Starting phenix.real_space_refine on Sat Feb 7 03:11:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e86_47708/02_2026/9e86_47708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e86_47708/02_2026/9e86_47708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e86_47708/02_2026/9e86_47708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e86_47708/02_2026/9e86_47708.map" model { file = "/net/cci-nas-00/data/ceres_data/9e86_47708/02_2026/9e86_47708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e86_47708/02_2026/9e86_47708.cif" } resolution = 3.8 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= 0.004 sd= 0.045 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 2 6.06 5 P 107 5.49 5 Mg 1 5.21 5 S 97 5.16 5 C 17977 2.51 5 N 5204 2.21 5 O 5819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29207 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1724 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 215} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8571 Classifications: {'peptide': 1113} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1050} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 9904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9904 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2373 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "N" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1073 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "T" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 972 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19062 SG CYS D 891 108.914 98.609 107.701 1.00120.10 S ATOM 19629 SG CYS D 968 105.690 98.308 105.701 1.00119.02 S ATOM 19671 SG CYS D 975 106.172 96.192 108.770 1.00118.37 S ATOM 19689 SG CYS D 978 105.654 99.836 109.058 1.00117.89 S ATOM 12501 SG CYS D 60 77.699 58.459 62.958 1.00166.35 S ATOM 12519 SG CYS D 62 76.758 58.234 59.264 1.00171.99 S ATOM 12628 SG CYS D 75 80.240 57.879 60.164 1.00177.56 S ATOM 12654 SG CYS D 78 78.639 61.136 60.373 1.00171.14 S Time building chain proxies: 6.05, per 1000 atoms: 0.21 Number of scatterers: 29207 At special positions: 0 Unit cell: (132.348, 161.4, 189.376, 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 2 29.99 S 97 16.00 P 107 15.00 Mg 1 11.99 O 5819 8.00 N 5204 7.00 C 17977 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 12 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6432 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 41 sheets defined 42.9% alpha, 15.1% beta 45 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.769A pdb=" N VAL A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.988A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.822A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.089A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.307A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.871A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.904A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 473 removed outlier: 3.597A pdb=" N VAL C 472 " --> pdb=" O GLY C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.746A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 588 through 593 removed outlier: 3.614A pdb=" N MET C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.902A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 783 removed outlier: 3.620A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 779 through 783' Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.731A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1070 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.351A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.088A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 185 removed outlier: 4.165A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 229 removed outlier: 4.203A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.542A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.661A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.918A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.731A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.759A pdb=" N ASN D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.669A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.110A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.893A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 727 removed outlier: 3.942A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.574A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.930A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.996A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 Proline residue: D1127 - end of helix Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.398A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.263A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1248 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.953A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.706A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 Processing helix chain 'F' and resid 274 through 311 removed outlier: 4.932A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.676A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 362 Processing helix chain 'F' and resid 369 through 390 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 418 Processing helix chain 'F' and resid 434 through 439 removed outlier: 3.813A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 467 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 516 removed outlier: 3.501A pdb=" N HIS F 516 " --> pdb=" O SER F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 520 through 525 removed outlier: 4.708A pdb=" N ASP F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 111 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.860A pdb=" N LEU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP M 68 " --> pdb=" O GLN M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.619A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 160 removed outlier: 3.581A pdb=" N ALA M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA M 160 " --> pdb=" O GLU M 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.732A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.900A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.545A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.604A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.887A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.138A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.203A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.203A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 141 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 146 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG M 47 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 149 " --> pdb=" O THR M 45 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.483A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.620A pdb=" N ASP C 188 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 212 through 216 removed outlier: 4.969A pdb=" N ILE C 226 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.701A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 559 through 562 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.644A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.581A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.007A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 748 through 760 removed outlier: 7.024A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.685A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.659A pdb=" N LEU D 497 " --> pdb=" O HIS D 544 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.364A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1069 removed outlier: 3.989A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 422 " --> pdb=" O GLN C1066 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.484A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 233 through 235 Processing sheet with id=AD7, first strand: chain 'F' and resid 421 through 422 removed outlier: 5.943A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER J 9 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.914A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1076 through 1081 removed outlier: 5.961A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.507A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE4, first strand: chain 'J' and resid 41 through 45 Processing sheet with id=AE5, first strand: chain 'M' and resid 26 through 27 1227 hydrogen bonds defined for protein. 3489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8340 1.33 - 1.46: 5560 1.46 - 1.58: 15631 1.58 - 1.70: 207 1.70 - 1.82: 171 Bond restraints: 29909 Sorted by residual: bond pdb=" O POP C2000 " pdb=" P1 POP C2000 " ideal model delta sigma weight residual 1.660 1.607 0.053 2.00e-02 2.50e+03 7.00e+00 bond pdb=" O POP C2000 " pdb=" P2 POP C2000 " ideal model delta sigma weight residual 1.661 1.608 0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" CA PRO D 31 " pdb=" CB PRO D 31 " ideal model delta sigma weight residual 1.531 1.544 -0.013 6.20e-03 2.60e+04 4.12e+00 bond pdb=" C ALA J 25 " pdb=" N PRO J 26 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.19e-02 7.06e+03 4.06e+00 bond pdb=" C THR D 253 " pdb=" N GLY D 254 " ideal model delta sigma weight residual 1.332 1.342 -0.010 5.00e-03 4.00e+04 4.00e+00 ... (remaining 29904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 40818 3.86 - 7.72: 144 7.72 - 11.58: 8 11.58 - 15.44: 0 15.44 - 19.30: 1 Bond angle restraints: 40971 Sorted by residual: angle pdb=" P1 POP C2000 " pdb=" O POP C2000 " pdb=" P2 POP C2000 " ideal model delta sigma weight residual 139.66 120.36 19.30 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C PRO B 28 " pdb=" N GLY B 29 " pdb=" CA GLY B 29 " ideal model delta sigma weight residual 121.70 131.09 -9.39 1.80e+00 3.09e-01 2.72e+01 angle pdb=" C ASP D1070 " pdb=" N GLY D1071 " pdb=" CA GLY D1071 " ideal model delta sigma weight residual 121.70 130.47 -8.77 1.80e+00 3.09e-01 2.37e+01 angle pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 111.50 105.25 6.25 1.40e+00 5.10e-01 2.00e+01 angle pdb=" C PRO M 12 " pdb=" N HIS M 13 " pdb=" CA HIS M 13 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.97e+01 ... (remaining 40966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 17174 33.75 - 67.49: 827 67.49 - 101.24: 34 101.24 - 134.98: 1 134.98 - 168.73: 1 Dihedral angle restraints: 18037 sinusoidal: 8042 harmonic: 9995 Sorted by residual: dihedral pdb=" CA ASP C 307 " pdb=" C ASP C 307 " pdb=" N LEU C 308 " pdb=" CA LEU C 308 " ideal model delta harmonic sigma weight residual 180.00 148.84 31.16 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA THR D1173 " pdb=" C THR D1173 " pdb=" N GLU D1174 " pdb=" CA GLU D1174 " ideal model delta harmonic sigma weight residual 180.00 149.68 30.32 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA PRO J 70 " pdb=" C PRO J 70 " pdb=" N GLU J 71 " pdb=" CA GLU J 71 " ideal model delta harmonic sigma weight residual 180.00 150.11 29.89 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3176 0.037 - 0.074: 1019 0.074 - 0.111: 372 0.111 - 0.148: 109 0.148 - 0.185: 5 Chirality restraints: 4681 Sorted by residual: chirality pdb=" C3' DC T 22 " pdb=" C4' DC T 22 " pdb=" O3' DC T 22 " pdb=" C2' DC T 22 " both_signs ideal model delta sigma weight residual False -2.66 -2.48 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA ILE C 769 " pdb=" N ILE C 769 " pdb=" C ILE C 769 " pdb=" CB ILE C 769 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB VAL D 490 " pdb=" CA VAL D 490 " pdb=" CG1 VAL D 490 " pdb=" CG2 VAL D 490 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 4678 not shown) Planarity restraints: 5019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 69 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO J 70 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO J 70 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO J 70 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 24 " -0.044 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 25 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 63 " -0.034 2.00e-02 2.50e+03 1.54e-02 6.55e+00 pdb=" N9 DA N 63 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DA N 63 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA N 63 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA N 63 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA N 63 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA N 63 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA N 63 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA N 63 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA N 63 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA N 63 " 0.004 2.00e-02 2.50e+03 ... (remaining 5016 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 260 2.52 - 3.11: 23434 3.11 - 3.71: 47851 3.71 - 4.30: 63577 4.30 - 4.90: 102268 Nonbonded interactions: 237390 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 1.925 2.170 nonbonded pdb=" OD1 ASP C 441 " pdb=" OG SER C 447 " model vdw 1.949 3.040 nonbonded pdb=" OG SER D 964 " pdb=" OE1 GLU D1155 " model vdw 1.968 3.040 nonbonded pdb=" OD1 ASP C 745 " pdb=" OG1 THR C 748 " model vdw 1.979 3.040 nonbonded pdb=" OG1 THR F 488 " pdb=" OE1 GLU F 491 " model vdw 2.023 3.040 ... (remaining 237385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 4 through 226) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 34.270 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.004 0.133 29917 Z= 0.190 Angle : 0.737 19.296 40983 Z= 0.399 Chirality : 0.043 0.185 4681 Planarity : 0.006 0.118 5019 Dihedral : 17.361 168.729 11605 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.78 % Favored : 93.16 % Rotamer: Outliers : 0.17 % Allowed : 18.14 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3466 helix: 0.12 (0.14), residues: 1382 sheet: -1.70 (0.26), residues: 370 loop : -1.93 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 27 TYR 0.028 0.002 TYR C 306 PHE 0.035 0.002 PHE C 252 TRP 0.015 0.002 TRP C 70 HIS 0.010 0.002 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00395 (29909) covalent geometry : angle 0.73718 (40971) hydrogen bonds : bond 0.08995 ( 1327) hydrogen bonds : angle 5.97900 ( 3709) metal coordination : bond 0.09314 ( 8) metal coordination : angle 0.04560 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1244 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6682 (m-80) cc_final: 0.6455 (m-80) REVERT: A 22 VAL cc_start: 0.9077 (t) cc_final: 0.8766 (p) REVERT: A 62 GLU cc_start: 0.8117 (mp0) cc_final: 0.7551 (mp0) REVERT: A 75 GLU cc_start: 0.8051 (tp30) cc_final: 0.7441 (tp30) REVERT: A 99 LYS cc_start: 0.8150 (tptt) cc_final: 0.7902 (tptm) REVERT: A 106 THR cc_start: 0.8811 (p) cc_final: 0.8115 (p) REVERT: A 129 ASN cc_start: 0.8642 (p0) cc_final: 0.8315 (p0) REVERT: A 133 LYS cc_start: 0.8816 (tttt) cc_final: 0.8290 (ttmm) REVERT: A 195 ASP cc_start: 0.7080 (t0) cc_final: 0.6102 (t0) REVERT: A 213 LYS cc_start: 0.8671 (tppt) cc_final: 0.8211 (tppt) REVERT: B 9 LEU cc_start: 0.8641 (tt) cc_final: 0.7958 (mp) REVERT: B 14 LEU cc_start: 0.8821 (mt) cc_final: 0.7775 (tt) REVERT: B 40 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8468 (mmm160) REVERT: B 72 ASP cc_start: 0.8484 (p0) cc_final: 0.7706 (p0) REVERT: B 138 LEU cc_start: 0.8235 (mp) cc_final: 0.7705 (mm) REVERT: B 191 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8073 (ttpt) REVERT: B 195 ASP cc_start: 0.7752 (t70) cc_final: 0.6895 (t70) REVERT: C 59 ASP cc_start: 0.8746 (m-30) cc_final: 0.8465 (m-30) REVERT: C 87 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8335 (mp0) REVERT: C 119 VAL cc_start: 0.9293 (t) cc_final: 0.8968 (p) REVERT: C 126 ASP cc_start: 0.8259 (m-30) cc_final: 0.8014 (m-30) REVERT: C 133 LEU cc_start: 0.9007 (mt) cc_final: 0.8800 (mt) REVERT: C 205 ILE cc_start: 0.9038 (tt) cc_final: 0.8679 (tt) REVERT: C 227 ASP cc_start: 0.8573 (t0) cc_final: 0.7910 (p0) REVERT: C 344 TYR cc_start: 0.8568 (t80) cc_final: 0.7829 (t80) REVERT: C 435 GLN cc_start: 0.8600 (pt0) cc_final: 0.8390 (pt0) REVERT: C 511 PHE cc_start: 0.7814 (m-80) cc_final: 0.7603 (m-10) REVERT: C 513 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8292 (mt-10) REVERT: C 631 GLU cc_start: 0.8214 (mp0) cc_final: 0.7676 (mp0) REVERT: C 814 LEU cc_start: 0.8655 (mm) cc_final: 0.8278 (mm) REVERT: C 846 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8416 (mtpp) REVERT: C 906 PHE cc_start: 0.8635 (p90) cc_final: 0.8269 (p90) REVERT: C 950 LYS cc_start: 0.8952 (pptt) cc_final: 0.8512 (mmtm) REVERT: C 1021 TYR cc_start: 0.8646 (m-80) cc_final: 0.8121 (m-10) REVERT: C 1051 MET cc_start: 0.7964 (tpp) cc_final: 0.7659 (tpp) REVERT: C 1079 TYR cc_start: 0.8067 (m-80) cc_final: 0.7738 (m-10) REVERT: C 1104 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8507 (tm-30) REVERT: C 1110 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7766 (mt-10) REVERT: C 1129 GLN cc_start: 0.8808 (mt0) cc_final: 0.8454 (tt0) REVERT: D 90 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8581 (mp0) REVERT: D 92 MET cc_start: 0.7648 (mtp) cc_final: 0.6743 (mtp) REVERT: D 94 HIS cc_start: 0.7697 (p-80) cc_final: 0.7203 (p-80) REVERT: D 136 ILE cc_start: 0.9476 (mm) cc_final: 0.9006 (tt) REVERT: D 263 LYS cc_start: 0.9241 (tppp) cc_final: 0.8992 (mtpt) REVERT: D 364 GLU cc_start: 0.9137 (tp30) cc_final: 0.8806 (tp30) REVERT: D 409 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7957 (tptp) REVERT: D 420 LYS cc_start: 0.7726 (mttt) cc_final: 0.7388 (mtmm) REVERT: D 517 VAL cc_start: 0.9122 (t) cc_final: 0.8600 (t) REVERT: D 523 GLN cc_start: 0.8376 (mt0) cc_final: 0.8121 (mt0) REVERT: D 556 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8479 (tpt-90) REVERT: D 750 GLU cc_start: 0.8687 (tp30) cc_final: 0.8188 (tp30) REVERT: D 754 ASP cc_start: 0.8650 (m-30) cc_final: 0.8355 (m-30) REVERT: D 784 GLU cc_start: 0.8135 (tp30) cc_final: 0.7814 (tp30) REVERT: D 848 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 869 ASP cc_start: 0.8030 (t0) cc_final: 0.7491 (t0) REVERT: D 918 THR cc_start: 0.8443 (p) cc_final: 0.8040 (p) REVERT: D 960 VAL cc_start: 0.9255 (m) cc_final: 0.9004 (p) REVERT: D 1036 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8397 (mm-30) REVERT: D 1139 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8516 (tp-100) REVERT: D 1150 HIS cc_start: 0.7772 (t-90) cc_final: 0.7316 (t-90) REVERT: D 1208 MET cc_start: 0.7808 (ptp) cc_final: 0.7514 (ptp) REVERT: D 1235 ASP cc_start: 0.8957 (p0) cc_final: 0.8660 (p0) REVERT: E 42 GLU cc_start: 0.8818 (mp0) cc_final: 0.8605 (mp0) REVERT: E 82 LEU cc_start: 0.9082 (tp) cc_final: 0.8450 (tp) REVERT: E 94 ILE cc_start: 0.9290 (mm) cc_final: 0.8846 (mm) REVERT: E 97 ARG cc_start: 0.9181 (mtp85) cc_final: 0.8855 (ttp-110) REVERT: E 98 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7548 (mt-10) REVERT: F 237 LYS cc_start: 0.9500 (pttt) cc_final: 0.9245 (pttm) REVERT: F 263 MET cc_start: 0.8947 (mtp) cc_final: 0.8484 (mtp) REVERT: F 282 MET cc_start: 0.8985 (mtm) cc_final: 0.8760 (mtp) REVERT: F 311 THR cc_start: 0.8611 (t) cc_final: 0.8223 (p) REVERT: F 319 ASP cc_start: 0.8897 (m-30) cc_final: 0.8684 (m-30) REVERT: F 366 ILE cc_start: 0.6991 (mm) cc_final: 0.5049 (tp) REVERT: F 478 ARG cc_start: 0.8689 (tpt170) cc_final: 0.8427 (tpm170) REVERT: J 32 TYR cc_start: 0.7827 (m-80) cc_final: 0.7361 (m-80) REVERT: J 85 LEU cc_start: 0.9023 (tp) cc_final: 0.8534 (mm) REVERT: M 55 TYR cc_start: 0.8264 (m-80) cc_final: 0.7912 (m-80) outliers start: 5 outliers final: 0 residues processed: 1247 average time/residue: 0.2141 time to fit residues: 400.3411 Evaluate side-chains 860 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 860 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN B 36 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN C1077 GLN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 693 GLN D 810 ASN ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1269 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097485 restraints weight = 71984.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101327 restraints weight = 36911.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103827 restraints weight = 24224.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105423 restraints weight = 18487.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106434 restraints weight = 15593.870| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29917 Z= 0.220 Angle : 0.800 14.163 40983 Z= 0.412 Chirality : 0.047 0.202 4681 Planarity : 0.006 0.073 5019 Dihedral : 16.358 177.945 5011 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 4.66 % Allowed : 21.53 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -1.37 (0.14), residues: 3466 helix: 0.23 (0.13), residues: 1386 sheet: -1.35 (0.27), residues: 353 loop : -1.79 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1054 TYR 0.026 0.002 TYR E 56 PHE 0.034 0.002 PHE D 302 TRP 0.040 0.003 TRP D 223 HIS 0.012 0.002 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00495 (29909) covalent geometry : angle 0.79267 (40971) hydrogen bonds : bond 0.05169 ( 1327) hydrogen bonds : angle 5.54089 ( 3709) metal coordination : bond 0.01451 ( 8) metal coordination : angle 6.37471 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 895 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7626 (mm-40) REVERT: A 21 PHE cc_start: 0.7619 (m-80) cc_final: 0.7338 (m-80) REVERT: A 22 VAL cc_start: 0.9216 (t) cc_final: 0.8848 (p) REVERT: A 24 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 25 PRO cc_start: 0.7501 (Cg_endo) cc_final: 0.6167 (Cg_exo) REVERT: A 75 GLU cc_start: 0.8364 (tp30) cc_final: 0.7575 (tp30) REVERT: A 129 ASN cc_start: 0.8854 (p0) cc_final: 0.8416 (p0) REVERT: A 194 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7350 (tt) REVERT: A 195 ASP cc_start: 0.7612 (t70) cc_final: 0.7239 (t0) REVERT: A 206 ASP cc_start: 0.8350 (m-30) cc_final: 0.8057 (m-30) REVERT: A 208 LEU cc_start: 0.9480 (tp) cc_final: 0.9275 (tt) REVERT: A 213 LYS cc_start: 0.8724 (tppt) cc_final: 0.8237 (tppt) REVERT: B 9 LEU cc_start: 0.8744 (tt) cc_final: 0.8113 (mt) REVERT: B 21 PHE cc_start: 0.8763 (m-80) cc_final: 0.8416 (m-80) REVERT: B 40 ARG cc_start: 0.9167 (mmm-85) cc_final: 0.8711 (mmm160) REVERT: B 42 LEU cc_start: 0.9443 (mp) cc_final: 0.9020 (mp) REVERT: B 72 ASP cc_start: 0.8169 (p0) cc_final: 0.7898 (p0) REVERT: B 191 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8389 (ttpt) REVERT: C 59 ASP cc_start: 0.8976 (m-30) cc_final: 0.8620 (m-30) REVERT: C 83 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.8989 (m) REVERT: C 121 GLU cc_start: 0.8796 (tt0) cc_final: 0.8033 (tp30) REVERT: C 127 MET cc_start: 0.7935 (mtm) cc_final: 0.6930 (mtm) REVERT: C 139 PHE cc_start: 0.9217 (t80) cc_final: 0.8211 (t80) REVERT: C 148 LYS cc_start: 0.9357 (mppt) cc_final: 0.8942 (mppt) REVERT: C 159 MET cc_start: 0.8918 (mmm) cc_final: 0.8621 (mmm) REVERT: C 163 LYS cc_start: 0.9105 (mmtp) cc_final: 0.8761 (mmtp) REVERT: C 227 ASP cc_start: 0.8722 (t0) cc_final: 0.7979 (p0) REVERT: C 278 TYR cc_start: 0.8387 (t80) cc_final: 0.7980 (t80) REVERT: C 376 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8026 (ttt90) REVERT: C 383 GLU cc_start: 0.8787 (tp30) cc_final: 0.8522 (tt0) REVERT: C 421 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8430 (ttp80) REVERT: C 458 LEU cc_start: 0.9083 (pp) cc_final: 0.8806 (pp) REVERT: C 487 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 513 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8536 (mt-10) REVERT: C 579 MET cc_start: 0.7832 (tmm) cc_final: 0.7572 (tmm) REVERT: C 586 MET cc_start: 0.8569 (pmm) cc_final: 0.7991 (pmm) REVERT: C 631 GLU cc_start: 0.8459 (mp0) cc_final: 0.7204 (pm20) REVERT: C 657 TYR cc_start: 0.8512 (p90) cc_final: 0.8310 (p90) REVERT: C 661 MET cc_start: 0.8465 (tpp) cc_final: 0.8087 (tpp) REVERT: C 712 GLU cc_start: 0.8532 (pm20) cc_final: 0.7910 (pm20) REVERT: C 814 LEU cc_start: 0.8896 (mm) cc_final: 0.8616 (mm) REVERT: C 819 ARG cc_start: 0.9362 (ttt180) cc_final: 0.8805 (ttt180) REVERT: C 835 THR cc_start: 0.8467 (p) cc_final: 0.8256 (p) REVERT: C 851 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8438 (mmp80) REVERT: C 897 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8757 (ttmm) REVERT: C 950 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8686 (mmtm) REVERT: C 965 GLU cc_start: 0.9024 (pp20) cc_final: 0.8692 (pp20) REVERT: C 982 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 1021 TYR cc_start: 0.8910 (m-80) cc_final: 0.8196 (m-10) REVERT: C 1074 TRP cc_start: 0.8486 (m-10) cc_final: 0.8138 (m-90) REVERT: C 1077 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8653 (mp10) REVERT: C 1104 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 1108 LYS cc_start: 0.9425 (tppt) cc_final: 0.8692 (tppt) REVERT: C 1110 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7350 (mp0) REVERT: C 1129 GLN cc_start: 0.8799 (mt0) cc_final: 0.8459 (pt0) REVERT: C 1131 LEU cc_start: 0.9067 (mt) cc_final: 0.8497 (mm) REVERT: C 1134 ASN cc_start: 0.8964 (t0) cc_final: 0.8243 (p0) REVERT: D 14 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8491 (tp) REVERT: D 49 GLU cc_start: 0.8581 (mp0) cc_final: 0.8359 (mp0) REVERT: D 90 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8641 (mp0) REVERT: D 92 MET cc_start: 0.8506 (mtp) cc_final: 0.7548 (mtp) REVERT: D 94 HIS cc_start: 0.8341 (p-80) cc_final: 0.7826 (p-80) REVERT: D 136 ILE cc_start: 0.9475 (mm) cc_final: 0.9014 (tt) REVERT: D 239 ASN cc_start: 0.9410 (p0) cc_final: 0.9160 (p0) REVERT: D 295 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8637 (mmt90) REVERT: D 364 GLU cc_start: 0.9453 (tp30) cc_final: 0.9034 (tp30) REVERT: D 372 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8168 (tmm-80) REVERT: D 376 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8604 (mt-10) REVERT: D 437 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8449 (mmmm) REVERT: D 450 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7312 (tm-30) REVERT: D 517 VAL cc_start: 0.9236 (t) cc_final: 0.8566 (t) REVERT: D 688 MET cc_start: 0.8717 (mmp) cc_final: 0.8381 (mmp) REVERT: D 784 GLU cc_start: 0.8646 (tp30) cc_final: 0.8137 (tp30) REVERT: D 848 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7895 (mt-10) REVERT: D 858 LYS cc_start: 0.9497 (tttt) cc_final: 0.9062 (tppt) REVERT: D 877 LEU cc_start: 0.9288 (tt) cc_final: 0.8919 (tt) REVERT: D 879 ASP cc_start: 0.8345 (p0) cc_final: 0.7895 (p0) REVERT: D 918 THR cc_start: 0.8582 (p) cc_final: 0.8378 (t) REVERT: D 990 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7716 (p0) REVERT: D 991 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8677 (tt) REVERT: D 993 GLU cc_start: 0.8480 (mm-30) cc_final: 0.6585 (mm-30) REVERT: D 1150 HIS cc_start: 0.8211 (t-90) cc_final: 0.7465 (t-170) REVERT: D 1152 LYS cc_start: 0.8753 (ptpt) cc_final: 0.8086 (ptpt) REVERT: D 1163 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7305 (mmm160) REVERT: D 1226 PHE cc_start: 0.7580 (t80) cc_final: 0.6871 (t80) REVERT: D 1248 LEU cc_start: 0.8536 (tp) cc_final: 0.8273 (tp) REVERT: D 1256 LYS cc_start: 0.9073 (tttp) cc_final: 0.8472 (tppt) REVERT: E 42 GLU cc_start: 0.9025 (mp0) cc_final: 0.8278 (tm-30) REVERT: E 51 TYR cc_start: 0.8451 (m-80) cc_final: 0.7565 (m-80) REVERT: E 55 ILE cc_start: 0.9362 (mm) cc_final: 0.9088 (mm) REVERT: E 59 LYS cc_start: 0.9465 (mmtt) cc_final: 0.9034 (mmtt) REVERT: E 60 ARG cc_start: 0.9343 (tpp-160) cc_final: 0.8980 (tpp-160) REVERT: E 67 TYR cc_start: 0.8609 (t80) cc_final: 0.8400 (t80) REVERT: E 70 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8010 (tm-30) REVERT: E 82 LEU cc_start: 0.9231 (tp) cc_final: 0.8596 (tp) REVERT: E 88 GLN cc_start: 0.8905 (tt0) cc_final: 0.8537 (tt0) REVERT: E 89 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8730 (mp0) REVERT: E 94 ILE cc_start: 0.9202 (mm) cc_final: 0.8837 (mm) REVERT: E 98 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7814 (mt-10) REVERT: E 100 HIS cc_start: 0.8837 (t-90) cc_final: 0.7083 (t-90) REVERT: F 310 TYR cc_start: 0.7971 (m-10) cc_final: 0.7761 (m-80) REVERT: F 353 GLN cc_start: 0.8952 (tm-30) cc_final: 0.7945 (pt0) REVERT: F 478 ARG cc_start: 0.9021 (tpt170) cc_final: 0.8406 (tpm170) REVERT: J 10 ARG cc_start: 0.8662 (mmm160) cc_final: 0.8429 (mmt180) REVERT: J 32 TYR cc_start: 0.8732 (m-80) cc_final: 0.7705 (m-80) REVERT: J 65 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6765 (mm) REVERT: J 82 TRP cc_start: 0.9248 (t-100) cc_final: 0.8967 (t-100) REVERT: J 85 LEU cc_start: 0.9107 (tp) cc_final: 0.8538 (mm) REVERT: M 34 TYR cc_start: 0.8854 (m-80) cc_final: 0.8132 (t80) REVERT: M 38 LYS cc_start: 0.9089 (tmtt) cc_final: 0.8749 (tptp) REVERT: M 52 ASN cc_start: 0.9364 (m-40) cc_final: 0.8847 (t0) REVERT: M 59 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8952 (mmm160) outliers start: 135 outliers final: 64 residues processed: 975 average time/residue: 0.1924 time to fit residues: 292.4735 Evaluate side-chains 835 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 760 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1149 ILE Chi-restraints excluded: chain D residue 1186 PHE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 128 optimal weight: 0.2980 chunk 255 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 258 optimal weight: 0.8980 chunk 250 optimal weight: 0.0870 chunk 322 optimal weight: 20.0000 chunk 346 optimal weight: 30.0000 chunk 141 optimal weight: 0.0370 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN B 17 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 GLN D 329 GLN D 369 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.149383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.099720 restraints weight = 71661.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103675 restraints weight = 36828.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106231 restraints weight = 24041.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107837 restraints weight = 18260.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108920 restraints weight = 15360.595| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29917 Z= 0.160 Angle : 0.780 18.368 40983 Z= 0.394 Chirality : 0.047 0.228 4681 Planarity : 0.006 0.090 5019 Dihedral : 16.266 178.547 5011 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 4.49 % Allowed : 22.91 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -1.21 (0.14), residues: 3466 helix: 0.32 (0.14), residues: 1374 sheet: -1.22 (0.26), residues: 368 loop : -1.64 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 279 TYR 0.021 0.002 TYR E 56 PHE 0.031 0.002 PHE B 189 TRP 0.055 0.003 TRP D 223 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00353 (29909) covalent geometry : angle 0.77023 (40971) hydrogen bonds : bond 0.04822 ( 1327) hydrogen bonds : angle 5.30272 ( 3709) metal coordination : bond 0.00903 ( 8) metal coordination : angle 7.37189 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 859 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7672 (mm-40) REVERT: A 21 PHE cc_start: 0.7639 (m-80) cc_final: 0.7359 (m-80) REVERT: A 25 PRO cc_start: 0.7447 (Cg_endo) cc_final: 0.6473 (Cg_exo) REVERT: A 75 GLU cc_start: 0.8362 (tp30) cc_final: 0.7494 (tp30) REVERT: A 133 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8450 (ttmm) REVERT: A 194 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7168 (tt) REVERT: A 195 ASP cc_start: 0.7559 (t70) cc_final: 0.7111 (t0) REVERT: A 206 ASP cc_start: 0.8335 (m-30) cc_final: 0.8084 (m-30) REVERT: A 213 LYS cc_start: 0.8665 (tppt) cc_final: 0.8169 (tppt) REVERT: B 9 LEU cc_start: 0.8719 (tt) cc_final: 0.8078 (mt) REVERT: B 17 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8099 (p0) REVERT: B 21 PHE cc_start: 0.8681 (m-80) cc_final: 0.8279 (m-80) REVERT: B 40 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8565 (mmm160) REVERT: B 42 LEU cc_start: 0.9461 (mp) cc_final: 0.9221 (mp) REVERT: B 72 ASP cc_start: 0.8130 (p0) cc_final: 0.7820 (p0) REVERT: B 189 PHE cc_start: 0.7952 (m-80) cc_final: 0.7734 (m-10) REVERT: B 191 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8299 (ttpt) REVERT: B 206 ASP cc_start: 0.8599 (p0) cc_final: 0.8235 (p0) REVERT: C 59 ASP cc_start: 0.8937 (m-30) cc_final: 0.8582 (m-30) REVERT: C 103 MET cc_start: 0.8932 (ttp) cc_final: 0.8720 (ppp) REVERT: C 121 GLU cc_start: 0.8799 (tt0) cc_final: 0.8054 (tp30) REVERT: C 127 MET cc_start: 0.7974 (mtm) cc_final: 0.7572 (mtm) REVERT: C 139 PHE cc_start: 0.8814 (t80) cc_final: 0.8530 (t80) REVERT: C 148 LYS cc_start: 0.9440 (mppt) cc_final: 0.9016 (mppt) REVERT: C 163 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8762 (mmmm) REVERT: C 227 ASP cc_start: 0.8720 (t0) cc_final: 0.7963 (p0) REVERT: C 293 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: C 376 ARG cc_start: 0.8901 (ttt180) cc_final: 0.8006 (ttt90) REVERT: C 384 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8952 (mp) REVERT: C 421 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8235 (ttp80) REVERT: C 487 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7856 (tm-30) REVERT: C 499 SER cc_start: 0.8392 (p) cc_final: 0.8024 (p) REVERT: C 513 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8424 (mt-10) REVERT: C 561 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7202 (p) REVERT: C 570 TYR cc_start: 0.8516 (m-80) cc_final: 0.8063 (t80) REVERT: C 579 MET cc_start: 0.7901 (tmm) cc_final: 0.7569 (tmm) REVERT: C 586 MET cc_start: 0.8519 (pmm) cc_final: 0.7878 (pmm) REVERT: C 593 MET cc_start: 0.9186 (mtp) cc_final: 0.8783 (mtm) REVERT: C 631 GLU cc_start: 0.8261 (mp0) cc_final: 0.7257 (pm20) REVERT: C 661 MET cc_start: 0.8435 (tpp) cc_final: 0.7978 (tpp) REVERT: C 724 MET cc_start: 0.8806 (ptm) cc_final: 0.8265 (ppp) REVERT: C 758 ASP cc_start: 0.6585 (p0) cc_final: 0.5976 (p0) REVERT: C 814 LEU cc_start: 0.8887 (mm) cc_final: 0.8639 (mm) REVERT: C 819 ARG cc_start: 0.9355 (ttt180) cc_final: 0.8820 (ttt180) REVERT: C 933 GLU cc_start: 0.8115 (tt0) cc_final: 0.7629 (pt0) REVERT: C 950 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8580 (mmtm) REVERT: C 965 GLU cc_start: 0.8935 (pp20) cc_final: 0.8618 (pp20) REVERT: C 982 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 984 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8491 (mp0) REVERT: C 1021 TYR cc_start: 0.8822 (m-80) cc_final: 0.8162 (m-10) REVERT: C 1074 TRP cc_start: 0.8365 (m-10) cc_final: 0.8069 (m-90) REVERT: C 1077 GLN cc_start: 0.9250 (mt0) cc_final: 0.8995 (mp10) REVERT: C 1104 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 1108 LYS cc_start: 0.9466 (tppt) cc_final: 0.8913 (tppt) REVERT: C 1110 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 1125 LEU cc_start: 0.9534 (mm) cc_final: 0.9308 (mm) REVERT: C 1129 GLN cc_start: 0.8712 (mt0) cc_final: 0.8442 (tt0) REVERT: C 1134 ASN cc_start: 0.8836 (t0) cc_final: 0.8404 (p0) REVERT: D 11 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8178 (tpp80) REVERT: D 14 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (mm) REVERT: D 65 TYR cc_start: 0.8802 (m-10) cc_final: 0.8465 (m-10) REVERT: D 92 MET cc_start: 0.8359 (mtp) cc_final: 0.7318 (mtp) REVERT: D 94 HIS cc_start: 0.8371 (p-80) cc_final: 0.7779 (p-80) REVERT: D 136 ILE cc_start: 0.9558 (mm) cc_final: 0.9095 (tt) REVERT: D 295 ARG cc_start: 0.9050 (mmt90) cc_final: 0.8557 (mmt90) REVERT: D 310 MET cc_start: 0.8412 (mmt) cc_final: 0.8092 (mmm) REVERT: D 364 GLU cc_start: 0.9433 (tp30) cc_final: 0.8981 (tp30) REVERT: D 373 MET cc_start: 0.8817 (mtp) cc_final: 0.8210 (ptp) REVERT: D 437 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8438 (mmmm) REVERT: D 450 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 457 MET cc_start: 0.8705 (mtm) cc_final: 0.8392 (mtm) REVERT: D 475 MET cc_start: 0.8693 (tpp) cc_final: 0.8355 (tpp) REVERT: D 517 VAL cc_start: 0.9192 (t) cc_final: 0.8044 (p) REVERT: D 518 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8127 (mm-30) REVERT: D 554 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8048 (mt-10) REVERT: D 556 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8439 (ttt90) REVERT: D 639 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7914 (mm110) REVERT: D 688 MET cc_start: 0.8737 (mmp) cc_final: 0.8490 (mmp) REVERT: D 706 MET cc_start: 0.8459 (mmp) cc_final: 0.8186 (mmm) REVERT: D 733 MET cc_start: 0.8058 (ttp) cc_final: 0.7855 (ttt) REVERT: D 754 ASP cc_start: 0.9191 (m-30) cc_final: 0.8884 (p0) REVERT: D 784 GLU cc_start: 0.8540 (tp30) cc_final: 0.8020 (tp30) REVERT: D 848 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7812 (mt-10) REVERT: D 858 LYS cc_start: 0.9457 (tttt) cc_final: 0.9174 (ttpt) REVERT: D 877 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9114 (tt) REVERT: D 918 THR cc_start: 0.8557 (p) cc_final: 0.7927 (p) REVERT: D 990 ASP cc_start: 0.8349 (m-30) cc_final: 0.7806 (p0) REVERT: D 991 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8733 (tp) REVERT: D 993 GLU cc_start: 0.8509 (mm-30) cc_final: 0.6793 (mm-30) REVERT: D 1112 MET cc_start: 0.7673 (tpp) cc_final: 0.7352 (tpp) REVERT: D 1151 ASP cc_start: 0.8661 (p0) cc_final: 0.8421 (p0) REVERT: D 1161 MET cc_start: 0.8653 (mtp) cc_final: 0.8417 (mtp) REVERT: D 1190 ASN cc_start: 0.8801 (t0) cc_final: 0.8476 (m-40) REVERT: D 1243 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: D 1248 LEU cc_start: 0.8380 (tp) cc_final: 0.8081 (tt) REVERT: D 1249 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8767 (pttt) REVERT: D 1256 LYS cc_start: 0.8976 (tttp) cc_final: 0.8370 (ttmm) REVERT: E 42 GLU cc_start: 0.9020 (mp0) cc_final: 0.8308 (tm-30) REVERT: E 55 ILE cc_start: 0.9334 (mm) cc_final: 0.8906 (mm) REVERT: E 59 LYS cc_start: 0.9492 (mmtt) cc_final: 0.8931 (mmtt) REVERT: E 60 ARG cc_start: 0.9334 (tpp-160) cc_final: 0.8857 (tpp-160) REVERT: E 70 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8035 (tm-30) REVERT: E 82 LEU cc_start: 0.9135 (tp) cc_final: 0.8460 (tp) REVERT: E 88 GLN cc_start: 0.8725 (tt0) cc_final: 0.8455 (tt0) REVERT: E 89 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8705 (mp0) REVERT: E 94 ILE cc_start: 0.9158 (mm) cc_final: 0.8824 (mm) REVERT: E 97 ARG cc_start: 0.9501 (mtp-110) cc_final: 0.9266 (ttm110) REVERT: E 98 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 100 HIS cc_start: 0.8614 (t-90) cc_final: 0.6692 (t-90) REVERT: F 308 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8414 (ttmt) REVERT: F 310 TYR cc_start: 0.7991 (m-10) cc_final: 0.7626 (m-80) REVERT: F 353 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8026 (pt0) REVERT: F 438 PHE cc_start: 0.8058 (m-80) cc_final: 0.7794 (m-80) REVERT: F 467 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6177 (tp) REVERT: F 478 ARG cc_start: 0.9005 (tpt170) cc_final: 0.8411 (tpm170) REVERT: F 526 TYR cc_start: 0.5555 (m-80) cc_final: 0.5250 (m-80) REVERT: J 10 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8092 (mmm-85) REVERT: J 32 TYR cc_start: 0.8761 (m-80) cc_final: 0.7808 (m-80) REVERT: J 60 MET cc_start: 0.4291 (mtm) cc_final: 0.3558 (ptt) REVERT: J 65 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6602 (mm) REVERT: J 69 LEU cc_start: 0.6428 (tt) cc_final: 0.6002 (mt) REVERT: J 85 LEU cc_start: 0.9009 (tp) cc_final: 0.8731 (pp) REVERT: M 52 ASN cc_start: 0.9323 (m-40) cc_final: 0.8833 (p0) REVERT: M 59 ARG cc_start: 0.9147 (mmm-85) cc_final: 0.8918 (mmm160) outliers start: 130 outliers final: 56 residues processed: 940 average time/residue: 0.1963 time to fit residues: 287.1408 Evaluate side-chains 840 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 771 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1243 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 60 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 257 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1077 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.146850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097058 restraints weight = 71252.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100898 restraints weight = 36530.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103375 restraints weight = 23882.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104966 restraints weight = 18172.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106003 restraints weight = 15286.687| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29917 Z= 0.193 Angle : 0.744 12.832 40983 Z= 0.383 Chirality : 0.046 0.303 4681 Planarity : 0.005 0.067 5019 Dihedral : 16.200 179.517 5011 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 5.25 % Allowed : 23.57 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -1.12 (0.14), residues: 3466 helix: 0.37 (0.14), residues: 1387 sheet: -1.28 (0.25), residues: 409 loop : -1.55 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 56 TYR 0.021 0.002 TYR E 56 PHE 0.021 0.002 PHE D 811 TRP 0.050 0.003 TRP D 223 HIS 0.014 0.002 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00433 (29909) covalent geometry : angle 0.73788 (40971) hydrogen bonds : bond 0.04629 ( 1327) hydrogen bonds : angle 5.30102 ( 3709) metal coordination : bond 0.01116 ( 8) metal coordination : angle 5.78383 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 782 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8517 (mm-40) cc_final: 0.7913 (mm-40) REVERT: A 75 GLU cc_start: 0.8440 (tp30) cc_final: 0.7622 (tp30) REVERT: A 133 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8500 (ttmm) REVERT: A 159 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 194 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 195 ASP cc_start: 0.7633 (t70) cc_final: 0.7158 (t0) REVERT: A 206 ASP cc_start: 0.8367 (m-30) cc_final: 0.8120 (m-30) REVERT: A 213 LYS cc_start: 0.8779 (tppt) cc_final: 0.8258 (tppt) REVERT: B 9 LEU cc_start: 0.8800 (tt) cc_final: 0.8106 (mt) REVERT: B 17 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.7970 (p0) REVERT: B 21 PHE cc_start: 0.8731 (m-80) cc_final: 0.8341 (m-80) REVERT: B 40 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8773 (mmm160) REVERT: B 72 ASP cc_start: 0.7926 (p0) cc_final: 0.7660 (p0) REVERT: B 81 LYS cc_start: 0.9680 (tppt) cc_final: 0.9384 (mmtp) REVERT: B 189 PHE cc_start: 0.8064 (m-10) cc_final: 0.7861 (m-10) REVERT: B 191 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8378 (ttpt) REVERT: C 59 ASP cc_start: 0.8921 (m-30) cc_final: 0.8581 (m-30) REVERT: C 103 MET cc_start: 0.9092 (ttp) cc_final: 0.8883 (ppp) REVERT: C 121 GLU cc_start: 0.8813 (tt0) cc_final: 0.8155 (tp30) REVERT: C 127 MET cc_start: 0.8094 (mtm) cc_final: 0.7766 (mtm) REVERT: C 139 PHE cc_start: 0.8801 (t80) cc_final: 0.8510 (t80) REVERT: C 148 LYS cc_start: 0.9460 (mppt) cc_final: 0.8932 (mppt) REVERT: C 159 MET cc_start: 0.8842 (mmm) cc_final: 0.8204 (mmm) REVERT: C 163 LYS cc_start: 0.9075 (mmtp) cc_final: 0.8842 (mmmm) REVERT: C 227 ASP cc_start: 0.8809 (t0) cc_final: 0.8470 (t0) REVERT: C 258 MET cc_start: 0.7740 (tmm) cc_final: 0.7504 (tmm) REVERT: C 279 ARG cc_start: 0.8826 (mmm160) cc_final: 0.8293 (mmm160) REVERT: C 293 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: C 376 ARG cc_start: 0.8987 (ttt180) cc_final: 0.7993 (ttt90) REVERT: C 421 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8414 (tmm-80) REVERT: C 487 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 513 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8449 (mt-10) REVERT: C 518 LYS cc_start: 0.8870 (tmtt) cc_final: 0.8580 (tmtt) REVERT: C 570 TYR cc_start: 0.8655 (m-80) cc_final: 0.8137 (t80) REVERT: C 579 MET cc_start: 0.7737 (tmm) cc_final: 0.7449 (tmm) REVERT: C 631 GLU cc_start: 0.8320 (mp0) cc_final: 0.7473 (pm20) REVERT: C 738 SER cc_start: 0.8975 (p) cc_final: 0.8754 (m) REVERT: C 758 ASP cc_start: 0.6589 (p0) cc_final: 0.5979 (p0) REVERT: C 814 LEU cc_start: 0.8909 (mm) cc_final: 0.8684 (mm) REVERT: C 816 PRO cc_start: 0.9253 (Cg_exo) cc_final: 0.9024 (Cg_endo) REVERT: C 819 ARG cc_start: 0.9412 (ttt180) cc_final: 0.8872 (ttt180) REVERT: C 832 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (p) REVERT: C 915 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8839 (pt) REVERT: C 933 GLU cc_start: 0.8254 (tt0) cc_final: 0.7638 (pt0) REVERT: C 950 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8630 (mmtm) REVERT: C 965 GLU cc_start: 0.8998 (pp20) cc_final: 0.8614 (pp20) REVERT: C 1021 TYR cc_start: 0.8889 (m-80) cc_final: 0.8238 (m-10) REVERT: C 1051 MET cc_start: 0.8057 (tpp) cc_final: 0.7616 (tpp) REVERT: C 1074 TRP cc_start: 0.8387 (m-10) cc_final: 0.8080 (m-90) REVERT: C 1077 GLN cc_start: 0.9166 (mt0) cc_final: 0.8954 (mt0) REVERT: C 1104 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8536 (tm-30) REVERT: C 1108 LYS cc_start: 0.9488 (tppt) cc_final: 0.9166 (tppt) REVERT: C 1110 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 1125 LEU cc_start: 0.9517 (mm) cc_final: 0.9269 (mm) REVERT: C 1129 GLN cc_start: 0.8766 (mt0) cc_final: 0.8538 (tt0) REVERT: C 1134 ASN cc_start: 0.8834 (t0) cc_final: 0.8405 (p0) REVERT: D 11 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8202 (tpp80) REVERT: D 14 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8478 (mm) REVERT: D 92 MET cc_start: 0.8354 (mtp) cc_final: 0.7911 (mtp) REVERT: D 94 HIS cc_start: 0.8381 (p-80) cc_final: 0.7453 (p-80) REVERT: D 151 LEU cc_start: 0.9381 (mt) cc_final: 0.9173 (tp) REVERT: D 164 ASP cc_start: 0.8939 (m-30) cc_final: 0.8701 (t70) REVERT: D 223 TRP cc_start: 0.8372 (t-100) cc_final: 0.7557 (t60) REVERT: D 263 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8889 (ttpt) REVERT: D 295 ARG cc_start: 0.9035 (mmt90) cc_final: 0.8596 (mmm-85) REVERT: D 310 MET cc_start: 0.8538 (mmt) cc_final: 0.8249 (mmm) REVERT: D 364 GLU cc_start: 0.9416 (tp30) cc_final: 0.8988 (tp30) REVERT: D 373 MET cc_start: 0.8862 (mtp) cc_final: 0.8222 (ptp) REVERT: D 450 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7121 (tm-30) REVERT: D 517 VAL cc_start: 0.9105 (t) cc_final: 0.8759 (p) REVERT: D 530 GLU cc_start: 0.8712 (mm-30) cc_final: 0.7957 (mm-30) REVERT: D 556 ARG cc_start: 0.9025 (tpp80) cc_final: 0.8422 (ttt90) REVERT: D 688 MET cc_start: 0.8808 (mmp) cc_final: 0.8558 (mmp) REVERT: D 706 MET cc_start: 0.8469 (mmp) cc_final: 0.8241 (mmm) REVERT: D 717 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8676 (ptmm) REVERT: D 750 GLU cc_start: 0.9030 (tp30) cc_final: 0.8826 (tp30) REVERT: D 784 GLU cc_start: 0.8618 (tp30) cc_final: 0.8071 (tp30) REVERT: D 842 GLU cc_start: 0.9085 (tp30) cc_final: 0.8686 (tp30) REVERT: D 848 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 877 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9203 (tt) REVERT: D 918 THR cc_start: 0.8644 (p) cc_final: 0.8414 (p) REVERT: D 990 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7387 (p0) REVERT: D 991 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8715 (tp) REVERT: D 993 GLU cc_start: 0.8499 (mm-30) cc_final: 0.6395 (mm-30) REVERT: D 1011 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7505 (p) REVERT: D 1112 MET cc_start: 0.8176 (tpp) cc_final: 0.7933 (tpp) REVERT: D 1161 MET cc_start: 0.8594 (mtp) cc_final: 0.8338 (mtp) REVERT: D 1163 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7373 (mmm160) REVERT: D 1183 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7526 (ptp-170) REVERT: D 1190 ASN cc_start: 0.8855 (t0) cc_final: 0.8476 (t0) REVERT: D 1248 LEU cc_start: 0.8606 (tp) cc_final: 0.8265 (tt) REVERT: D 1249 LYS cc_start: 0.8971 (ptmt) cc_final: 0.8724 (pttt) REVERT: D 1256 LYS cc_start: 0.8989 (tttp) cc_final: 0.8207 (ttmm) REVERT: E 42 GLU cc_start: 0.9029 (mp0) cc_final: 0.8359 (tm-30) REVERT: E 51 TYR cc_start: 0.8470 (m-80) cc_final: 0.7393 (m-80) REVERT: E 59 LYS cc_start: 0.9523 (mmtt) cc_final: 0.9054 (mmtt) REVERT: E 82 LEU cc_start: 0.9170 (tp) cc_final: 0.8552 (tp) REVERT: E 88 GLN cc_start: 0.8761 (tt0) cc_final: 0.8488 (tt0) REVERT: E 89 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8685 (mp0) REVERT: E 94 ILE cc_start: 0.9186 (mm) cc_final: 0.8859 (mm) REVERT: E 97 ARG cc_start: 0.9492 (mtp-110) cc_final: 0.9095 (tpp80) REVERT: E 98 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7882 (mt-10) REVERT: E 100 HIS cc_start: 0.8564 (t-90) cc_final: 0.6909 (t-90) REVERT: F 257 LEU cc_start: 0.8959 (tp) cc_final: 0.8751 (pp) REVERT: F 353 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8133 (pt0) REVERT: F 438 PHE cc_start: 0.8067 (m-80) cc_final: 0.7825 (m-80) REVERT: F 467 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6260 (tp) REVERT: F 478 ARG cc_start: 0.8948 (tpt170) cc_final: 0.8348 (tpm170) REVERT: J 10 ARG cc_start: 0.8319 (mmm160) cc_final: 0.8111 (mmm160) REVERT: J 32 TYR cc_start: 0.8941 (m-80) cc_final: 0.7907 (m-80) REVERT: J 60 MET cc_start: 0.4006 (mtm) cc_final: 0.3342 (ptt) REVERT: J 65 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6590 (mm) REVERT: J 69 LEU cc_start: 0.6522 (tt) cc_final: 0.6072 (mt) REVERT: J 85 LEU cc_start: 0.9012 (tp) cc_final: 0.8660 (mm) REVERT: M 52 ASN cc_start: 0.9314 (m-40) cc_final: 0.8902 (p0) REVERT: M 127 MET cc_start: 0.7003 (mtp) cc_final: 0.6799 (mtt) outliers start: 152 outliers final: 91 residues processed: 872 average time/residue: 0.1972 time to fit residues: 268.1408 Evaluate side-chains 845 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 738 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1149 ILE Chi-restraints excluded: chain D residue 1183 ARG Chi-restraints excluded: chain D residue 1243 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 208 optimal weight: 0.3980 chunk 243 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 291 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 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 = 0.4137 r_free = 0.4137 target = 0.147822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097855 restraints weight = 71885.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101743 restraints weight = 36589.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104277 restraints weight = 23869.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105906 restraints weight = 18107.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106908 restraints weight = 15266.941| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29917 Z= 0.158 Angle : 0.738 12.415 40983 Z= 0.375 Chirality : 0.045 0.277 4681 Planarity : 0.005 0.066 5019 Dihedral : 16.114 179.682 5011 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 5.04 % Allowed : 25.05 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -1.01 (0.14), residues: 3466 helix: 0.43 (0.14), residues: 1389 sheet: -1.07 (0.26), residues: 402 loop : -1.51 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 25 TYR 0.031 0.002 TYR E 56 PHE 0.024 0.002 PHE J 40 TRP 0.039 0.002 TRP D 656 HIS 0.011 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00357 (29909) covalent geometry : angle 0.73332 (40971) hydrogen bonds : bond 0.04466 ( 1327) hydrogen bonds : angle 5.15474 ( 3709) metal coordination : bond 0.00861 ( 8) metal coordination : angle 4.67969 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 788 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7794 (mm-40) REVERT: A 75 GLU cc_start: 0.8435 (tp30) cc_final: 0.7601 (tp30) REVERT: A 133 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8591 (ttmm) REVERT: A 159 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8698 (tp) REVERT: A 177 LYS cc_start: 0.7950 (ptpt) cc_final: 0.7504 (ptmm) REVERT: A 194 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7259 (tt) REVERT: A 195 ASP cc_start: 0.7620 (t70) cc_final: 0.7168 (t0) REVERT: A 206 ASP cc_start: 0.8361 (m-30) cc_final: 0.8104 (m-30) REVERT: A 208 LEU cc_start: 0.9514 (tp) cc_final: 0.9222 (tt) REVERT: A 213 LYS cc_start: 0.8755 (tppt) cc_final: 0.8226 (tppt) REVERT: B 9 LEU cc_start: 0.8811 (tt) cc_final: 0.8421 (mt) REVERT: B 12 ASP cc_start: 0.8176 (p0) cc_final: 0.7832 (p0) REVERT: B 21 PHE cc_start: 0.8650 (m-80) cc_final: 0.8429 (m-80) REVERT: B 40 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8733 (mmm160) REVERT: B 72 ASP cc_start: 0.7801 (p0) cc_final: 0.7541 (p0) REVERT: B 191 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8411 (ttpt) REVERT: B 206 ASP cc_start: 0.8500 (p0) cc_final: 0.8096 (p0) REVERT: C 59 ASP cc_start: 0.8847 (m-30) cc_final: 0.8494 (m-30) REVERT: C 65 ILE cc_start: 0.9451 (mm) cc_final: 0.9138 (tp) REVERT: C 127 MET cc_start: 0.8120 (mtm) cc_final: 0.7394 (ptp) REVERT: C 148 LYS cc_start: 0.9458 (mppt) cc_final: 0.8856 (mmtm) REVERT: C 159 MET cc_start: 0.8776 (mmm) cc_final: 0.8279 (mmm) REVERT: C 163 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8703 (mmtp) REVERT: C 227 ASP cc_start: 0.8795 (t0) cc_final: 0.8445 (t0) REVERT: C 279 ARG cc_start: 0.8833 (mmm160) cc_final: 0.8173 (mmm160) REVERT: C 285 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 293 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: C 376 ARG cc_start: 0.9070 (ttt180) cc_final: 0.8081 (ttt90) REVERT: C 401 ARG cc_start: 0.9074 (ttm170) cc_final: 0.8462 (mtt90) REVERT: C 415 GLN cc_start: 0.9473 (tp40) cc_final: 0.9104 (mm-40) REVERT: C 421 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8396 (tmm-80) REVERT: C 440 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.6891 (tpt) REVERT: C 487 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8247 (tm-30) REVERT: C 513 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8448 (mt-10) REVERT: C 570 TYR cc_start: 0.8589 (m-80) cc_final: 0.8133 (t80) REVERT: C 579 MET cc_start: 0.7937 (tmm) cc_final: 0.7671 (tmm) REVERT: C 580 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7840 (t0) REVERT: C 586 MET cc_start: 0.8390 (pmm) cc_final: 0.7865 (pmm) REVERT: C 593 MET cc_start: 0.9202 (mtp) cc_final: 0.8913 (mtm) REVERT: C 661 MET cc_start: 0.8378 (tpp) cc_final: 0.7968 (tpp) REVERT: C 672 MET cc_start: 0.7590 (mmm) cc_final: 0.6977 (mmt) REVERT: C 744 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8225 (mt-10) REVERT: C 819 ARG cc_start: 0.9416 (ttt180) cc_final: 0.8860 (ttt180) REVERT: C 933 GLU cc_start: 0.8240 (tt0) cc_final: 0.7613 (pt0) REVERT: C 965 GLU cc_start: 0.8944 (pp20) cc_final: 0.8577 (pp20) REVERT: C 982 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6467 (mt-10) REVERT: C 1021 TYR cc_start: 0.8860 (m-80) cc_final: 0.8218 (m-10) REVERT: C 1074 TRP cc_start: 0.8326 (m-10) cc_final: 0.8024 (m-90) REVERT: C 1077 GLN cc_start: 0.9120 (mt0) cc_final: 0.8880 (mt0) REVERT: C 1104 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 1108 LYS cc_start: 0.9519 (tppt) cc_final: 0.9075 (tppt) REVERT: C 1110 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 1125 LEU cc_start: 0.9501 (mm) cc_final: 0.9249 (mm) REVERT: C 1134 ASN cc_start: 0.8788 (t0) cc_final: 0.8435 (p0) REVERT: D 11 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8211 (tpp80) REVERT: D 14 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8513 (mm) REVERT: D 37 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8436 (mmm160) REVERT: D 92 MET cc_start: 0.8235 (mtp) cc_final: 0.7765 (mtp) REVERT: D 94 HIS cc_start: 0.8263 (p-80) cc_final: 0.7738 (p-80) REVERT: D 136 ILE cc_start: 0.9627 (mm) cc_final: 0.9227 (tt) REVERT: D 164 ASP cc_start: 0.8928 (m-30) cc_final: 0.8703 (t70) REVERT: D 295 ARG cc_start: 0.9040 (mmt90) cc_final: 0.8740 (mmt90) REVERT: D 310 MET cc_start: 0.8474 (mmt) cc_final: 0.8097 (mmm) REVERT: D 364 GLU cc_start: 0.9399 (tp30) cc_final: 0.8981 (tp30) REVERT: D 373 MET cc_start: 0.8858 (mtp) cc_final: 0.8282 (ptp) REVERT: D 450 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7052 (tm-30) REVERT: D 475 MET cc_start: 0.8571 (tpp) cc_final: 0.8132 (tpp) REVERT: D 517 VAL cc_start: 0.9163 (t) cc_final: 0.8724 (t) REVERT: D 523 GLN cc_start: 0.8365 (mt0) cc_final: 0.7999 (mt0) REVERT: D 556 ARG cc_start: 0.8979 (tpp80) cc_final: 0.8349 (ttt90) REVERT: D 754 ASP cc_start: 0.9283 (m-30) cc_final: 0.8924 (p0) REVERT: D 784 GLU cc_start: 0.8598 (tp30) cc_final: 0.8062 (tp30) REVERT: D 820 MET cc_start: 0.8370 (tpp) cc_final: 0.8043 (tpt) REVERT: D 842 GLU cc_start: 0.9094 (tp30) cc_final: 0.8614 (tp30) REVERT: D 848 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 877 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9131 (tt) REVERT: D 918 THR cc_start: 0.8747 (p) cc_final: 0.8426 (p) REVERT: D 993 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7732 (mm-30) REVERT: D 1011 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7484 (p) REVERT: D 1163 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7522 (mmm160) REVERT: D 1190 ASN cc_start: 0.8872 (t0) cc_final: 0.8523 (t0) REVERT: D 1241 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8590 (tpp80) REVERT: D 1243 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: D 1248 LEU cc_start: 0.8575 (tp) cc_final: 0.8218 (tt) REVERT: D 1249 LYS cc_start: 0.8973 (ptmt) cc_final: 0.8765 (pttt) REVERT: D 1256 LYS cc_start: 0.9005 (tttp) cc_final: 0.8335 (ttmm) REVERT: E 42 GLU cc_start: 0.8985 (mp0) cc_final: 0.8446 (tm-30) REVERT: E 59 LYS cc_start: 0.9519 (mmtt) cc_final: 0.9090 (mmtt) REVERT: E 70 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 82 LEU cc_start: 0.9103 (tp) cc_final: 0.8459 (tp) REVERT: E 88 GLN cc_start: 0.8733 (tt0) cc_final: 0.8498 (tt0) REVERT: E 89 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8720 (mp0) REVERT: E 94 ILE cc_start: 0.9209 (mm) cc_final: 0.8886 (mm) REVERT: E 96 LEU cc_start: 0.9497 (mp) cc_final: 0.9276 (mp) REVERT: E 97 ARG cc_start: 0.9482 (mtp-110) cc_final: 0.9195 (tpp80) REVERT: E 98 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7690 (mt-10) REVERT: F 257 LEU cc_start: 0.8892 (tp) cc_final: 0.8556 (pp) REVERT: F 263 MET cc_start: 0.8707 (mtt) cc_final: 0.8099 (mtt) REVERT: F 282 MET cc_start: 0.8751 (mtm) cc_final: 0.7990 (mtm) REVERT: F 308 LYS cc_start: 0.8679 (tttp) cc_final: 0.8452 (tppt) REVERT: F 343 PHE cc_start: 0.9109 (t80) cc_final: 0.8769 (t80) REVERT: F 438 PHE cc_start: 0.8004 (m-80) cc_final: 0.7366 (m-10) REVERT: F 467 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6214 (tp) REVERT: F 476 ARG cc_start: 0.9485 (ptp-170) cc_final: 0.9223 (ptp90) REVERT: F 478 ARG cc_start: 0.8964 (tpt170) cc_final: 0.8338 (tpm170) REVERT: J 10 ARG cc_start: 0.8266 (mmm160) cc_final: 0.8057 (mmm160) REVERT: J 32 TYR cc_start: 0.8908 (m-80) cc_final: 0.7755 (m-80) REVERT: J 40 PHE cc_start: 0.6584 (m-80) cc_final: 0.6059 (m-80) REVERT: J 60 MET cc_start: 0.3660 (mtm) cc_final: 0.2947 (ptt) REVERT: J 65 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6402 (mm) REVERT: J 69 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6138 (mt) REVERT: J 85 LEU cc_start: 0.8975 (tp) cc_final: 0.8307 (mm) REVERT: M 52 ASN cc_start: 0.9318 (m-40) cc_final: 0.8860 (p0) REVERT: M 59 ARG cc_start: 0.9160 (mmm-85) cc_final: 0.8756 (mmm160) REVERT: M 85 TRP cc_start: 0.8332 (OUTLIER) cc_final: 0.7912 (t60) REVERT: M 126 ARG cc_start: 0.6600 (mpt180) cc_final: 0.6379 (mmt-90) REVERT: M 127 MET cc_start: 0.6907 (mtp) cc_final: 0.6630 (mtp) REVERT: M 151 GLU cc_start: 0.8949 (tp30) cc_final: 0.8379 (mp0) outliers start: 146 outliers final: 96 residues processed: 869 average time/residue: 0.1984 time to fit residues: 269.6267 Evaluate side-chains 847 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 736 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 915 TYR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1149 ILE Chi-restraints excluded: chain D residue 1152 LYS Chi-restraints excluded: chain D residue 1183 ARG Chi-restraints excluded: chain D residue 1243 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 0.0770 chunk 343 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 290 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN C 57 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN C1129 GLN ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.145305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094758 restraints weight = 72315.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098468 restraints weight = 37562.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100889 restraints weight = 24826.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102374 restraints weight = 19073.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103370 restraints weight = 16227.450| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29917 Z= 0.210 Angle : 0.763 13.946 40983 Z= 0.391 Chirality : 0.046 0.289 4681 Planarity : 0.005 0.068 5019 Dihedral : 16.086 179.902 5011 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.17 % Rotamer: Outliers : 5.98 % Allowed : 25.33 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -1.03 (0.14), residues: 3466 helix: 0.36 (0.14), residues: 1401 sheet: -1.00 (0.26), residues: 414 loop : -1.50 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 182 TYR 0.026 0.002 TYR E 56 PHE 0.020 0.002 PHE C 430 TRP 0.058 0.003 TRP D 223 HIS 0.011 0.002 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00469 (29909) covalent geometry : angle 0.75824 (40971) hydrogen bonds : bond 0.04553 ( 1327) hydrogen bonds : angle 5.21400 ( 3709) metal coordination : bond 0.01235 ( 8) metal coordination : angle 4.86450 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 766 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7838 (mm-40) REVERT: A 133 LYS cc_start: 0.8925 (ttpp) cc_final: 0.8491 (ttmm) REVERT: A 159 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8750 (mt) REVERT: A 194 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7456 (tt) REVERT: A 195 ASP cc_start: 0.7593 (t70) cc_final: 0.7070 (t0) REVERT: A 199 LYS cc_start: 0.9390 (ptpt) cc_final: 0.8701 (ptpp) REVERT: A 206 ASP cc_start: 0.8363 (m-30) cc_final: 0.8059 (m-30) REVERT: A 213 LYS cc_start: 0.8837 (tppt) cc_final: 0.8315 (tppt) REVERT: B 179 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7945 (t0) REVERT: B 191 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8411 (ttpt) REVERT: B 206 ASP cc_start: 0.8481 (p0) cc_final: 0.8074 (p0) REVERT: C 59 ASP cc_start: 0.8887 (m-30) cc_final: 0.8567 (m-30) REVERT: C 103 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8459 (tmm) REVERT: C 121 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8312 (tp30) REVERT: C 127 MET cc_start: 0.8277 (mtm) cc_final: 0.7421 (ptp) REVERT: C 139 PHE cc_start: 0.8995 (t80) cc_final: 0.8729 (t80) REVERT: C 163 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8725 (mmtp) REVERT: C 186 TYR cc_start: 0.8911 (m-80) cc_final: 0.8539 (m-80) REVERT: C 227 ASP cc_start: 0.8785 (t0) cc_final: 0.8436 (t0) REVERT: C 279 ARG cc_start: 0.8864 (mmm160) cc_final: 0.8262 (mmm160) REVERT: C 293 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: C 376 ARG cc_start: 0.9060 (ttt180) cc_final: 0.8083 (ttt90) REVERT: C 397 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8686 (tm-30) REVERT: C 401 ARG cc_start: 0.9112 (ttm170) cc_final: 0.8761 (mtt180) REVERT: C 415 GLN cc_start: 0.9493 (tp40) cc_final: 0.9126 (mm-40) REVERT: C 421 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8450 (tmm-80) REVERT: C 440 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6995 (tpt) REVERT: C 487 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 513 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8423 (mt-10) REVERT: C 570 TYR cc_start: 0.8638 (m-80) cc_final: 0.8193 (t80) REVERT: C 586 MET cc_start: 0.8308 (pmm) cc_final: 0.7874 (pmm) REVERT: C 631 GLU cc_start: 0.8305 (mp0) cc_final: 0.7936 (mp0) REVERT: C 744 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8335 (mt-10) REVERT: C 814 LEU cc_start: 0.9017 (mm) cc_final: 0.8680 (mm) REVERT: C 816 PRO cc_start: 0.9231 (Cg_exo) cc_final: 0.8937 (Cg_endo) REVERT: C 819 ARG cc_start: 0.9431 (ttt180) cc_final: 0.8912 (ttt180) REVERT: C 915 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8945 (pt) REVERT: C 933 GLU cc_start: 0.8168 (tt0) cc_final: 0.7587 (pt0) REVERT: C 984 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8196 (mp0) REVERT: C 993 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8478 (pp) REVERT: C 1021 TYR cc_start: 0.8872 (m-80) cc_final: 0.8250 (m-10) REVERT: C 1074 TRP cc_start: 0.8431 (m-10) cc_final: 0.7966 (m-90) REVERT: C 1077 GLN cc_start: 0.9143 (mt0) cc_final: 0.8906 (mt0) REVERT: C 1104 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 1108 LYS cc_start: 0.9545 (tppt) cc_final: 0.9212 (tppt) REVERT: C 1110 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7474 (mt-10) REVERT: C 1125 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9260 (mm) REVERT: C 1129 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: C 1134 ASN cc_start: 0.8652 (t0) cc_final: 0.8361 (p0) REVERT: D 14 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8510 (mm) REVERT: D 46 LEU cc_start: 0.9662 (mm) cc_final: 0.9461 (mm) REVERT: D 65 TYR cc_start: 0.8948 (m-10) cc_final: 0.8633 (m-10) REVERT: D 143 MET cc_start: 0.3250 (ptm) cc_final: 0.3021 (mmt) REVERT: D 164 ASP cc_start: 0.8907 (m-30) cc_final: 0.8704 (t70) REVERT: D 295 ARG cc_start: 0.9070 (mmt90) cc_final: 0.8723 (mmm-85) REVERT: D 310 MET cc_start: 0.8546 (mmt) cc_final: 0.8191 (mmm) REVERT: D 364 GLU cc_start: 0.9361 (tp30) cc_final: 0.8872 (tp30) REVERT: D 373 MET cc_start: 0.8899 (mtp) cc_final: 0.8630 (mtp) REVERT: D 450 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7156 (tm-30) REVERT: D 453 LYS cc_start: 0.9259 (tttp) cc_final: 0.8749 (tmtt) REVERT: D 475 MET cc_start: 0.8540 (tpp) cc_final: 0.7940 (tpp) REVERT: D 489 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8614 (mt-10) REVERT: D 517 VAL cc_start: 0.9295 (t) cc_final: 0.8986 (t) REVERT: D 523 GLN cc_start: 0.8201 (mt0) cc_final: 0.7927 (mt0) REVERT: D 556 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8341 (ttt90) REVERT: D 574 LEU cc_start: 0.9356 (tp) cc_final: 0.9084 (tt) REVERT: D 688 MET cc_start: 0.8651 (mmp) cc_final: 0.8391 (mmp) REVERT: D 706 MET cc_start: 0.8409 (mmp) cc_final: 0.8155 (mmm) REVERT: D 717 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8545 (ptmt) REVERT: D 750 GLU cc_start: 0.9016 (tp30) cc_final: 0.8807 (tp30) REVERT: D 784 GLU cc_start: 0.8613 (tp30) cc_final: 0.8075 (tp30) REVERT: D 820 MET cc_start: 0.8522 (tpp) cc_final: 0.8172 (tpt) REVERT: D 848 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7771 (mt-10) REVERT: D 858 LYS cc_start: 0.9491 (tttt) cc_final: 0.9045 (tppt) REVERT: D 877 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9019 (tt) REVERT: D 991 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8542 (tp) REVERT: D 993 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 1011 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7699 (p) REVERT: D 1112 MET cc_start: 0.7799 (tpp) cc_final: 0.7440 (tpp) REVERT: D 1137 GLU cc_start: 0.8839 (tp30) cc_final: 0.8538 (tp30) REVERT: D 1243 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: D 1248 LEU cc_start: 0.8692 (tp) cc_final: 0.8258 (tt) REVERT: D 1249 LYS cc_start: 0.9107 (ptmt) cc_final: 0.8760 (ptmm) REVERT: D 1256 LYS cc_start: 0.8987 (tttp) cc_final: 0.8202 (ttmm) REVERT: D 1267 TYR cc_start: 0.8875 (m-80) cc_final: 0.8411 (m-80) REVERT: E 42 GLU cc_start: 0.8928 (mp0) cc_final: 0.8336 (tm-30) REVERT: E 51 TYR cc_start: 0.8630 (m-80) cc_final: 0.8030 (m-80) REVERT: E 59 LYS cc_start: 0.9521 (mmtt) cc_final: 0.9101 (mmtt) REVERT: E 82 LEU cc_start: 0.9134 (tp) cc_final: 0.8551 (tp) REVERT: E 88 GLN cc_start: 0.8742 (tt0) cc_final: 0.8501 (tt0) REVERT: E 89 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8723 (mp0) REVERT: E 94 ILE cc_start: 0.9203 (mm) cc_final: 0.8896 (mm) REVERT: E 96 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9236 (mp) REVERT: E 97 ARG cc_start: 0.9463 (mtp-110) cc_final: 0.9234 (tpp80) REVERT: E 98 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7945 (mt-10) REVERT: F 246 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8935 (mp0) REVERT: F 257 LEU cc_start: 0.8796 (tp) cc_final: 0.8596 (pp) REVERT: F 273 LEU cc_start: 0.7552 (mp) cc_final: 0.7095 (mm) REVERT: F 281 MET cc_start: 0.7319 (ppp) cc_final: 0.6220 (ppp) REVERT: F 282 MET cc_start: 0.8178 (mtm) cc_final: 0.7893 (mtm) REVERT: F 308 LYS cc_start: 0.8669 (tttp) cc_final: 0.8428 (tppt) REVERT: F 343 PHE cc_start: 0.9099 (t80) cc_final: 0.8805 (t80) REVERT: F 353 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8693 (pp30) REVERT: F 403 MET cc_start: 0.8803 (tpp) cc_final: 0.8562 (tpp) REVERT: F 467 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6213 (tp) REVERT: F 478 ARG cc_start: 0.8980 (tpt170) cc_final: 0.8370 (tpm170) REVERT: J 10 ARG cc_start: 0.8223 (mmm160) cc_final: 0.8020 (mmm160) REVERT: J 32 TYR cc_start: 0.8919 (m-80) cc_final: 0.7830 (m-80) REVERT: J 60 MET cc_start: 0.4194 (mtm) cc_final: 0.3321 (ptt) REVERT: J 65 ILE cc_start: 0.6624 (OUTLIER) cc_final: 0.6310 (mm) REVERT: J 69 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6214 (mt) REVERT: M 59 ARG cc_start: 0.9141 (mmm-85) cc_final: 0.8748 (mmm160) REVERT: M 126 ARG cc_start: 0.6451 (mpt180) cc_final: 0.4376 (mmt-90) REVERT: M 151 GLU cc_start: 0.8983 (tp30) cc_final: 0.8443 (mp0) outliers start: 173 outliers final: 116 residues processed: 864 average time/residue: 0.1867 time to fit residues: 253.6141 Evaluate side-chains 861 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 724 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1129 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 915 TYR Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1148 SER Chi-restraints excluded: chain D residue 1183 ARG Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1243 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 283 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 344 optimal weight: 50.0000 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 318 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 HIS C 679 ASN C 935 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.148078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.098638 restraints weight = 71101.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102319 restraints weight = 37479.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104715 restraints weight = 24896.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106211 restraints weight = 19145.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.107229 restraints weight = 16261.102| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29917 Z= 0.153 Angle : 0.770 13.151 40983 Z= 0.388 Chirality : 0.046 0.262 4681 Planarity : 0.005 0.064 5019 Dihedral : 16.035 179.923 5011 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.31 % Favored : 94.63 % Rotamer: Outliers : 4.66 % Allowed : 28.02 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -0.93 (0.14), residues: 3466 helix: 0.40 (0.14), residues: 1386 sheet: -0.86 (0.27), residues: 386 loop : -1.42 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 478 TYR 0.033 0.002 TYR B 168 PHE 0.030 0.002 PHE B 189 TRP 0.061 0.003 TRP D 223 HIS 0.010 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00346 (29909) covalent geometry : angle 0.76715 (40971) hydrogen bonds : bond 0.04403 ( 1327) hydrogen bonds : angle 5.11942 ( 3709) metal coordination : bond 0.00628 ( 8) metal coordination : angle 3.85537 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 778 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7660 (mm-40) REVERT: A 159 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8710 (mt) REVERT: A 194 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7196 (tt) REVERT: A 195 ASP cc_start: 0.7643 (t70) cc_final: 0.7177 (t0) REVERT: A 199 LYS cc_start: 0.9372 (ptpt) cc_final: 0.8665 (ptpp) REVERT: A 206 ASP cc_start: 0.8321 (m-30) cc_final: 0.8033 (m-30) REVERT: A 213 LYS cc_start: 0.8693 (tppt) cc_final: 0.8160 (tppt) REVERT: B 9 LEU cc_start: 0.8972 (tt) cc_final: 0.7935 (mp) REVERT: B 146 TYR cc_start: 0.7426 (t80) cc_final: 0.6809 (t80) REVERT: B 168 TYR cc_start: 0.8341 (m-80) cc_final: 0.7928 (m-80) REVERT: B 179 ASP cc_start: 0.8196 (m-30) cc_final: 0.7930 (t0) REVERT: B 191 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8406 (ttpt) REVERT: B 206 ASP cc_start: 0.8520 (p0) cc_final: 0.8267 (p0) REVERT: C 59 ASP cc_start: 0.8878 (m-30) cc_final: 0.8524 (m-30) REVERT: C 65 ILE cc_start: 0.9449 (mm) cc_final: 0.9159 (tp) REVERT: C 103 MET cc_start: 0.8745 (tmm) cc_final: 0.8428 (tmm) REVERT: C 121 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8188 (tp30) REVERT: C 127 MET cc_start: 0.8314 (mtm) cc_final: 0.7419 (ptp) REVERT: C 139 PHE cc_start: 0.9071 (t80) cc_final: 0.8830 (t80) REVERT: C 159 MET cc_start: 0.8718 (mmm) cc_final: 0.7942 (mmm) REVERT: C 163 LYS cc_start: 0.9220 (mmtp) cc_final: 0.8840 (mmtp) REVERT: C 174 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.7545 (t) REVERT: C 186 TYR cc_start: 0.8899 (m-80) cc_final: 0.8546 (m-80) REVERT: C 227 ASP cc_start: 0.8813 (t0) cc_final: 0.8445 (t0) REVERT: C 279 ARG cc_start: 0.8826 (mmm160) cc_final: 0.8226 (mmm160) REVERT: C 293 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: C 376 ARG cc_start: 0.9072 (ttt180) cc_final: 0.8606 (ttt180) REVERT: C 421 ARG cc_start: 0.8817 (ttp80) cc_final: 0.8430 (tmm-80) REVERT: C 440 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.6795 (tpt) REVERT: C 487 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8317 (tm-30) REVERT: C 513 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8443 (mt-10) REVERT: C 518 LYS cc_start: 0.8852 (tmtt) cc_final: 0.8518 (tmmt) REVERT: C 570 TYR cc_start: 0.8660 (m-80) cc_final: 0.8199 (t80) REVERT: C 586 MET cc_start: 0.8270 (pmm) cc_final: 0.7836 (pmm) REVERT: C 593 MET cc_start: 0.9038 (mtp) cc_final: 0.8747 (mtm) REVERT: C 652 GLU cc_start: 0.8123 (tp30) cc_final: 0.7737 (tp30) REVERT: C 672 MET cc_start: 0.7772 (mmm) cc_final: 0.7316 (mtt) REVERT: C 814 LEU cc_start: 0.9044 (mm) cc_final: 0.8698 (mm) REVERT: C 816 PRO cc_start: 0.9224 (Cg_exo) cc_final: 0.8956 (Cg_endo) REVERT: C 819 ARG cc_start: 0.9443 (ttt180) cc_final: 0.8906 (ttt180) REVERT: C 933 GLU cc_start: 0.8235 (tt0) cc_final: 0.7685 (pt0) REVERT: C 1021 TYR cc_start: 0.8830 (m-80) cc_final: 0.8035 (m-10) REVERT: C 1074 TRP cc_start: 0.8278 (m-10) cc_final: 0.7826 (m-90) REVERT: C 1077 GLN cc_start: 0.9124 (mt0) cc_final: 0.8842 (mt0) REVERT: C 1125 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9260 (mm) REVERT: C 1126 LYS cc_start: 0.9449 (mmmm) cc_final: 0.9149 (mmtm) REVERT: C 1129 GLN cc_start: 0.8961 (tt0) cc_final: 0.8186 (tm-30) REVERT: C 1134 ASN cc_start: 0.8634 (t0) cc_final: 0.8382 (p0) REVERT: D 1 MET cc_start: 0.7273 (ppp) cc_final: 0.6965 (ppp) REVERT: D 14 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8468 (mm) REVERT: D 37 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8340 (mmm160) REVERT: D 136 ILE cc_start: 0.9538 (mm) cc_final: 0.9183 (tp) REVERT: D 295 ARG cc_start: 0.9064 (mmt90) cc_final: 0.8698 (mmm-85) REVERT: D 310 MET cc_start: 0.8642 (mmt) cc_final: 0.8307 (mmp) REVERT: D 323 GLU cc_start: 0.8943 (mp0) cc_final: 0.8366 (mt-10) REVERT: D 364 GLU cc_start: 0.9334 (tp30) cc_final: 0.8867 (tp30) REVERT: D 373 MET cc_start: 0.8917 (mtp) cc_final: 0.8651 (mtp) REVERT: D 450 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7371 (tm-30) REVERT: D 453 LYS cc_start: 0.9178 (tttp) cc_final: 0.8879 (tmtt) REVERT: D 475 MET cc_start: 0.8595 (tpp) cc_final: 0.8369 (tpp) REVERT: D 517 VAL cc_start: 0.9276 (t) cc_final: 0.8797 (p) REVERT: D 523 GLN cc_start: 0.8185 (mt0) cc_final: 0.7977 (mt0) REVERT: D 556 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8605 (mmm-85) REVERT: D 574 LEU cc_start: 0.9348 (tp) cc_final: 0.9111 (tt) REVERT: D 620 MET cc_start: 0.8966 (ppp) cc_final: 0.8576 (ppp) REVERT: D 688 MET cc_start: 0.8779 (mmp) cc_final: 0.8452 (mmp) REVERT: D 706 MET cc_start: 0.8350 (mmp) cc_final: 0.8138 (mmm) REVERT: D 717 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8646 (ptmt) REVERT: D 750 GLU cc_start: 0.9056 (tp30) cc_final: 0.8785 (tp30) REVERT: D 784 GLU cc_start: 0.8644 (tp30) cc_final: 0.8095 (tp30) REVERT: D 820 MET cc_start: 0.8405 (tpp) cc_final: 0.8090 (tpt) REVERT: D 842 GLU cc_start: 0.9222 (tp30) cc_final: 0.8538 (tp30) REVERT: D 848 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7781 (mt-10) REVERT: D 877 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9059 (tt) REVERT: D 993 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 1011 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7452 (p) REVERT: D 1112 MET cc_start: 0.7771 (tpp) cc_final: 0.7557 (tpp) REVERT: D 1161 MET cc_start: 0.8586 (mtm) cc_final: 0.8322 (mtp) REVERT: D 1163 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7130 (mmm160) REVERT: D 1248 LEU cc_start: 0.8501 (tp) cc_final: 0.8119 (tt) REVERT: D 1249 LYS cc_start: 0.9079 (ptmt) cc_final: 0.8721 (pttt) REVERT: D 1256 LYS cc_start: 0.9000 (tttp) cc_final: 0.8243 (ttmm) REVERT: D 1267 TYR cc_start: 0.8921 (m-80) cc_final: 0.8282 (m-80) REVERT: E 51 TYR cc_start: 0.8531 (m-80) cc_final: 0.7913 (m-80) REVERT: E 55 ILE cc_start: 0.9434 (mm) cc_final: 0.8960 (mm) REVERT: E 59 LYS cc_start: 0.9536 (mmtt) cc_final: 0.9059 (mmtt) REVERT: E 70 GLN cc_start: 0.8593 (pp30) cc_final: 0.8008 (pp30) REVERT: E 82 LEU cc_start: 0.9111 (tp) cc_final: 0.8510 (tp) REVERT: E 94 ILE cc_start: 0.9214 (mm) cc_final: 0.8910 (mm) REVERT: E 97 ARG cc_start: 0.9446 (mtp-110) cc_final: 0.9231 (tpp80) REVERT: E 98 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7938 (mt-10) REVERT: F 246 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8811 (mp0) REVERT: F 257 LEU cc_start: 0.8763 (tp) cc_final: 0.8336 (pp) REVERT: F 273 LEU cc_start: 0.7188 (mp) cc_final: 0.6834 (mm) REVERT: F 308 LYS cc_start: 0.8612 (tttp) cc_final: 0.8384 (tppt) REVERT: F 343 PHE cc_start: 0.9074 (t80) cc_final: 0.8823 (t80) REVERT: F 353 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8731 (pp30) REVERT: F 467 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6205 (tp) REVERT: F 478 ARG cc_start: 0.8921 (tpt170) cc_final: 0.8301 (tpm170) REVERT: J 32 TYR cc_start: 0.8888 (m-80) cc_final: 0.7716 (m-80) REVERT: J 40 PHE cc_start: 0.6594 (m-80) cc_final: 0.6123 (m-80) REVERT: J 60 MET cc_start: 0.4084 (mtm) cc_final: 0.3141 (ptt) REVERT: J 65 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6370 (mm) REVERT: J 69 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6233 (mt) REVERT: J 85 LEU cc_start: 0.9043 (tp) cc_final: 0.8395 (mm) REVERT: M 59 ARG cc_start: 0.9139 (mmm-85) cc_final: 0.8773 (mmm160) REVERT: M 126 ARG cc_start: 0.6385 (mpt180) cc_final: 0.6061 (mmt-90) outliers start: 135 outliers final: 92 residues processed: 854 average time/residue: 0.1798 time to fit residues: 239.1726 Evaluate side-chains 829 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 723 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 915 TYR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 159 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 331 optimal weight: 0.0000 chunk 59 optimal weight: 0.6980 chunk 340 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1150 HIS ** E 70 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 = 0.4132 r_free = 0.4132 target = 0.146679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097332 restraints weight = 71936.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100931 restraints weight = 37960.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103253 restraints weight = 25276.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104764 restraints weight = 19505.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105680 restraints weight = 16559.090| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29917 Z= 0.182 Angle : 0.790 13.024 40983 Z= 0.399 Chirality : 0.046 0.270 4681 Planarity : 0.005 0.064 5019 Dihedral : 16.065 179.578 5011 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 4.98 % Allowed : 28.30 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -0.91 (0.14), residues: 3466 helix: 0.39 (0.14), residues: 1400 sheet: -0.82 (0.27), residues: 383 loop : -1.39 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 578 TYR 0.028 0.002 TYR F 258 PHE 0.025 0.002 PHE C 61 TRP 0.052 0.003 TRP F 349 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00413 (29909) covalent geometry : angle 0.78698 (40971) hydrogen bonds : bond 0.04425 ( 1327) hydrogen bonds : angle 5.13672 ( 3709) metal coordination : bond 0.00982 ( 8) metal coordination : angle 4.03575 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 744 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.8739 (t) cc_final: 0.8249 (p) REVERT: A 20 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7746 (mm-40) REVERT: A 159 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8705 (mt) REVERT: A 194 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7308 (tt) REVERT: A 195 ASP cc_start: 0.7583 (t70) cc_final: 0.6874 (t0) REVERT: A 213 LYS cc_start: 0.8789 (tppt) cc_final: 0.8175 (tppt) REVERT: B 12 ASP cc_start: 0.8443 (p0) cc_final: 0.8077 (p0) REVERT: B 44 SER cc_start: 0.7840 (m) cc_final: 0.7628 (p) REVERT: B 146 TYR cc_start: 0.7656 (t80) cc_final: 0.6875 (t80) REVERT: B 168 TYR cc_start: 0.8421 (m-80) cc_final: 0.8006 (m-80) REVERT: B 191 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8526 (ttpt) REVERT: B 205 ARG cc_start: 0.8607 (ptm-80) cc_final: 0.7954 (ptm-80) REVERT: B 206 ASP cc_start: 0.8608 (p0) cc_final: 0.7365 (p0) REVERT: C 59 ASP cc_start: 0.8897 (m-30) cc_final: 0.8532 (m-30) REVERT: C 103 MET cc_start: 0.8842 (tmm) cc_final: 0.8579 (tmm) REVERT: C 121 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8243 (tp30) REVERT: C 127 MET cc_start: 0.8376 (mtm) cc_final: 0.7495 (ptp) REVERT: C 139 PHE cc_start: 0.9084 (t80) cc_final: 0.8835 (t80) REVERT: C 159 MET cc_start: 0.8889 (mmm) cc_final: 0.8225 (mmm) REVERT: C 163 LYS cc_start: 0.9259 (mmtp) cc_final: 0.8775 (mmmm) REVERT: C 174 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7393 (t) REVERT: C 186 TYR cc_start: 0.8941 (m-80) cc_final: 0.8601 (m-80) REVERT: C 227 ASP cc_start: 0.8805 (t0) cc_final: 0.8450 (t0) REVERT: C 279 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8280 (mmm160) REVERT: C 293 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: C 376 ARG cc_start: 0.9076 (ttt180) cc_final: 0.8041 (ttt90) REVERT: C 383 GLU cc_start: 0.8712 (tp30) cc_final: 0.8484 (tp30) REVERT: C 420 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9047 (mm) REVERT: C 421 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8358 (tmm-80) REVERT: C 440 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6813 (tpt) REVERT: C 487 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 513 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8459 (mt-10) REVERT: C 518 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8535 (tmmt) REVERT: C 570 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8234 (t80) REVERT: C 586 MET cc_start: 0.8253 (pmm) cc_final: 0.7860 (pmm) REVERT: C 593 MET cc_start: 0.9081 (mtp) cc_final: 0.8751 (mtm) REVERT: C 652 GLU cc_start: 0.8229 (tp30) cc_final: 0.7835 (tp30) REVERT: C 672 MET cc_start: 0.7941 (mmm) cc_final: 0.7410 (mmm) REVERT: C 744 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8047 (mp0) REVERT: C 816 PRO cc_start: 0.9247 (Cg_exo) cc_final: 0.8967 (Cg_endo) REVERT: C 819 ARG cc_start: 0.9462 (ttt180) cc_final: 0.8995 (ttt180) REVERT: C 820 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9357 (mt) REVERT: C 832 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8714 (p) REVERT: C 915 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8869 (pt) REVERT: C 933 GLU cc_start: 0.8240 (tt0) cc_final: 0.7622 (pt0) REVERT: C 1021 TYR cc_start: 0.8850 (m-80) cc_final: 0.8107 (m-10) REVERT: C 1024 THR cc_start: 0.9026 (m) cc_final: 0.8686 (p) REVERT: C 1074 TRP cc_start: 0.8310 (m-10) cc_final: 0.7843 (m-90) REVERT: C 1077 GLN cc_start: 0.9168 (mt0) cc_final: 0.8924 (mt0) REVERT: C 1110 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 1125 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9262 (mm) REVERT: C 1126 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9078 (mmtm) REVERT: C 1129 GLN cc_start: 0.8952 (tt0) cc_final: 0.8393 (pt0) REVERT: C 1134 ASN cc_start: 0.8679 (t0) cc_final: 0.8223 (p0) REVERT: D 14 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8437 (mm) REVERT: D 23 TRP cc_start: 0.8675 (m-10) cc_final: 0.8466 (m-10) REVERT: D 37 ARG cc_start: 0.8834 (mmm160) cc_final: 0.8322 (mmm160) REVERT: D 56 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8507 (mmm160) REVERT: D 65 TYR cc_start: 0.8857 (m-10) cc_final: 0.8580 (m-80) REVERT: D 143 MET cc_start: 0.3594 (mmt) cc_final: 0.1908 (ptm) REVERT: D 238 GLU cc_start: 0.9522 (pm20) cc_final: 0.9185 (mm-30) REVERT: D 295 ARG cc_start: 0.9035 (mmt90) cc_final: 0.8662 (mmm-85) REVERT: D 310 MET cc_start: 0.8727 (mmt) cc_final: 0.8396 (mmp) REVERT: D 364 GLU cc_start: 0.9336 (tp30) cc_final: 0.8883 (tp30) REVERT: D 373 MET cc_start: 0.8901 (mtp) cc_final: 0.8538 (mtp) REVERT: D 450 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7416 (tm-30) REVERT: D 475 MET cc_start: 0.8630 (tpp) cc_final: 0.8411 (tpp) REVERT: D 489 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8475 (tp30) REVERT: D 517 VAL cc_start: 0.9274 (t) cc_final: 0.8896 (p) REVERT: D 518 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7899 (mm-30) REVERT: D 620 MET cc_start: 0.8978 (ppp) cc_final: 0.8579 (ppp) REVERT: D 688 MET cc_start: 0.8783 (mmp) cc_final: 0.8451 (mmp) REVERT: D 706 MET cc_start: 0.8344 (mmp) cc_final: 0.8135 (mmm) REVERT: D 717 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8638 (ptmt) REVERT: D 750 GLU cc_start: 0.9065 (tp30) cc_final: 0.8769 (tp30) REVERT: D 784 GLU cc_start: 0.8672 (tp30) cc_final: 0.8131 (tp30) REVERT: D 820 MET cc_start: 0.8433 (tpp) cc_final: 0.8149 (tpt) REVERT: D 832 ILE cc_start: 0.8855 (mm) cc_final: 0.8547 (mp) REVERT: D 842 GLU cc_start: 0.9246 (tp30) cc_final: 0.8571 (tp30) REVERT: D 848 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7785 (mt-10) REVERT: D 877 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9081 (tt) REVERT: D 993 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7711 (mm-30) REVERT: D 1011 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7512 (p) REVERT: D 1112 MET cc_start: 0.7931 (tpp) cc_final: 0.7680 (tpp) REVERT: D 1137 GLU cc_start: 0.8909 (tp30) cc_final: 0.8698 (tm-30) REVERT: D 1155 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8454 (tt0) REVERT: D 1163 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7335 (mmm160) REVERT: D 1226 PHE cc_start: 0.7976 (t80) cc_final: 0.7425 (t80) REVERT: D 1249 LYS cc_start: 0.9063 (ptmt) cc_final: 0.8667 (ptmm) REVERT: D 1256 LYS cc_start: 0.9061 (tttp) cc_final: 0.8274 (ttmm) REVERT: D 1267 TYR cc_start: 0.8904 (m-80) cc_final: 0.8686 (m-80) REVERT: E 42 GLU cc_start: 0.8965 (mp0) cc_final: 0.8744 (mp0) REVERT: E 51 TYR cc_start: 0.8641 (m-80) cc_final: 0.7904 (m-80) REVERT: E 55 ILE cc_start: 0.9436 (mm) cc_final: 0.9000 (mm) REVERT: E 59 LYS cc_start: 0.9546 (mmtt) cc_final: 0.9092 (mmtt) REVERT: E 70 GLN cc_start: 0.8663 (pp30) cc_final: 0.8137 (pp30) REVERT: E 82 LEU cc_start: 0.9169 (tp) cc_final: 0.8591 (tp) REVERT: E 94 ILE cc_start: 0.9257 (mm) cc_final: 0.8977 (mm) REVERT: E 98 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8000 (mt-10) REVERT: F 246 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: F 258 TYR cc_start: 0.8246 (t80) cc_final: 0.7914 (t80) REVERT: F 273 LEU cc_start: 0.7122 (mp) cc_final: 0.6853 (mm) REVERT: F 308 LYS cc_start: 0.8642 (tttp) cc_final: 0.8286 (tptt) REVERT: F 343 PHE cc_start: 0.9045 (t80) cc_final: 0.8799 (t80) REVERT: F 386 LEU cc_start: 0.9292 (tp) cc_final: 0.8900 (pp) REVERT: F 409 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9083 (pttm) REVERT: F 467 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6415 (tp) REVERT: F 478 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8236 (tpm170) REVERT: J 32 TYR cc_start: 0.8819 (m-80) cc_final: 0.7714 (m-80) REVERT: J 40 PHE cc_start: 0.6624 (m-80) cc_final: 0.6102 (m-80) REVERT: J 60 MET cc_start: 0.4393 (mtm) cc_final: 0.3363 (ptt) REVERT: J 65 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6290 (mm) REVERT: J 69 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6254 (mt) REVERT: J 82 TRP cc_start: 0.8805 (t-100) cc_final: 0.8506 (t-100) REVERT: M 11 TYR cc_start: 0.8840 (t80) cc_final: 0.8176 (t80) REVERT: M 52 ASN cc_start: 0.9318 (m-40) cc_final: 0.8883 (m110) REVERT: M 59 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8687 (mmm160) REVERT: M 85 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7953 (t60) REVERT: M 87 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6976 (ttp80) REVERT: M 126 ARG cc_start: 0.6402 (mpt180) cc_final: 0.6075 (mmt-90) outliers start: 144 outliers final: 106 residues processed: 816 average time/residue: 0.1792 time to fit residues: 230.5349 Evaluate side-chains 832 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 705 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 915 TYR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1148 SER Chi-restraints excluded: chain D residue 1149 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 81 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 116 optimal weight: 0.2980 chunk 259 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097584 restraints weight = 71920.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101208 restraints weight = 38025.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103551 restraints weight = 25254.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105080 restraints weight = 19432.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105963 restraints weight = 16465.151| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29917 Z= 0.173 Angle : 0.821 17.872 40983 Z= 0.411 Chirality : 0.047 0.274 4681 Planarity : 0.005 0.071 5019 Dihedral : 16.046 179.728 5011 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 4.63 % Allowed : 29.20 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -0.93 (0.14), residues: 3466 helix: 0.34 (0.14), residues: 1396 sheet: -0.75 (0.27), residues: 387 loop : -1.39 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 242 TYR 0.024 0.002 TYR F 258 PHE 0.024 0.002 PHE F 438 TRP 0.047 0.002 TRP D 656 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00395 (29909) covalent geometry : angle 0.81883 (40971) hydrogen bonds : bond 0.04372 ( 1327) hydrogen bonds : angle 5.09423 ( 3709) metal coordination : bond 0.00855 ( 8) metal coordination : angle 3.60413 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 723 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.8792 (t) cc_final: 0.8245 (p) REVERT: A 20 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7508 (mm-40) REVERT: A 133 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8503 (ttmm) REVERT: A 159 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8799 (tp) REVERT: A 177 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7679 (ptmm) REVERT: A 194 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7255 (tt) REVERT: A 195 ASP cc_start: 0.7488 (t70) cc_final: 0.6894 (t0) REVERT: A 213 LYS cc_start: 0.8848 (tppt) cc_final: 0.8238 (tppt) REVERT: A 215 LEU cc_start: 0.9409 (mp) cc_final: 0.9102 (mp) REVERT: B 44 SER cc_start: 0.7731 (m) cc_final: 0.7452 (p) REVERT: B 146 TYR cc_start: 0.7619 (t80) cc_final: 0.6943 (t80) REVERT: B 168 TYR cc_start: 0.8345 (m-80) cc_final: 0.8019 (m-80) REVERT: B 191 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8498 (ttpt) REVERT: B 205 ARG cc_start: 0.8588 (ptm-80) cc_final: 0.7933 (ptm-80) REVERT: B 206 ASP cc_start: 0.8545 (p0) cc_final: 0.7316 (p0) REVERT: C 59 ASP cc_start: 0.8876 (m-30) cc_final: 0.8525 (m-30) REVERT: C 121 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8204 (tp30) REVERT: C 127 MET cc_start: 0.8322 (mtm) cc_final: 0.7614 (ptp) REVERT: C 139 PHE cc_start: 0.9007 (t80) cc_final: 0.8765 (t80) REVERT: C 159 MET cc_start: 0.8859 (mmm) cc_final: 0.8325 (mmm) REVERT: C 163 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8944 (mmtt) REVERT: C 174 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.7560 (t) REVERT: C 186 TYR cc_start: 0.8906 (m-80) cc_final: 0.8596 (m-80) REVERT: C 227 ASP cc_start: 0.8696 (t0) cc_final: 0.8321 (t0) REVERT: C 279 ARG cc_start: 0.8883 (mmm160) cc_final: 0.8265 (mmm160) REVERT: C 293 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: C 376 ARG cc_start: 0.9010 (ttt180) cc_final: 0.8018 (ttt90) REVERT: C 420 ILE cc_start: 0.9548 (pp) cc_final: 0.9100 (mm) REVERT: C 421 ARG cc_start: 0.8784 (ttp80) cc_final: 0.8301 (tmm-80) REVERT: C 440 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6840 (tpt) REVERT: C 487 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 518 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8565 (tmmt) REVERT: C 570 TYR cc_start: 0.8546 (m-80) cc_final: 0.8144 (t80) REVERT: C 586 MET cc_start: 0.8170 (pmm) cc_final: 0.7821 (pmm) REVERT: C 593 MET cc_start: 0.8983 (mtp) cc_final: 0.8669 (mtm) REVERT: C 744 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8045 (mp0) REVERT: C 832 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 915 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8907 (pt) REVERT: C 933 GLU cc_start: 0.8114 (tt0) cc_final: 0.7503 (pt0) REVERT: C 1021 TYR cc_start: 0.8757 (m-80) cc_final: 0.8132 (m-10) REVERT: C 1024 THR cc_start: 0.9042 (m) cc_final: 0.8661 (p) REVERT: C 1062 GLN cc_start: 0.7642 (pm20) cc_final: 0.7361 (pm20) REVERT: C 1074 TRP cc_start: 0.8306 (m-10) cc_final: 0.7804 (m-90) REVERT: C 1077 GLN cc_start: 0.9144 (mt0) cc_final: 0.8886 (mt0) REVERT: C 1079 TYR cc_start: 0.8326 (m-80) cc_final: 0.7947 (m-80) REVERT: C 1110 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7364 (tm-30) REVERT: C 1125 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9233 (mm) REVERT: C 1126 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9060 (mmtm) REVERT: C 1129 GLN cc_start: 0.8960 (tt0) cc_final: 0.8395 (pt0) REVERT: C 1134 ASN cc_start: 0.8609 (t0) cc_final: 0.8218 (p0) REVERT: D 14 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8429 (mm) REVERT: D 37 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8397 (mmm160) REVERT: D 65 TYR cc_start: 0.8866 (m-10) cc_final: 0.8564 (m-10) REVERT: D 71 LYS cc_start: 0.9318 (mmtt) cc_final: 0.8731 (tppt) REVERT: D 143 MET cc_start: 0.3856 (mmt) cc_final: 0.2275 (ptm) REVERT: D 238 GLU cc_start: 0.9409 (pm20) cc_final: 0.9179 (mm-30) REVERT: D 295 ARG cc_start: 0.9008 (mmt90) cc_final: 0.8701 (mmm-85) REVERT: D 310 MET cc_start: 0.8692 (mmt) cc_final: 0.8326 (mmp) REVERT: D 364 GLU cc_start: 0.9302 (tp30) cc_final: 0.8638 (tp30) REVERT: D 368 ASN cc_start: 0.9231 (p0) cc_final: 0.8608 (p0) REVERT: D 373 MET cc_start: 0.8874 (mtp) cc_final: 0.8537 (mtp) REVERT: D 450 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 475 MET cc_start: 0.8537 (tpp) cc_final: 0.8296 (tpp) REVERT: D 620 MET cc_start: 0.8957 (ppp) cc_final: 0.8657 (ppp) REVERT: D 688 MET cc_start: 0.8658 (mmp) cc_final: 0.8389 (mmp) REVERT: D 717 LYS cc_start: 0.9011 (ptmm) cc_final: 0.8797 (ptmt) REVERT: D 718 ASP cc_start: 0.9058 (t0) cc_final: 0.8753 (m-30) REVERT: D 750 GLU cc_start: 0.9000 (tp30) cc_final: 0.8684 (tp30) REVERT: D 784 GLU cc_start: 0.8596 (tp30) cc_final: 0.8142 (tp30) REVERT: D 811 PHE cc_start: 0.9059 (t80) cc_final: 0.8805 (t80) REVERT: D 842 GLU cc_start: 0.9162 (tp30) cc_final: 0.8480 (tp30) REVERT: D 848 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 877 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9196 (tt) REVERT: D 948 GLU cc_start: 0.9261 (mp0) cc_final: 0.8990 (mp0) REVERT: D 993 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7624 (mm-30) REVERT: D 1011 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7482 (p) REVERT: D 1112 MET cc_start: 0.7880 (tpp) cc_final: 0.7647 (tpp) REVERT: D 1137 GLU cc_start: 0.8775 (tp30) cc_final: 0.8530 (tm-30) REVERT: D 1226 PHE cc_start: 0.7920 (t80) cc_final: 0.7341 (t80) REVERT: D 1243 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7050 (m-30) REVERT: D 1249 LYS cc_start: 0.9085 (ptmt) cc_final: 0.8593 (pttt) REVERT: D 1256 LYS cc_start: 0.9002 (tttp) cc_final: 0.8273 (ttmm) REVERT: D 1267 TYR cc_start: 0.8817 (m-80) cc_final: 0.8593 (m-80) REVERT: E 42 GLU cc_start: 0.8911 (mp0) cc_final: 0.8630 (mp0) REVERT: E 51 TYR cc_start: 0.8583 (m-80) cc_final: 0.7741 (m-80) REVERT: E 55 ILE cc_start: 0.9448 (mm) cc_final: 0.8953 (mm) REVERT: E 59 LYS cc_start: 0.9519 (mmtt) cc_final: 0.9070 (mmtt) REVERT: E 70 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8179 (pp30) REVERT: E 82 LEU cc_start: 0.9126 (tp) cc_final: 0.8570 (tp) REVERT: E 94 ILE cc_start: 0.9256 (mm) cc_final: 0.9043 (mm) REVERT: E 98 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8112 (mt-10) REVERT: F 308 LYS cc_start: 0.8706 (tttp) cc_final: 0.8325 (tptt) REVERT: F 366 ILE cc_start: 0.6848 (mm) cc_final: 0.5220 (tp) REVERT: F 386 LEU cc_start: 0.9296 (tp) cc_final: 0.8921 (pp) REVERT: F 467 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6594 (tp) REVERT: F 478 ARG cc_start: 0.8902 (tpt170) cc_final: 0.8184 (tpm170) REVERT: J 32 TYR cc_start: 0.8749 (m-80) cc_final: 0.7714 (m-80) REVERT: J 40 PHE cc_start: 0.6930 (m-80) cc_final: 0.6523 (m-80) REVERT: J 60 MET cc_start: 0.4457 (mtm) cc_final: 0.3412 (ptt) REVERT: J 65 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6192 (mm) REVERT: J 69 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6199 (mt) REVERT: J 82 TRP cc_start: 0.8645 (t-100) cc_final: 0.8386 (t-100) REVERT: M 11 TYR cc_start: 0.8775 (t80) cc_final: 0.8069 (t80) REVERT: M 52 ASN cc_start: 0.9316 (m-40) cc_final: 0.8894 (m110) REVERT: M 59 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8688 (mmm160) REVERT: M 87 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6391 (ttp80) outliers start: 134 outliers final: 105 residues processed: 792 average time/residue: 0.1788 time to fit residues: 222.4203 Evaluate side-chains 816 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 694 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 915 TYR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1148 SER Chi-restraints excluded: chain D residue 1149 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1243 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 149 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 289 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 340 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 137 optimal weight: 0.0570 chunk 329 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 300 optimal weight: 20.0000 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 493 ASN C 612 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.147175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097747 restraints weight = 71175.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101470 restraints weight = 36932.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103927 restraints weight = 24279.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105494 restraints weight = 18452.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.106473 restraints weight = 15619.516| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29917 Z= 0.168 Angle : 0.844 15.825 40983 Z= 0.422 Chirality : 0.047 0.309 4681 Planarity : 0.006 0.068 5019 Dihedral : 16.060 179.672 5011 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 4.22 % Allowed : 29.89 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -0.93 (0.14), residues: 3466 helix: 0.31 (0.14), residues: 1392 sheet: -0.66 (0.27), residues: 387 loop : -1.39 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 556 TYR 0.022 0.002 TYR D 36 PHE 0.034 0.002 PHE F 479 TRP 0.062 0.003 TRP D 23 HIS 0.008 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00387 (29909) covalent geometry : angle 0.84165 (40971) hydrogen bonds : bond 0.04390 ( 1327) hydrogen bonds : angle 5.10435 ( 3709) metal coordination : bond 0.00808 ( 8) metal coordination : angle 3.39748 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 717 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7569 (mm-40) REVERT: A 133 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8526 (ttmm) REVERT: A 159 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 172 LEU cc_start: 0.9339 (tp) cc_final: 0.9024 (mp) REVERT: A 173 LYS cc_start: 0.8626 (tttp) cc_final: 0.8377 (tptp) REVERT: A 177 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7625 (ptmm) REVERT: A 194 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7332 (tt) REVERT: A 195 ASP cc_start: 0.7503 (t70) cc_final: 0.6924 (t0) REVERT: A 199 LYS cc_start: 0.9342 (ptpt) cc_final: 0.9096 (ptpt) REVERT: A 213 LYS cc_start: 0.8819 (tppt) cc_final: 0.8205 (tppt) REVERT: B 40 ARG cc_start: 0.8539 (mmm160) cc_final: 0.7773 (mmm160) REVERT: B 146 TYR cc_start: 0.7664 (t80) cc_final: 0.7289 (t80) REVERT: B 168 TYR cc_start: 0.8349 (m-80) cc_final: 0.7989 (m-80) REVERT: B 206 ASP cc_start: 0.8564 (p0) cc_final: 0.8294 (p0) REVERT: C 59 ASP cc_start: 0.8877 (m-30) cc_final: 0.8541 (m-30) REVERT: C 121 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8153 (tp30) REVERT: C 127 MET cc_start: 0.8364 (mtm) cc_final: 0.7642 (ptp) REVERT: C 159 MET cc_start: 0.8884 (mmm) cc_final: 0.8352 (mmm) REVERT: C 163 LYS cc_start: 0.9167 (mmtp) cc_final: 0.8861 (mmtt) REVERT: C 174 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.7490 (t) REVERT: C 186 TYR cc_start: 0.8898 (m-80) cc_final: 0.8596 (m-80) REVERT: C 227 ASP cc_start: 0.8751 (t0) cc_final: 0.8368 (t0) REVERT: C 279 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8054 (mmm160) REVERT: C 285 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: C 293 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: C 376 ARG cc_start: 0.9039 (ttt180) cc_final: 0.8585 (ttt180) REVERT: C 420 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9145 (mm) REVERT: C 421 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8295 (tmm-80) REVERT: C 440 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6799 (tpt) REVERT: C 487 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 513 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8546 (mt-10) REVERT: C 518 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8534 (tmmt) REVERT: C 570 TYR cc_start: 0.8584 (m-80) cc_final: 0.8167 (t80) REVERT: C 586 MET cc_start: 0.8174 (pmm) cc_final: 0.7829 (pmm) REVERT: C 593 MET cc_start: 0.9031 (mtp) cc_final: 0.8610 (mtm) REVERT: C 744 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7980 (mp0) REVERT: C 795 GLU cc_start: 0.7906 (tp30) cc_final: 0.7515 (tt0) REVERT: C 819 ARG cc_start: 0.9514 (ttt180) cc_final: 0.8999 (ttt180) REVERT: C 832 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 915 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8891 (pt) REVERT: C 933 GLU cc_start: 0.8120 (tt0) cc_final: 0.7516 (pt0) REVERT: C 1021 TYR cc_start: 0.8784 (m-80) cc_final: 0.8122 (m-10) REVERT: C 1024 THR cc_start: 0.9023 (m) cc_final: 0.8669 (p) REVERT: C 1062 GLN cc_start: 0.7575 (pm20) cc_final: 0.7296 (pm20) REVERT: C 1074 TRP cc_start: 0.8306 (m-10) cc_final: 0.7808 (m-90) REVERT: C 1077 GLN cc_start: 0.9156 (mt0) cc_final: 0.8899 (mt0) REVERT: C 1079 TYR cc_start: 0.8302 (m-80) cc_final: 0.7889 (m-80) REVERT: C 1110 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 1125 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9247 (mm) REVERT: C 1126 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9234 (mmtm) REVERT: C 1129 GLN cc_start: 0.8982 (tt0) cc_final: 0.8536 (tt0) REVERT: C 1134 ASN cc_start: 0.8518 (t0) cc_final: 0.8187 (p0) REVERT: D 14 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8418 (mm) REVERT: D 37 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8289 (mmm160) REVERT: D 42 GLU cc_start: 0.6984 (mp0) cc_final: 0.6774 (mp0) REVERT: D 65 TYR cc_start: 0.8873 (m-10) cc_final: 0.8567 (m-10) REVERT: D 71 LYS cc_start: 0.9321 (mmtt) cc_final: 0.8734 (tppt) REVERT: D 136 ILE cc_start: 0.9481 (mm) cc_final: 0.9133 (tp) REVERT: D 143 MET cc_start: 0.3977 (mmt) cc_final: 0.2478 (ptm) REVERT: D 238 GLU cc_start: 0.9491 (pm20) cc_final: 0.9171 (mm-30) REVERT: D 295 ARG cc_start: 0.9044 (mmt90) cc_final: 0.8561 (mmt90) REVERT: D 310 MET cc_start: 0.8734 (mmt) cc_final: 0.8379 (mmp) REVERT: D 364 GLU cc_start: 0.9306 (tp30) cc_final: 0.8800 (tp30) REVERT: D 373 MET cc_start: 0.8856 (mtp) cc_final: 0.8548 (mtp) REVERT: D 450 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7353 (tm-30) REVERT: D 475 MET cc_start: 0.8596 (tpp) cc_final: 0.8358 (tpp) REVERT: D 620 MET cc_start: 0.8990 (ppp) cc_final: 0.8772 (ppp) REVERT: D 718 ASP cc_start: 0.9100 (t0) cc_final: 0.8764 (m-30) REVERT: D 750 GLU cc_start: 0.9034 (tp30) cc_final: 0.8725 (tp30) REVERT: D 784 GLU cc_start: 0.8615 (tp30) cc_final: 0.8172 (tp30) REVERT: D 811 PHE cc_start: 0.9074 (t80) cc_final: 0.8822 (t80) REVERT: D 842 GLU cc_start: 0.9185 (tp30) cc_final: 0.8480 (tp30) REVERT: D 848 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 858 LYS cc_start: 0.9386 (ttmt) cc_final: 0.8933 (ttmt) REVERT: D 877 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9187 (tt) REVERT: D 948 GLU cc_start: 0.9291 (mp0) cc_final: 0.9039 (mp0) REVERT: D 993 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7663 (mm-30) REVERT: D 1011 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7463 (p) REVERT: D 1112 MET cc_start: 0.7889 (tpp) cc_final: 0.7636 (tpp) REVERT: D 1137 GLU cc_start: 0.8816 (tp30) cc_final: 0.8564 (tm-30) REVERT: D 1226 PHE cc_start: 0.7959 (t80) cc_final: 0.7391 (t80) REVERT: D 1243 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: D 1249 LYS cc_start: 0.9143 (ptmt) cc_final: 0.8942 (pttt) REVERT: D 1250 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8057 (mt-10) REVERT: D 1256 LYS cc_start: 0.9016 (tttp) cc_final: 0.8223 (ttmm) REVERT: E 42 GLU cc_start: 0.8957 (mp0) cc_final: 0.8628 (mp0) REVERT: E 51 TYR cc_start: 0.8581 (m-80) cc_final: 0.7771 (m-80) REVERT: E 55 ILE cc_start: 0.9434 (mm) cc_final: 0.8957 (mm) REVERT: E 59 LYS cc_start: 0.9526 (mmtt) cc_final: 0.9063 (mmtt) REVERT: E 70 GLN cc_start: 0.8679 (pp30) cc_final: 0.8161 (pp30) REVERT: E 82 LEU cc_start: 0.9112 (tp) cc_final: 0.8526 (tp) REVERT: E 90 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8507 (mmtp) REVERT: E 94 ILE cc_start: 0.9185 (mm) cc_final: 0.8971 (mm) REVERT: E 98 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8139 (mt-10) REVERT: F 246 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8759 (mp0) REVERT: F 308 LYS cc_start: 0.8699 (tttp) cc_final: 0.8309 (tptt) REVERT: F 366 ILE cc_start: 0.6818 (mm) cc_final: 0.5204 (tp) REVERT: F 386 LEU cc_start: 0.9292 (tp) cc_final: 0.8893 (pp) REVERT: F 467 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6528 (tp) REVERT: F 478 ARG cc_start: 0.8826 (tpt170) cc_final: 0.8024 (tpm170) REVERT: J 32 TYR cc_start: 0.8750 (m-80) cc_final: 0.7705 (m-80) REVERT: J 40 PHE cc_start: 0.6747 (m-80) cc_final: 0.6355 (m-80) REVERT: J 60 MET cc_start: 0.4457 (mtm) cc_final: 0.3407 (ptt) REVERT: J 65 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6193 (mm) REVERT: J 69 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6219 (mt) REVERT: J 82 TRP cc_start: 0.8612 (t-100) cc_final: 0.8364 (t-100) REVERT: M 11 TYR cc_start: 0.8770 (t80) cc_final: 0.8108 (t80) REVERT: M 52 ASN cc_start: 0.9312 (m-40) cc_final: 0.8899 (m110) REVERT: M 59 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8680 (mmm160) REVERT: M 87 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7049 (ttp80) outliers start: 122 outliers final: 96 residues processed: 785 average time/residue: 0.1875 time to fit residues: 232.7786 Evaluate side-chains 811 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 697 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 355 LYS Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 915 TYR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1077 TYR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1243 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 165 optimal weight: 9.9990 chunk 62 optimal weight: 0.0030 chunk 30 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 99 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 353 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 = 0.4164 r_free = 0.4164 target = 0.149331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099948 restraints weight = 71621.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.103840 restraints weight = 36416.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106357 restraints weight = 23675.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108003 restraints weight = 17897.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109015 restraints weight = 15036.883| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29917 Z= 0.153 Angle : 0.848 15.426 40983 Z= 0.421 Chirality : 0.047 0.312 4681 Planarity : 0.005 0.066 5019 Dihedral : 16.064 179.659 5011 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 3.59 % Allowed : 30.96 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.09 % 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: -0.86 (0.14), residues: 3466 helix: 0.34 (0.14), residues: 1384 sheet: -0.64 (0.27), residues: 377 loop : -1.31 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 242 TYR 0.023 0.002 TYR F 526 PHE 0.025 0.002 PHE B 189 TRP 0.050 0.003 TRP D 656 HIS 0.010 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00348 (29909) covalent geometry : angle 0.84709 (40971) hydrogen bonds : bond 0.04334 ( 1327) hydrogen bonds : angle 5.04612 ( 3709) metal coordination : bond 0.00451 ( 8) metal coordination : angle 2.74332 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7722.32 seconds wall clock time: 133 minutes 8.19 seconds (7988.19 seconds total)