 removed outlier: 4.049A pdb=" N VAL B 630 " --> pdb=" O PRO B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.037A pdb=" N LEU B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.865A pdb=" N ASN B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 702 through 708 removed outlier: 4.045A pdb=" N LYS B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 911 through 917 removed outlier: 4.753A pdb=" N SER B 915 " --> pdb=" O HIS B 911 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 916 " --> pdb=" O GLY B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 4.194A pdb=" N LEU B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 removed outlier: 3.870A pdb=" N GLY B 945 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 959 removed outlier: 3.534A pdb=" N GLY B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 998 Processing helix chain 'B' and resid 1027 through 1038 Processing helix chain 'B' and resid 1039 through 1048 Processing helix chain 'B' and resid 1092 through 1105 removed outlier: 3.548A pdb=" N MET B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.506A pdb=" N ILE C 7 " --> pdb=" O SER C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 35 removed outlier: 3.628A pdb=" N TYR C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 58 Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.804A pdb=" N VAL C 69 " --> pdb=" O PRO C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.797A pdb=" N LEU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 148' Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.956A pdb=" N VAL C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.624A pdb=" N ILE C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 298 removed outlier: 3.619A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.982A pdb=" N ILE C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 309 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 310 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 3.563A pdb=" N LYS C 332 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.571A pdb=" N ARG C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 169 through 181 removed outlier: 4.029A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 260 removed outlier: 4.128A pdb=" N THR D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 26 removed outlier: 3.516A pdb=" N LYS G 20 " --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 61 removed outlier: 3.663A pdb=" N VAL G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 79 through 84 removed outlier: 3.677A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.527A pdb=" N TYR H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 54 Processing helix chain 'I' and resid 42 through 49 removed outlier: 3.557A pdb=" N LYS I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 21 Processing helix chain 'K' and resid 35 through 47 Processing helix chain 'L' and resid 21 through 33 removed outlier: 3.893A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 93 removed outlier: 3.736A pdb=" N ILE L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS L 83 " --> pdb=" O PHE L 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 27 removed outlier: 3.783A pdb=" N PHE N 21 " --> pdb=" O LYS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 39 Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.603A pdb=" N ARG N 46 " --> pdb=" O ARG N 42 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU N 49 " --> pdb=" O CYS N 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER N 51 " --> pdb=" O ARG N 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 removed outlier: 4.280A pdb=" N THR E 19 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 36 removed outlier: 4.503A pdb=" N GLY E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 173 through 189 Processing helix chain 'F' and resid 13 through 32 removed outlier: 3.782A pdb=" N GLU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 51 removed outlier: 3.802A pdb=" N PHE F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 removed outlier: 3.580A pdb=" N PHE F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.504A pdb=" N LEU F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 116 Processing sheet with id=AA1, first strand: chain 'B' and resid 1054 through 1059 removed outlier: 4.714A pdb=" N GLU B1090 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 5 " --> pdb=" O GLU B1090 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 5 " --> pdb=" O SER B1114 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER B1114 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1054 through 1059 removed outlier: 4.714A pdb=" N GLU B1090 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 5 " --> pdb=" O GLU B1090 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 81 removed outlier: 6.872A pdb=" N THR A 213 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N ARG A 78 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N VAL A 211 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.581A pdb=" N LYS A 319 " --> pdb=" O PHE B1026 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1000 through 1002 removed outlier: 3.539A pdb=" N SER A 324 " --> pdb=" O ARG B1002 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 327 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 340 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL A 342 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE A 445 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 328 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU A 447 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 330 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.651A pdb=" N ARG A 411 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR A 380 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.782A pdb=" N GLY A 495 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 517 through 518 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 570 removed outlier: 6.712A pdb=" N TYR A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.873A pdb=" N VAL A 858 " --> pdb=" O VAL A 866 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 52 through 53 removed outlier: 5.747A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 53 removed outlier: 5.747A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 102 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG B 119 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU B 117 " --> pdb=" O MET B 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB7, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB8, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.162A pdb=" N SER B 167 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AC1, first strand: chain 'B' and resid 485 through 486 Processing sheet with id=AC2, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC3, first strand: chain 'B' and resid 505 through 506 removed outlier: 7.195A pdb=" N VAL B 519 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 528 " --> pdb=" O TRP B 517 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP B 517 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.628A pdb=" N GLY B 689 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 843 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.628A pdb=" N GLY B 689 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA P 4 " --> pdb=" O LEU P 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU P 17 " --> pdb=" O ALA P 4 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AC7, first strand: chain 'B' and resid 965 through 966 removed outlier: 7.413A pdb=" N ILE B 735 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 889 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 737 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE B 982 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 806 through 808 removed outlier: 6.945A pdb=" N VAL B 835 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 811 through 812 Processing sheet with id=AD1, first strand: chain 'B' and resid 897 through 898 removed outlier: 3.543A pdb=" N TRP B 897 " --> pdb=" O TYR B 969 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1067 through 1069 removed outlier: 3.521A pdb=" N ARG B1074 " --> pdb=" O ASP B1069 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 233 through 239 removed outlier: 4.264A pdb=" N LYS C 233 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 248 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 242 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR C 243 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 122 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET C 118 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR C 121 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG C 265 " --> pdb=" O TYR C 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 149 through 155 Processing sheet with id=AD5, first strand: chain 'K' and resid 52 through 53 removed outlier: 4.899A pdb=" N LEU C 382 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 59 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 5 through 12 removed outlier: 6.592A pdb=" N LYS D 17 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS D 11 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 18 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR D 158 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ASN D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N LYS D 156 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N TYR D 222 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N TYR D 154 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N PHE D 224 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N PHE D 152 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 190 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 107 through 108 removed outlier: 3.502A pdb=" N LEU D 93 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 133 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG D 130 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN D 52 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 132 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS D 138 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL D 44 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY D 140 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE D 42 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.973A pdb=" N VAL D 123 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 66 through 69 removed outlier: 6.975A pdb=" N ARG G 9 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 69 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA G 7 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA G 35 " --> pdb=" O GLU G 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE I 35 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 18 through 20 removed outlier: 5.594A pdb=" N ILE H 43 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE3, first strand: chain 'L' and resid 2 through 9 removed outlier: 3.582A pdb=" N LYS L 2 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS L 8 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU L 12 " --> pdb=" O LYS L 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 44 through 54 removed outlier: 6.780A pdb=" N LEU E 75 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE E 48 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP E 73 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU E 50 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL E 71 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LYS E 52 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N GLU E 69 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ILE E 54 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N TYR E 67 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 66 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE E 4 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS F 10 " --> pdb=" O ILE E 4 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 105 through 109 removed outlier: 6.232A pdb=" N ARG E 100 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 89 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 145 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY E 162 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE E 149 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG E 160 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 105 through 109 removed outlier: 6.232A pdb=" N ARG E 100 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 89 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 143 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 118 through 121 1173 hydrogen bonds defined for protein. 3243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9219 1.34 - 1.46: 4981 1.46 - 1.58: 14700 1.58 - 1.70: 100 1.70 - 1.82: 200 Bond restraints: 29200 Sorted by residual: bond pdb=" C3' DG X 6 " pdb=" C2' DG X 6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.87e+00 bond pdb=" C1' DT X 7 " pdb=" N1 DT X 7 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.56e+00 bond pdb=" C3' DA Y 26 " pdb=" C2' DA Y 26 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.00e+00 bond pdb=" C3' DG Y 10 " pdb=" C2' DG Y 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.20e+00 bond pdb=" C3' DA X 8 " pdb=" C2' DA X 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.09e+00 ... (remaining 29195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 39185 2.27 - 4.53: 418 4.53 - 6.80: 33 6.80 - 9.06: 12 9.06 - 11.33: 1 Bond angle restraints: 39649 Sorted by residual: angle pdb=" N3 DT X 7 " pdb=" C4 DT X 7 " pdb=" O4 DT X 7 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4 DT X 7 " pdb=" C4 DT X 7 " pdb=" C5 DT X 7 " ideal model delta sigma weight residual 124.90 121.70 3.20 7.00e-01 2.04e+00 2.09e+01 angle pdb=" N3 DT X 20 " pdb=" C4 DT X 20 " pdb=" O4 DT X 20 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O4' DC X 15 " pdb=" C4' DC X 15 " pdb=" C3' DC X 15 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 39644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 17150 34.69 - 69.38: 633 69.38 - 104.07: 63 104.07 - 138.77: 1 138.77 - 173.46: 2 Dihedral angle restraints: 17849 sinusoidal: 7934 harmonic: 9915 Sorted by residual: dihedral pdb=" C4' DG Y 10 " pdb=" C3' DG Y 10 " pdb=" O3' DG Y 10 " pdb=" P DT Y 11 " ideal model delta sinusoidal sigma weight residual -140.00 33.46 -173.46 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT X 23 " pdb=" C3' DT X 23 " pdb=" O3' DT X 23 " pdb=" P DT X 24 " ideal model delta sinusoidal sigma weight residual 220.00 65.84 154.16 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" C4' DG X 6 " pdb=" C3' DG X 6 " pdb=" O3' DG X 6 " pdb=" P DT X 7 " ideal model delta sinusoidal sigma weight residual 220.00 86.06 133.94 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 17846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3118 0.039 - 0.077: 837 0.077 - 0.116: 395 0.116 - 0.155: 59 0.155 - 0.193: 3 Chirality restraints: 4412 Sorted by residual: chirality pdb=" CG LEU F 66 " pdb=" CB LEU F 66 " pdb=" CD1 LEU F 66 " pdb=" CD2 LEU F 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" C3' DT X 23 " pdb=" C4' DT X 23 " pdb=" O3' DT X 23 " pdb=" C2' DT X 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR E 33 " pdb=" CA THR E 33 " pdb=" OG1 THR E 33 " pdb=" CG2 THR E 33 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 4409 not shown) Planarity restraints: 4948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 175 " 0.025 2.00e-02 2.50e+03 2.71e-02 1.83e+01 pdb=" CG TRP E 175 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP E 175 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP E 175 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 175 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 175 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 175 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 175 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 175 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 175 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 80 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" CD GLU G 80 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU G 80 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU G 80 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 30 " 0.010 2.00e-02 2.50e+03 1.26e-02 3.97e+00 pdb=" CG TRP I 30 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP I 30 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP I 30 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 30 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 30 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 30 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 30 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 30 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 30 " -0.000 2.00e-02 2.50e+03 ... (remaining 4945 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 179 2.59 - 3.17: 22766 3.17 - 3.75: 42426 3.75 - 4.32: 57251 4.32 - 4.90: 97271 Nonbonded interactions: 219893 Sorted by model distance: nonbonded pdb=" O3' G Z 19 " pdb="MG MG A1002 " model vdw 2.014 2.170 nonbonded pdb=" OD1 ASP A 458 " pdb="MG MG A1002 " model vdw 2.016 2.170 nonbonded pdb=" OE2 GLU C 239 " pdb=" OH TYR C 246 " model vdw 2.158 3.040 nonbonded pdb=" O HIS E 82 " pdb=" ND1 HIS E 82 " model vdw 2.173 3.120 nonbonded pdb=" N GLU H 24 " pdb=" OE1 GLU H 24 " model vdw 2.180 3.120 ... (remaining 219888 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=0.18 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 34.010 Find NCS groups from input model: 0.100 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.045 29224 Z= 0.172 Angle : 0.575 11.417 39682 Z= 0.342 Chirality : 0.044 0.193 4412 Planarity : 0.004 0.042 4948 Dihedral : 17.177 173.456 11479 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.09 % Rotamer: Outliers : 0.17 % Allowed : 17.58 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.61 (0.15), residues: 3402 helix: 1.39 (0.16), residues: 1184 sheet: 0.18 (0.23), residues: 505 loop : -0.14 (0.16), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 100 TYR 0.017 0.001 TYR P 29 PHE 0.019 0.001 PHE E 95 TRP 0.070 0.002 TRP E 175 HIS 0.005 0.001 HIS B 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.17 (29200) covalent geometry : angle 0.56453 / 0.34 (39649) hydrogen bonds : bond 0.19060 / 13.04 ( 1189) hydrogen bonds : angle 6.71916 / 4.84 ( 3355) metal coordination : bond 0.00444 / 0.22 ( 24) metal coordination : angle 3.78690 / 2.07 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: F 14 ILE cc_start: 0.8238 (pt) cc_final: 0.7982 (mt) outliers start: 5 outliers final: 1 residues processed: 192 average time/residue: 0.1787 time to fit residues: 55.1132 Evaluate side-chains 179 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.3980 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 255 ASN A 273 GLN B 298 ASN B 718 ASN B 921 GLN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.077054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.048310 restraints weight = 83033.830| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.98 r_work: 0.2587 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29224 Z= 0.220 Angle : 0.598 8.367 39682 Z= 0.318 Chirality : 0.046 0.328 4412 Planarity : 0.005 0.047 4948 Dihedral : 12.246 172.743 4405 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.45 % Allowed : 16.77 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.47 (0.15), residues: 3402 helix: 1.25 (0.15), residues: 1215 sheet: 0.08 (0.22), residues: 523 loop : -0.23 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 423 TYR 0.022 0.001 TYR B 369 PHE 0.018 0.002 PHE E 95 TRP 0.017 0.001 TRP I 30 HIS 0.005 0.001 HIS B 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (29200) covalent geometry : angle 0.58814 / 0.32 (39649) hydrogen bonds : bond 0.05931 / 4.10 ( 1189) hydrogen bonds : angle 5.19546 / 3.74 ( 3355) metal coordination : bond 0.00647 / 0.40 ( 24) metal coordination : angle 3.82646 / 2.37 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.997 Fit side-chains REVERT: A 357 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8420 (p) REVERT: B 426 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8705 (tpt170) REVERT: C 23 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8859 (mtmm) REVERT: G 77 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9087 (tppt) REVERT: E 100 ARG cc_start: 0.1231 (tpt90) cc_final: 0.0892 (tpt90) outliers start: 43 outliers final: 16 residues processed: 216 average time/residue: 0.1828 time to fit residues: 63.9302 Evaluate side-chains 194 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain F residue 90 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 13 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 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 = 0.3435 r_free = 0.3435 target = 0.076735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.047979 restraints weight = 83385.727| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.99 r_work: 0.2579 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29224 Z= 0.210 Angle : 0.574 8.122 39682 Z= 0.304 Chirality : 0.046 0.347 4412 Planarity : 0.004 0.046 4948 Dihedral : 12.257 172.948 4403 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.92 % Allowed : 16.74 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.41 (0.15), residues: 3402 helix: 1.27 (0.15), residues: 1216 sheet: -0.10 (0.22), residues: 538 loop : -0.27 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 236 TYR 0.013 0.001 TYR H 73 PHE 0.018 0.001 PHE C 193 TRP 0.030 0.001 TRP E 175 HIS 0.016 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (29200) covalent geometry : angle 0.56063 / 0.30 (39649) hydrogen bonds : bond 0.05736 / 3.96 ( 1189) hydrogen bonds : angle 4.93642 / 3.55 ( 3355) metal coordination : bond 0.00656 / 0.40 ( 24) metal coordination : angle 4.25325 / 2.66 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 426 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8668 (tpt170) REVERT: C 118 MET cc_start: 0.8651 (mtm) cc_final: 0.8355 (mtp) REVERT: C 309 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9109 (tt) REVERT: G 77 LYS cc_start: 0.9337 (ttmm) cc_final: 0.9083 (tppt) REVERT: H 53 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8539 (mm) REVERT: I 30 TRP cc_start: 0.6204 (p-90) cc_final: 0.5686 (p-90) REVERT: E 85 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7827 (m) REVERT: F 42 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6895 (ptt90) outliers start: 57 outliers final: 31 residues processed: 225 average time/residue: 0.1713 time to fit residues: 63.0306 Evaluate side-chains 215 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 90 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 86 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 HIS B 298 ASN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.077873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.049124 restraints weight = 82775.107| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.01 r_work: 0.2601 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29224 Z= 0.144 Angle : 0.533 7.968 39682 Z= 0.282 Chirality : 0.045 0.351 4412 Planarity : 0.004 0.048 4948 Dihedral : 12.214 173.042 4403 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.55 % Allowed : 16.20 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.50 (0.15), residues: 3402 helix: 1.37 (0.16), residues: 1215 sheet: -0.08 (0.22), residues: 533 loop : -0.23 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 236 TYR 0.014 0.001 TYR P 29 PHE 0.013 0.001 PHE E 95 TRP 0.027 0.001 TRP E 175 HIS 0.004 0.001 HIS B 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (29200) covalent geometry : angle 0.52103 / 0.28 (39649) hydrogen bonds : bond 0.05058 / 3.48 ( 1189) hydrogen bonds : angle 4.71546 / 3.39 ( 3355) metal coordination : bond 0.00480 / 0.28 ( 24) metal coordination : angle 3.96499 / 2.45 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 428 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8726 (p90) REVERT: B 426 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8668 (tpt170) REVERT: B 447 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8411 (mp-120) REVERT: C 23 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8885 (mtmm) REVERT: C 118 MET cc_start: 0.8659 (mtm) cc_final: 0.8371 (mtp) REVERT: C 309 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9084 (tt) REVERT: G 77 LYS cc_start: 0.9398 (ttmm) cc_final: 0.9120 (tppt) REVERT: H 53 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8564 (mm) REVERT: I 30 TRP cc_start: 0.6269 (p-90) cc_final: 0.5777 (p-90) REVERT: F 42 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6891 (ptt90) outliers start: 76 outliers final: 41 residues processed: 250 average time/residue: 0.1778 time to fit residues: 72.0350 Evaluate side-chains 225 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 323 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 chunk 279 optimal weight: 50.0000 chunk 292 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 147 ASN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.047940 restraints weight = 83804.423| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.96 r_work: 0.2563 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 29224 Z= 0.250 Angle : 0.592 8.172 39682 Z= 0.312 Chirality : 0.046 0.346 4412 Planarity : 0.004 0.047 4948 Dihedral : 12.279 173.622 4403 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.66 % Allowed : 17.01 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.32 (0.15), residues: 3402 helix: 1.26 (0.15), residues: 1217 sheet: -0.21 (0.22), residues: 538 loop : -0.36 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 50 TYR 0.016 0.001 TYR P 29 PHE 0.012 0.001 PHE E 95 TRP 0.024 0.001 TRP E 175 HIS 0.013 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (29200) covalent geometry : angle 0.58137 / 0.31 (39649) hydrogen bonds : bond 0.05699 / 3.92 ( 1189) hydrogen bonds : angle 4.78213 / 3.43 ( 3355) metal coordination : bond 0.00729 / 0.46 ( 24) metal coordination : angle 3.95078 / 2.50 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 174 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 357 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8511 (p) REVERT: A 570 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8103 (mtm180) REVERT: B 426 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8682 (tpt170) REVERT: B 447 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8609 (mp-120) REVERT: C 23 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.8842 (mtmm) REVERT: C 118 MET cc_start: 0.8703 (mtm) cc_final: 0.8400 (mtp) REVERT: C 309 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9084 (tt) REVERT: G 34 TYR cc_start: 0.6733 (m-10) cc_final: 0.6473 (m-80) REVERT: G 77 LYS cc_start: 0.9432 (ttmm) cc_final: 0.9109 (tppt) REVERT: H 53 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8595 (mm) REVERT: I 30 TRP cc_start: 0.6268 (p-90) cc_final: 0.5732 (p-90) REVERT: F 42 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6904 (ptt90) outliers start: 79 outliers final: 49 residues processed: 239 average time/residue: 0.1852 time to fit residues: 71.1852 Evaluate side-chains 230 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain F residue 42 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 256 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 222 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 0.0270 chunk 57 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 2 optimal weight: 0.0020 overall best weight: 1.0052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.078460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.050216 restraints weight = 82423.133| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.96 r_work: 0.2626 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29224 Z= 0.101 Angle : 0.513 8.385 39682 Z= 0.270 Chirality : 0.044 0.358 4412 Planarity : 0.004 0.048 4948 Dihedral : 12.188 173.504 4403 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.08 % Allowed : 17.78 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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 (0.15), residues: 3402 helix: 1.45 (0.16), residues: 1219 sheet: -0.07 (0.22), residues: 540 loop : -0.20 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 230 TYR 0.016 0.001 TYR P 29 PHE 0.020 0.001 PHE C 193 TRP 0.028 0.001 TRP E 175 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (29200) covalent geometry : angle 0.50136 / 0.27 (39649) hydrogen bonds : bond 0.04405 / 3.03 ( 1189) hydrogen bonds : angle 4.48759 / 3.23 ( 3355) metal coordination : bond 0.00419 / 0.21 ( 24) metal coordination : angle 3.75009 / 2.25 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 118 MET cc_start: 0.8603 (mtm) cc_final: 0.8304 (mtp) REVERT: C 309 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9060 (tt) REVERT: G 14 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: G 16 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: G 34 TYR cc_start: 0.6773 (m-10) cc_final: 0.6415 (m-80) REVERT: G 58 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: G 73 GLU cc_start: 0.7948 (tt0) cc_final: 0.7663 (tt0) REVERT: G 77 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9124 (tppt) REVERT: H 53 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (mm) REVERT: I 30 TRP cc_start: 0.6253 (p-90) cc_final: 0.5770 (p-90) REVERT: F 42 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6892 (ptt90) outliers start: 62 outliers final: 36 residues processed: 233 average time/residue: 0.1788 time to fit residues: 67.2159 Evaluate side-chains 215 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 175 TRP Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 90 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 15 optimal weight: 6.9990 chunk 216 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 312 optimal weight: 0.0470 chunk 225 optimal weight: 0.0970 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049770 restraints weight = 82271.812| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.02 r_work: 0.2614 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29224 Z= 0.125 Angle : 0.513 8.156 39682 Z= 0.269 Chirality : 0.044 0.351 4412 Planarity : 0.004 0.048 4948 Dihedral : 12.172 174.059 4403 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.98 % Allowed : 18.08 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.62 (0.15), residues: 3402 helix: 1.48 (0.16), residues: 1219 sheet: -0.05 (0.22), residues: 538 loop : -0.16 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 13 TYR 0.017 0.001 TYR P 29 PHE 0.011 0.001 PHE D 18 TRP 0.027 0.001 TRP E 175 HIS 0.018 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (29200) covalent geometry : angle 0.50292 / 0.27 (39649) hydrogen bonds : bond 0.04483 / 3.09 ( 1189) hydrogen bonds : angle 4.44615 / 3.20 ( 3355) metal coordination : bond 0.00405 / 0.23 ( 24) metal coordination : angle 3.52043 / 2.16 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8416 (p) REVERT: C 118 MET cc_start: 0.8684 (mtm) cc_final: 0.8352 (mtp) REVERT: C 223 HIS cc_start: 0.7543 (t-90) cc_final: 0.7286 (t-90) REVERT: C 309 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9076 (tt) REVERT: G 34 TYR cc_start: 0.6746 (m-10) cc_final: 0.6341 (m-80) REVERT: G 73 GLU cc_start: 0.7940 (tt0) cc_final: 0.7673 (tt0) REVERT: G 77 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9098 (tppt) REVERT: H 53 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8581 (mm) REVERT: I 30 TRP cc_start: 0.6271 (p-90) cc_final: 0.5773 (p-90) REVERT: F 42 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6932 (ptt90) outliers start: 59 outliers final: 39 residues processed: 224 average time/residue: 0.1658 time to fit residues: 60.4657 Evaluate side-chains 215 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 175 TRP Chi-restraints excluded: chain F residue 42 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 320 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 222 optimal weight: 40.0000 chunk 44 optimal weight: 0.8980 chunk 308 optimal weight: 50.0000 chunk 37 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 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 = 0.3467 r_free = 0.3467 target = 0.077549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.049189 restraints weight = 82276.220| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.05 r_work: 0.2628 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29224 Z= 0.110 Angle : 0.506 7.848 39682 Z= 0.266 Chirality : 0.043 0.353 4412 Planarity : 0.004 0.047 4948 Dihedral : 12.143 174.522 4403 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.75 % Allowed : 18.42 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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 (0.15), residues: 3402 helix: 1.51 (0.16), residues: 1225 sheet: -0.02 (0.22), residues: 540 loop : -0.12 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 23 TYR 0.014 0.001 TYR P 29 PHE 0.011 0.001 PHE D 18 TRP 0.027 0.001 TRP E 175 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (29200) covalent geometry : angle 0.49655 / 0.27 (39649) hydrogen bonds : bond 0.04223 / 2.92 ( 1189) hydrogen bonds : angle 4.34973 / 3.13 ( 3355) metal coordination : bond 0.00395 / 0.22 ( 24) metal coordination : angle 3.40348 / 2.07 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8414 (p) REVERT: C 118 MET cc_start: 0.8670 (mtm) cc_final: 0.8331 (mtp) REVERT: C 309 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9082 (tt) REVERT: G 34 TYR cc_start: 0.6659 (m-10) cc_final: 0.6160 (m-80) REVERT: G 73 GLU cc_start: 0.7951 (tt0) cc_final: 0.7680 (tt0) REVERT: G 77 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9092 (tppt) REVERT: H 53 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8617 (mm) REVERT: I 30 TRP cc_start: 0.6339 (p-90) cc_final: 0.5844 (p-90) REVERT: F 42 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6975 (ptt90) outliers start: 52 outliers final: 37 residues processed: 220 average time/residue: 0.1732 time to fit residues: 61.3940 Evaluate side-chains 212 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 175 TRP Chi-restraints excluded: chain F residue 42 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 194 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 313 optimal weight: 8.9990 chunk 287 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.078387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050096 restraints weight = 81934.166| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.99 r_work: 0.2652 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29224 Z= 0.096 Angle : 0.503 12.308 39682 Z= 0.263 Chirality : 0.043 0.349 4412 Planarity : 0.004 0.047 4948 Dihedral : 12.088 174.833 4403 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.61 % Allowed : 18.55 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.76 (0.15), residues: 3402 helix: 1.57 (0.16), residues: 1223 sheet: 0.12 (0.23), residues: 526 loop : -0.10 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 13 TYR 0.014 0.001 TYR P 29 PHE 0.020 0.001 PHE F 96 TRP 0.028 0.001 TRP E 175 HIS 0.004 0.001 HIS B 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (29200) covalent geometry : angle 0.49465 / 0.26 (39649) hydrogen bonds : bond 0.03860 / 2.66 ( 1189) hydrogen bonds : angle 4.25218 / 3.06 ( 3355) metal coordination : bond 0.00367 / 0.19 ( 24) metal coordination : angle 3.25507 / 1.96 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8372 (p) REVERT: B 109 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9056 (mmtp) REVERT: C 118 MET cc_start: 0.8626 (mtm) cc_final: 0.8296 (mtp) REVERT: C 309 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9079 (tt) REVERT: G 34 TYR cc_start: 0.6677 (m-10) cc_final: 0.6050 (m-80) REVERT: G 73 GLU cc_start: 0.7963 (tt0) cc_final: 0.7681 (tt0) REVERT: G 77 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9085 (tppt) REVERT: H 53 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8619 (mm) REVERT: H 66 LYS cc_start: 0.9063 (mttm) cc_final: 0.8836 (mttp) REVERT: I 30 TRP cc_start: 0.6295 (p-90) cc_final: 0.5777 (p-90) REVERT: F 25 ARG cc_start: 0.9151 (tpp80) cc_final: 0.8834 (tpp80) REVERT: F 42 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6981 (ptt90) outliers start: 48 outliers final: 36 residues processed: 218 average time/residue: 0.1777 time to fit residues: 62.9043 Evaluate side-chains 211 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 175 TRP Chi-restraints excluded: chain F residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 160 optimal weight: 0.0470 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 314 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 258 optimal weight: 0.4980 chunk 283 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.078095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.049726 restraints weight = 81872.914| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.02 r_work: 0.2680 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29224 Z= 0.108 Angle : 0.508 10.327 39682 Z= 0.264 Chirality : 0.043 0.336 4412 Planarity : 0.004 0.099 4948 Dihedral : 12.079 175.079 4403 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 18.82 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.77 (0.15), residues: 3402 helix: 1.57 (0.15), residues: 1228 sheet: 0.05 (0.22), residues: 547 loop : -0.06 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 13 TYR 0.017 0.001 TYR A 152 PHE 0.011 0.001 PHE D 18 TRP 0.028 0.001 TRP E 175 HIS 0.003 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (29200) covalent geometry : angle 0.49986 / 0.26 (39649) hydrogen bonds : bond 0.03945 / 2.73 ( 1189) hydrogen bonds : angle 4.22691 / 3.05 ( 3355) metal coordination : bond 0.00377 / 0.21 ( 24) metal coordination : angle 3.20845 / 1.94 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 109 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9058 (mmtp) REVERT: C 118 MET cc_start: 0.8585 (mtm) cc_final: 0.8256 (mtp) REVERT: C 309 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9076 (tt) REVERT: G 34 TYR cc_start: 0.6656 (m-10) cc_final: 0.5967 (m-80) REVERT: G 73 GLU cc_start: 0.7975 (tt0) cc_final: 0.7699 (tt0) REVERT: G 77 LYS cc_start: 0.9467 (ttmm) cc_final: 0.9087 (tppt) REVERT: H 66 LYS cc_start: 0.9023 (mttm) cc_final: 0.8801 (mttp) REVERT: I 30 TRP cc_start: 0.6310 (p-90) cc_final: 0.5788 (p-90) outliers start: 43 outliers final: 33 residues processed: 209 average time/residue: 0.1877 time to fit residues: 63.7000 Evaluate side-chains 208 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 30 CYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 175 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 34 optimal weight: 3.9990 chunk 215 optimal weight: 40.0000 chunk 106 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 337 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 335 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.048368 restraints weight = 83769.238| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.02 r_work: 0.2564 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 29224 Z= 0.284 Angle : 0.629 13.013 39682 Z= 0.326 Chirality : 0.047 0.296 4412 Planarity : 0.005 0.068 4948 Dihedral : 12.209 175.435 4403 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.45 % Allowed : 18.92 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.48 (0.15), residues: 3402 helix: 1.34 (0.15), residues: 1236 sheet: -0.02 (0.23), residues: 507 loop : -0.29 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 157 TYR 0.016 0.001 TYR B 340 PHE 0.017 0.002 PHE F 70 TRP 0.027 0.002 TRP E 175 HIS 0.007 0.001 HIS B 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.28 (29200) covalent geometry : angle 0.62077 / 0.33 (39649) hydrogen bonds : bond 0.05556 / 3.84 ( 1189) hydrogen bonds : angle 4.53985 / 3.25 ( 3355) metal coordination : bond 0.00884 / 0.57 ( 24) metal coordination : angle 3.54936 / 2.27 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.99 seconds wall clock time: 103 minutes 42.84 seconds (6222.84 seconds total)