Starting phenix.real_space_refine on Mon Sep 14 20:00:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.cif" model { file = "/net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c17_30268/09_2026/7c17_30268.map" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ag 1 8.66 5 Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 20403 2.51 5 N 5838 2.21 5 O 6576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33061 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2307 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1692 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10450 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 8, 'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 10168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10168 Classifications: {'peptide': 1331} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1275} Chain breaks: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 17, 'GLU:plan': 10, 'ASP:plan': 4, 'PHE:plan': 2, 'GLN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 145 Chain: "E" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3726 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'TYR:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 48 Chain: "1" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1188 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "2" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "G" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 987 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 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} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' AG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14883 SG CYS D 70 70.244 43.888 65.111 1.00 68.22 S ATOM 14897 SG CYS D 72 72.300 43.074 61.706 1.00 73.04 S ATOM 20661 SG CYS D 814 84.245 65.453 125.016 1.00 67.56 S ATOM 21218 SG CYS D 888 83.708 66.957 121.680 1.00 58.93 S ATOM 21269 SG CYS D 895 80.688 64.504 122.682 1.00 61.58 S ATOM 21290 SG CYS D 898 81.676 68.279 124.949 1.00 56.03 S ATOM 31964 SG CYS G 112 37.725 60.162 23.976 1.00216.41 S ATOM 32016 SG CYS G 120 37.167 56.837 26.883 1.00241.50 S Time building chain proxies: 6.51, per 1000 atoms: 0.20 Number of scatterers: 33061 At special positions: 0 Unit cell: (158, 149, 169, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ag 1 46.95 Zn 2 29.99 S 137 16.00 P 103 15.00 Mg 1 11.99 O 6576 8.00 N 5838 7.00 C 20403 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7430 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 40 sheets defined 42.7% alpha, 10.1% beta 40 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.759A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.548A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.709A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.698A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.567A pdb=" N GLU A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.570A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.925A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.824A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.088A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.360A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.782A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.627A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.132A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.789A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.618A pdb=" N MET C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.929A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.883A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.415A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.617A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.657A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.631A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.686A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.369A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 removed outlier: 3.847A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.510A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 998' Processing helix chain 'C' and resid 1005 through 1037 removed outlier: 3.518A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.722A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.792A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1148 removed outlier: 3.548A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.686A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1333 Processing helix chain 'D' and resid 26 through 35 removed outlier: 4.616A pdb=" N PHE D 35 " --> pdb=" O ARG D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.877A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.910A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 230 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.590A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.705A pdb=" N GLN D 335 " --> pdb=" O LYS D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.149A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.657A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 634 removed outlier: 3.602A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.628A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.779A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.735A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 801 removed outlier: 3.871A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 874 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.595A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 924 removed outlier: 3.655A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.127A pdb=" N THR D 928 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1074 Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.781A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.752A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D1245 " --> pdb=" O TYR D1241 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1261 removed outlier: 4.147A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 3.571A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 3.811A pdb=" N PHE D1325 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.512A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.707A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1370 removed outlier: 3.979A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.540A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.535A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 134 removed outlier: 3.922A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 138 through 151 removed outlier: 4.085A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 154 No H-bonds generated for 'chain 'F' and resid 152 through 154' Processing helix chain 'F' and resid 213 through 220 removed outlier: 3.752A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.630A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 removed outlier: 3.507A pdb=" N GLN F 246 " --> pdb=" O HIS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.624A pdb=" N ASP F 267 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.814A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 319 removed outlier: 3.729A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA F 319 " --> pdb=" O TRP F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 352 removed outlier: 4.302A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 382 removed outlier: 3.600A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.718A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.918A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.727A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.663A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.661A pdb=" N LEU F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 500 removed outlier: 3.565A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 548 removed outlier: 4.492A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 564 removed outlier: 4.342A pdb=" N LYS F 557 " --> pdb=" O ALA F 553 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.847A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.950A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 610 through 612 No H-bonds generated for 'chain 'F' and resid 610 through 612' Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.548A pdb=" N VAL G 6 " --> pdb=" O ASN G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 23 removed outlier: 3.741A pdb=" N ILE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 57 removed outlier: 3.519A pdb=" N VAL G 56 " --> pdb=" O GLN G 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.845A pdb=" N LEU G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 106 Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'H' and resid 4 through 11 Processing helix chain 'H' and resid 13 through 23 removed outlier: 3.664A pdb=" N ILE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 55 removed outlier: 3.645A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 71 removed outlier: 4.187A pdb=" N GLU H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 108 Processing helix chain 'H' and resid 121 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.201A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.870A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.778A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.979A pdb=" N THR B 101 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.644A pdb=" N ARG C 97 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 74 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.576A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.526A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.564A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 236 through 240 removed outlier: 3.892A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 228 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.732A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.820A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.820A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 615 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP C 654 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA C 617 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.937A pdb=" N LYS C1234 " --> pdb=" O VAL C 690 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AB9, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.511A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.530A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 1076 through 1079 removed outlier: 8.267A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 833 removed outlier: 7.238A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 833 removed outlier: 4.634A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 888 through 889 Processing sheet with id=AC8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.290A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 146 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 147 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD3, first strand: chain 'D' and resid 350 through 353 Processing sheet with id=AD4, first strand: chain 'D' and resid 355 through 357 removed outlier: 6.039A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.507A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.720A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 949 through 951 removed outlier: 7.649A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D1017 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 991 through 994 removed outlier: 3.617A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 3.604A pdb=" N ILE D1124 " --> pdb=" O MET D1025 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE2, first strand: chain 'D' and resid 1187 through 1188 removed outlier: 3.902A pdb=" N GLU D1202 " --> pdb=" O VAL D1163 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AE4, first strand: chain 'H' and resid 30 through 31 1240 hydrogen bonds defined for protein. 3543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9949 1.34 - 1.46: 5255 1.46 - 1.58: 18117 1.58 - 1.70: 204 1.70 - 1.82: 238 Bond restraints: 33763 Sorted by residual: bond pdb=" C3' DC 1 39 " pdb=" O3' DC 1 39 " ideal model delta sigma weight residual 1.435 1.514 -0.079 1.30e-02 5.92e+03 3.68e+01 bond pdb=" C3' DA 2 54 " pdb=" O3' DA 2 54 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.22e+01 bond pdb=" C ASP C 354 " pdb=" N PRO C 355 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.10e+01 bond pdb=" CD2 TRP D1020 " pdb=" CE2 TRP D1020 " ideal model delta sigma weight residual 1.409 1.484 -0.075 1.70e-02 3.46e+03 1.95e+01 bond pdb=" CD2 TRP F 315 " pdb=" CE2 TRP F 315 " ideal model delta sigma weight residual 1.409 1.484 -0.075 1.70e-02 3.46e+03 1.94e+01 ... (remaining 33758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 45751 3.15 - 6.31: 269 6.31 - 9.46: 36 9.46 - 12.62: 9 12.62 - 15.77: 4 Bond angle restraints: 46069 Sorted by residual: angle pdb=" N ALA F 501 " pdb=" CA ALA F 501 " pdb=" C ALA F 501 " ideal model delta sigma weight residual 111.36 123.20 -11.84 1.09e+00 8.42e-01 1.18e+02 angle pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " pdb=" CZ3 TRP F 315 " ideal model delta sigma weight residual 118.60 129.35 -10.75 1.30e+00 5.92e-01 6.84e+01 angle pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " pdb=" CZ3 TRP D1020 " ideal model delta sigma weight residual 118.60 129.34 -10.74 1.30e+00 5.92e-01 6.82e+01 angle pdb=" N VAL D 839 " pdb=" CA VAL D 839 " pdb=" C VAL D 839 " ideal model delta sigma weight residual 111.91 106.36 5.55 8.90e-01 1.26e+00 3.88e+01 angle pdb=" CE2 TRP D1020 " pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " ideal model delta sigma weight residual 118.80 124.87 -6.07 1.00e+00 1.00e+00 3.68e+01 ... (remaining 46064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 19637 33.14 - 66.28: 850 66.28 - 99.41: 37 99.41 - 132.55: 0 132.55 - 165.69: 4 Dihedral angle restraints: 20528 sinusoidal: 9023 harmonic: 11505 Sorted by residual: dihedral pdb=" CA ALA F 321 " pdb=" C ALA F 321 " pdb=" N MET F 322 " pdb=" CA MET F 322 " ideal model delta harmonic sigma weight residual 180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE F 580 " pdb=" C PHE F 580 " pdb=" N ASP F 581 " pdb=" CA ASP F 581 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN F 258 " pdb=" C GLN F 258 " pdb=" N PHE F 259 " pdb=" CA PHE F 259 " ideal model delta harmonic sigma weight residual 180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 20525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4772 0.083 - 0.167: 499 0.167 - 0.250: 18 0.250 - 0.333: 3 0.333 - 0.416: 1 Chirality restraints: 5293 Sorted by residual: chirality pdb=" CA ALA F 501 " pdb=" N ALA F 501 " pdb=" C ALA F 501 " pdb=" CB ALA F 501 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB ILE H 3 " pdb=" CA ILE H 3 " pdb=" CG1 ILE H 3 " pdb=" CG2 ILE H 3 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C1182 " pdb=" CA ILE C1182 " pdb=" CG1 ILE C1182 " pdb=" CG2 ILE C1182 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 5290 not shown) Planarity restraints: 5664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 500 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ILE F 500 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE F 500 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA F 501 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO C 190 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO D 502 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.036 5.00e-02 4.00e+02 ... (remaining 5661 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.60: 315 2.60 - 3.20: 26860 3.20 - 3.80: 58279 3.80 - 4.40: 77351 4.40 - 5.00: 125211 Nonbonded interactions: 288016 Sorted by model distance: nonbonded pdb=" C2 DA 1 34 " pdb=" O2 DT 2 56 " model vdw 1.995 3.340 nonbonded pdb=" O LEU C 363 " pdb=" CG2 ILE C 366 " model vdw 2.005 3.460 nonbonded pdb=" SG CYS G 120 " pdb="AG AG G 201 " model vdw 2.183 3.140 nonbonded pdb=" OG1 THR C 715 " pdb=" O ALA C 784 " model vdw 2.262 3.040 nonbonded pdb=" CG2 THR D 262 " pdb=" CG PRO F 504 " model vdw 2.265 3.860 ... (remaining 288011 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 'G' and (resid 1 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 114 or (resid 115 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 127)) \ selection = (chain 'H' and (resid 1 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 43 or (resid 44 and (name N \ or name CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 \ and (name N or name CA or name C or name O or name CB )) or resid 48 or (resid \ 49 and (name N or name CA or name C or name O or name CB )) or resid 50 through \ 127)) } 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=0.30 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 35.780 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.672 33769 Z= 0.303 Angle : 0.761 17.846 46075 Z= 0.466 Chirality : 0.049 0.416 5293 Planarity : 0.005 0.070 5664 Dihedral : 16.452 165.691 13098 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.21 % Allowed : 6.79 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.63 (0.10), residues: 3971 helix: -3.12 (0.08), residues: 1516 sheet: -3.06 (0.24), residues: 308 loop : -3.09 (0.11), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1246 TYR 0.017 0.001 TYR F 421 PHE 0.025 0.001 PHE F 259 TRP 0.016 0.001 TRP F 315 HIS 0.017 0.001 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.25 (33763) covalent geometry : angle 0.74919 / 0.47 (46069) hydrogen bonds : bond 0.17886 / 12.02 ( 1327) hydrogen bonds : angle 7.73474 / 5.35 ( 3729) metal coordination : bond 0.37412 / 19.55 ( 6) metal coordination : angle 11.49911 / 5.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 996 time to evaluate : 1.031 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 199 ASP cc_start: 0.5692 (m-30) cc_final: 0.4984 (m-30) REVERT: A 206 GLU cc_start: 0.6109 (tp30) cc_final: 0.5219 (tp30) REVERT: B 46 ILE cc_start: 0.8597 (pt) cc_final: 0.8276 (tt) REVERT: C 136 PHE cc_start: 0.8368 (m-80) cc_final: 0.7603 (m-10) REVERT: C 171 LEU cc_start: 0.6511 (mp) cc_final: 0.6248 (pp) REVERT: C 367 TYR cc_start: 0.8078 (t80) cc_final: 0.7576 (t80) REVERT: C 555 TYR cc_start: 0.7965 (t80) cc_final: 0.7711 (t80) REVERT: C 616 ILE cc_start: 0.7941 (mm) cc_final: 0.6795 (mm) REVERT: C 662 SER cc_start: 0.8479 (m) cc_final: 0.8277 (p) REVERT: C 739 ASP cc_start: 0.7192 (p0) cc_final: 0.6024 (t0) REVERT: C 742 TYR cc_start: 0.6748 (m-80) cc_final: 0.6490 (m-10) REVERT: C 829 THR cc_start: 0.7853 (p) cc_final: 0.7650 (p) REVERT: C 882 ILE cc_start: 0.7535 (mt) cc_final: 0.6646 (mt) REVERT: C 1064 ASP cc_start: 0.7891 (t0) cc_final: 0.7550 (t0) REVERT: C 1187 PHE cc_start: 0.7644 (m-80) cc_final: 0.7433 (m-80) REVERT: C 1240 ASP cc_start: 0.7145 (m-30) cc_final: 0.6877 (t0) REVERT: C 1242 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8389 (mmtp) REVERT: C 1257 GLN cc_start: 0.6820 (tt0) cc_final: 0.6583 (mt0) REVERT: C 1281 TYR cc_start: 0.7775 (m-80) cc_final: 0.7350 (m-80) REVERT: D 24 LEU cc_start: 0.7188 (mt) cc_final: 0.6685 (mt) REVERT: D 117 LEU cc_start: 0.8736 (tp) cc_final: 0.8473 (tp) REVERT: D 298 MET cc_start: 0.7177 (mtp) cc_final: 0.4672 (mtp) REVERT: D 300 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 341 ASN cc_start: 0.7576 (m110) cc_final: 0.7160 (m110) REVERT: D 355 ILE cc_start: 0.9233 (pt) cc_final: 0.8875 (mm) REVERT: D 443 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7416 (tp30) REVERT: D 450 HIS cc_start: 0.8628 (t-90) cc_final: 0.8031 (t70) REVERT: D 464 ASP cc_start: 0.8120 (m-30) cc_final: 0.7185 (m-30) REVERT: D 681 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8619 (mmtp) REVERT: D 903 LEU cc_start: 0.8497 (tp) cc_final: 0.8247 (tp) REVERT: D 925 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7241 (tm-30) REVERT: D 958 ILE cc_start: 0.7660 (mm) cc_final: 0.7433 (mp) REVERT: D 1037 PHE cc_start: 0.2816 (m-10) cc_final: 0.2061 (m-80) REVERT: D 1250 ASP cc_start: 0.7076 (p0) cc_final: 0.6415 (p0) REVERT: D 1350 ASN cc_start: 0.7938 (m-40) cc_final: 0.7545 (t0) REVERT: F 100 MET cc_start: 0.8088 (ptp) cc_final: 0.6467 (ptp) REVERT: F 150 ARG cc_start: 0.5947 (mtt90) cc_final: 0.5355 (tmm160) REVERT: F 277 MET cc_start: 0.7255 (tpt) cc_final: 0.7028 (tpp) REVERT: F 297 MET cc_start: 0.3685 (ptt) cc_final: 0.3167 (ptm) REVERT: F 322 MET cc_start: 0.1819 (pmm) cc_final: 0.0727 (tmm) REVERT: F 393 LYS cc_start: 0.4187 (mttp) cc_final: 0.3654 (tptt) REVERT: F 418 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8373 (tptp) REVERT: F 430 TYR cc_start: 0.6251 (t80) cc_final: 0.5282 (t80) REVERT: F 578 LYS cc_start: 0.8499 (mttt) cc_final: 0.8256 (ttpt) REVERT: G 1 MET cc_start: 0.4992 (mpp) cc_final: 0.4295 (ttp) REVERT: G 50 LEU cc_start: 0.7288 (tp) cc_final: 0.7037 (tp) REVERT: H 58 PHE cc_start: 0.7468 (m-10) cc_final: 0.7253 (m-80) REVERT: H 91 ILE cc_start: 0.7438 (pt) cc_final: 0.7198 (pt) outliers start: 7 outliers final: 3 residues processed: 1002 average time/residue: 0.2385 time to fit residues: 364.2062 Evaluate side-chains 576 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 573 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 66 HIS B 137 ASN B 208 ASN B 227 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 932 GLN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1264 GLN C1299 ASN C1313 HIS ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN D 768 ASN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D 929 GLN D1010 GLN D1195 GLN D1197 ASN D1259 GLN E 15 ASN F 129 GLN F 246 GLN F 258 GLN F 357 GLN F 383 ASN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.122583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.104830 restraints weight = 106576.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105998 restraints weight = 71430.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106318 restraints weight = 52001.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.106852 restraints weight = 43572.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107065 restraints weight = 38806.843| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 33769 Z= 0.239 Angle : 0.719 10.732 46075 Z= 0.381 Chirality : 0.046 0.362 5293 Planarity : 0.006 0.079 5664 Dihedral : 15.863 163.495 5475 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.24 % Allowed : 5.13 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.12), residues: 3971 helix: -1.34 (0.12), residues: 1581 sheet: -2.75 (0.24), residues: 311 loop : -2.63 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 247 TYR 0.031 0.002 TYR G 20 PHE 0.032 0.002 PHE E 17 TRP 0.014 0.002 TRP D 236 HIS 0.016 0.002 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 (33763) covalent geometry : angle 0.71764 / 0.38 (46069) hydrogen bonds : bond 0.05018 / 3.64 ( 1327) hydrogen bonds : angle 5.57288 / 3.86 ( 3729) metal coordination : bond 0.01848 / 1.01 ( 6) metal coordination : angle 3.51845 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 708 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8272 (p90) cc_final: 0.8048 (p-80) REVERT: A 199 ASP cc_start: 0.6459 (m-30) cc_final: 0.6220 (m-30) REVERT: A 206 GLU cc_start: 0.6625 (tp30) cc_final: 0.5685 (tp30) REVERT: B 39 LEU cc_start: 0.8426 (mm) cc_final: 0.8210 (mm) REVERT: C 182 SER cc_start: 0.8077 (p) cc_final: 0.7860 (p) REVERT: C 458 GLU cc_start: 0.8014 (tt0) cc_final: 0.7735 (tt0) REVERT: C 516 ASP cc_start: 0.7353 (p0) cc_final: 0.6836 (p0) REVERT: C 739 ASP cc_start: 0.7536 (p0) cc_final: 0.6628 (t0) REVERT: C 741 MET cc_start: 0.7992 (mtt) cc_final: 0.7369 (mtt) REVERT: C 791 LEU cc_start: 0.8824 (tp) cc_final: 0.8624 (tt) REVERT: C 1053 TYR cc_start: 0.8684 (m-80) cc_final: 0.8481 (m-10) REVERT: C 1220 GLN cc_start: 0.7221 (pp30) cc_final: 0.6930 (pp30) REVERT: C 1225 VAL cc_start: 0.9309 (t) cc_final: 0.9036 (p) REVERT: C 1232 MET cc_start: 0.6999 (ptp) cc_final: 0.6761 (ptp) REVERT: C 1240 ASP cc_start: 0.8170 (m-30) cc_final: 0.7611 (t0) REVERT: C 1257 GLN cc_start: 0.7283 (tt0) cc_final: 0.7044 (mt0) REVERT: C 1306 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7532 (tmtt) REVERT: C 1310 ASP cc_start: 0.7861 (m-30) cc_final: 0.7613 (m-30) REVERT: D 24 LEU cc_start: 0.7513 (mt) cc_final: 0.7246 (mt) REVERT: D 39 LYS cc_start: 0.8521 (mmtm) cc_final: 0.7340 (pttp) REVERT: D 246 PRO cc_start: 0.8922 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: D 267 ASP cc_start: 0.8053 (t0) cc_final: 0.7498 (t0) REVERT: D 299 LEU cc_start: 0.9317 (tp) cc_final: 0.9022 (tt) REVERT: D 341 ASN cc_start: 0.8048 (m110) cc_final: 0.7666 (m-40) REVERT: D 450 HIS cc_start: 0.8655 (t-90) cc_final: 0.8368 (t70) REVERT: D 631 TYR cc_start: 0.6144 (m-80) cc_final: 0.5817 (m-10) REVERT: D 646 ILE cc_start: 0.7053 (mm) cc_final: 0.6630 (mm) REVERT: D 681 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8715 (mmtp) REVERT: D 743 MET cc_start: 0.7328 (ppp) cc_final: 0.6863 (ppp) REVERT: D 925 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 958 ILE cc_start: 0.8053 (mm) cc_final: 0.7735 (mp) REVERT: D 1037 PHE cc_start: 0.2715 (m-10) cc_final: 0.1916 (m-80) REVERT: D 1095 MET cc_start: 0.6816 (tmm) cc_final: 0.5944 (tmm) REVERT: D 1227 HIS cc_start: 0.7055 (m-70) cc_final: 0.6424 (m-70) REVERT: D 1256 ILE cc_start: 0.9110 (mm) cc_final: 0.8869 (mm) REVERT: D 1350 ASN cc_start: 0.8600 (m-40) cc_final: 0.7937 (t0) REVERT: E 17 PHE cc_start: 0.7779 (m-10) cc_final: 0.7466 (m-80) REVERT: E 72 GLN cc_start: 0.6684 (mt0) cc_final: 0.6483 (tm-30) REVERT: F 100 MET cc_start: 0.8122 (ptp) cc_final: 0.7735 (ptp) REVERT: F 150 ARG cc_start: 0.6124 (mtt90) cc_final: 0.5555 (tmm160) REVERT: F 297 MET cc_start: 0.4195 (ptt) cc_final: 0.3180 (ptm) REVERT: F 378 GLU cc_start: 0.8973 (pt0) cc_final: 0.8137 (pt0) REVERT: F 393 LYS cc_start: 0.4994 (mttp) cc_final: 0.4231 (tptt) REVERT: F 401 PHE cc_start: 0.8387 (t80) cc_final: 0.8182 (t80) REVERT: F 578 LYS cc_start: 0.8604 (mttt) cc_final: 0.8402 (ttmt) REVERT: F 612 ASP cc_start: 0.7732 (m-30) cc_final: 0.7491 (m-30) REVERT: G 1 MET cc_start: 0.5539 (mpp) cc_final: 0.4827 (ttm) REVERT: G 59 ASN cc_start: 0.8461 (p0) cc_final: 0.8069 (p0) REVERT: H 1 MET cc_start: 0.3174 (mtp) cc_final: 0.2720 (tmm) REVERT: H 30 MET cc_start: 0.6090 (tpt) cc_final: 0.5851 (tpt) outliers start: 8 outliers final: 2 residues processed: 714 average time/residue: 0.2062 time to fit residues: 237.5262 Evaluate side-chains 493 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 491 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 90 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 402 optimal weight: 0.0870 chunk 374 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D 929 GLN D1235 ASN F 258 GLN F 400 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.120111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.101632 restraints weight = 106529.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103054 restraints weight = 68877.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103777 restraints weight = 45657.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103989 restraints weight = 43559.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104073 restraints weight = 37814.458| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 33769 Z= 0.218 Angle : 0.678 12.900 46075 Z= 0.361 Chirality : 0.045 0.355 5293 Planarity : 0.005 0.095 5664 Dihedral : 15.828 165.543 5475 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.12), residues: 3971 helix: -0.78 (0.12), residues: 1600 sheet: -2.47 (0.25), residues: 289 loop : -2.42 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 102 TYR 0.026 0.002 TYR C 70 PHE 0.030 0.002 PHE C 186 TRP 0.019 0.002 TRP D 115 HIS 0.014 0.002 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (33763) covalent geometry : angle 0.67694 / 0.36 (46069) hydrogen bonds : bond 0.04727 / 3.43 ( 1327) hydrogen bonds : angle 5.27237 / 3.65 ( 3729) metal coordination : bond 0.00825 / 0.43 ( 6) metal coordination : angle 3.30220 / 1.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 669 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9118 (tt) cc_final: 0.8868 (tt) REVERT: A 66 HIS cc_start: 0.8423 (p90) cc_final: 0.8078 (p-80) REVERT: B 39 LEU cc_start: 0.8544 (mm) cc_final: 0.8321 (mm) REVERT: C 130 MET cc_start: 0.8063 (tpt) cc_final: 0.7653 (tpt) REVERT: C 135 THR cc_start: 0.9014 (m) cc_final: 0.8671 (p) REVERT: C 136 PHE cc_start: 0.8542 (m-80) cc_final: 0.7951 (m-80) REVERT: C 149 LEU cc_start: 0.9283 (tp) cc_final: 0.8954 (tp) REVERT: C 458 GLU cc_start: 0.7943 (tt0) cc_final: 0.7715 (tt0) REVERT: C 459 MET cc_start: 0.7945 (mmm) cc_final: 0.7695 (mmm) REVERT: C 516 ASP cc_start: 0.7865 (p0) cc_final: 0.7363 (p0) REVERT: C 739 ASP cc_start: 0.7579 (p0) cc_final: 0.6695 (t0) REVERT: C 791 LEU cc_start: 0.8904 (tp) cc_final: 0.8683 (tp) REVERT: C 800 MET cc_start: 0.8892 (pmm) cc_final: 0.8564 (pmm) REVERT: C 816 ILE cc_start: 0.9458 (mm) cc_final: 0.9132 (mm) REVERT: C 898 GLU cc_start: 0.9468 (mp0) cc_final: 0.9242 (mp0) REVERT: C 1220 GLN cc_start: 0.7298 (pp30) cc_final: 0.6924 (pp30) REVERT: C 1240 ASP cc_start: 0.8100 (m-30) cc_final: 0.7537 (t0) REVERT: C 1279 GLU cc_start: 0.8663 (tt0) cc_final: 0.8420 (tt0) REVERT: C 1299 ASN cc_start: 0.7849 (p0) cc_final: 0.7616 (p0) REVERT: D 24 LEU cc_start: 0.7895 (mt) cc_final: 0.7518 (mt) REVERT: D 106 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: D 300 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8135 (tm-30) REVERT: D 341 ASN cc_start: 0.8047 (m110) cc_final: 0.7473 (m-40) REVERT: D 355 ILE cc_start: 0.9331 (pt) cc_final: 0.8965 (mt) REVERT: D 450 HIS cc_start: 0.8681 (t-90) cc_final: 0.8328 (t70) REVERT: D 625 MET cc_start: 0.8502 (ttp) cc_final: 0.8248 (ttp) REVERT: D 646 ILE cc_start: 0.7350 (mm) cc_final: 0.6944 (mm) REVERT: D 681 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8729 (mmtp) REVERT: D 743 MET cc_start: 0.7447 (ppp) cc_final: 0.6961 (ppp) REVERT: D 925 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 958 ILE cc_start: 0.8001 (mm) cc_final: 0.7673 (mp) REVERT: D 1037 PHE cc_start: 0.2848 (m-10) cc_final: 0.2083 (m-80) REVERT: D 1256 ILE cc_start: 0.9088 (mm) cc_final: 0.8781 (mm) REVERT: E 17 PHE cc_start: 0.7610 (m-10) cc_final: 0.7063 (m-10) REVERT: F 150 ARG cc_start: 0.6160 (mtt90) cc_final: 0.5513 (tmm160) REVERT: F 297 MET cc_start: 0.4160 (ptt) cc_final: 0.3174 (ptm) REVERT: F 322 MET cc_start: 0.1958 (pmm) cc_final: 0.1743 (tmm) REVERT: F 378 GLU cc_start: 0.8598 (pt0) cc_final: 0.8333 (pt0) REVERT: F 400 GLN cc_start: 0.7540 (mt0) cc_final: 0.7286 (mt0) REVERT: G 1 MET cc_start: 0.5562 (mpp) cc_final: 0.4828 (ttm) REVERT: G 17 ILE cc_start: 0.8548 (pt) cc_final: 0.8309 (pt) REVERT: H 1 MET cc_start: 0.3491 (mtp) cc_final: 0.3208 (ttp) REVERT: H 52 GLN cc_start: 0.4945 (mm110) cc_final: 0.4624 (pp30) REVERT: H 91 ILE cc_start: 0.7818 (pt) cc_final: 0.7447 (pt) REVERT: H 94 HIS cc_start: 0.8100 (m90) cc_final: 0.7857 (m90) outliers start: 6 outliers final: 1 residues processed: 674 average time/residue: 0.2032 time to fit residues: 222.6097 Evaluate side-chains 490 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 488 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 220 optimal weight: 0.6980 chunk 340 optimal weight: 8.9990 chunk 387 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 289 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 ASN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D 929 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN F 362 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.118478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099212 restraints weight = 106293.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100947 restraints weight = 68888.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101329 restraints weight = 50419.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102172 restraints weight = 40752.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102340 restraints weight = 32710.935| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33769 Z= 0.192 Angle : 0.657 11.815 46075 Z= 0.347 Chirality : 0.044 0.352 5293 Planarity : 0.005 0.104 5664 Dihedral : 15.829 163.112 5475 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.12 % Allowed : 4.77 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 3971 helix: -0.46 (0.13), residues: 1590 sheet: -2.12 (0.26), residues: 302 loop : -2.34 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 54 TYR 0.026 0.002 TYR C1281 PHE 0.017 0.002 PHE C 195 TRP 0.015 0.001 TRP D 236 HIS 0.016 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (33763) covalent geometry : angle 0.65621 / 0.35 (46069) hydrogen bonds : bond 0.04423 / 3.22 ( 1327) hydrogen bonds : angle 5.14155 / 3.56 ( 3729) metal coordination : bond 0.00761 / 0.41 ( 6) metal coordination : angle 3.26450 / 1.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 641 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.6769 (tp30) cc_final: 0.5646 (tp30) REVERT: C 130 MET cc_start: 0.8455 (tpp) cc_final: 0.7293 (tpt) REVERT: C 136 PHE cc_start: 0.8458 (m-80) cc_final: 0.7637 (m-80) REVERT: C 149 LEU cc_start: 0.9297 (tp) cc_final: 0.8970 (tp) REVERT: C 182 SER cc_start: 0.8204 (p) cc_final: 0.7986 (p) REVERT: C 458 GLU cc_start: 0.7998 (tt0) cc_final: 0.7657 (tt0) REVERT: C 516 ASP cc_start: 0.7970 (p0) cc_final: 0.7304 (p0) REVERT: C 680 LEU cc_start: 0.8980 (pp) cc_final: 0.8778 (pp) REVERT: C 739 ASP cc_start: 0.7576 (p0) cc_final: 0.6763 (t0) REVERT: C 800 MET cc_start: 0.8907 (pmm) cc_final: 0.8656 (pmm) REVERT: C 898 GLU cc_start: 0.9458 (mp0) cc_final: 0.9187 (mp0) REVERT: C 1107 MET cc_start: 0.7861 (mmt) cc_final: 0.7629 (mmt) REVERT: C 1180 MET cc_start: 0.8326 (tpp) cc_final: 0.8063 (tpp) REVERT: C 1220 GLN cc_start: 0.7237 (pp30) cc_final: 0.6995 (pp30) REVERT: C 1240 ASP cc_start: 0.8005 (m-30) cc_final: 0.7539 (t0) REVERT: C 1276 TRP cc_start: 0.8557 (m-10) cc_final: 0.8311 (m-10) REVERT: C 1328 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8286 (mmtm) REVERT: D 24 LEU cc_start: 0.8025 (mt) cc_final: 0.7750 (mt) REVERT: D 341 ASN cc_start: 0.8254 (m110) cc_final: 0.7810 (m-40) REVERT: D 355 ILE cc_start: 0.9336 (pt) cc_final: 0.8891 (mt) REVERT: D 619 ILE cc_start: 0.8883 (mt) cc_final: 0.8626 (tp) REVERT: D 625 MET cc_start: 0.8490 (ttp) cc_final: 0.8208 (ttp) REVERT: D 681 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8697 (mmtp) REVERT: D 743 MET cc_start: 0.7574 (ppp) cc_final: 0.7065 (ppp) REVERT: D 800 LEU cc_start: 0.8793 (mt) cc_final: 0.8560 (mt) REVERT: D 903 LEU cc_start: 0.8522 (tp) cc_final: 0.8309 (tp) REVERT: D 925 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 958 ILE cc_start: 0.8002 (mm) cc_final: 0.7595 (mp) REVERT: D 1037 PHE cc_start: 0.3284 (m-10) cc_final: 0.2488 (m-80) REVERT: D 1095 MET cc_start: 0.6593 (tmm) cc_final: 0.6386 (tmm) REVERT: D 1256 ILE cc_start: 0.9151 (mm) cc_final: 0.8807 (mm) REVERT: D 1329 THR cc_start: 0.8686 (p) cc_final: 0.8338 (p) REVERT: D 1357 ILE cc_start: 0.8999 (mp) cc_final: 0.8579 (mt) REVERT: E 17 PHE cc_start: 0.7648 (m-10) cc_final: 0.7286 (m-80) REVERT: E 19 LEU cc_start: 0.6652 (tt) cc_final: 0.6186 (tp) REVERT: E 30 MET cc_start: 0.5883 (ttm) cc_final: 0.5631 (ttm) REVERT: F 150 ARG cc_start: 0.5941 (mtt90) cc_final: 0.5508 (ttp80) REVERT: F 297 MET cc_start: 0.2406 (ptt) cc_final: 0.2118 (ppp) REVERT: F 322 MET cc_start: 0.2039 (pmm) cc_final: 0.1525 (tmm) REVERT: F 403 ASP cc_start: 0.7792 (m-30) cc_final: 0.7506 (m-30) REVERT: F 487 MET cc_start: 0.6362 (tpp) cc_final: 0.5800 (tpp) REVERT: F 508 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7757 (pm20) REVERT: G 1 MET cc_start: 0.5700 (mpp) cc_final: 0.5028 (ttm) REVERT: H 1 MET cc_start: 0.3388 (mtp) cc_final: 0.2938 (ttp) REVERT: H 91 ILE cc_start: 0.7736 (pt) cc_final: 0.7520 (pt) REVERT: H 94 HIS cc_start: 0.8142 (m90) cc_final: 0.7882 (m-70) outliers start: 4 outliers final: 1 residues processed: 643 average time/residue: 0.2017 time to fit residues: 211.0185 Evaluate side-chains 474 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 147 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 358 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS C 86 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D 910 ASN D 929 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 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 = 0.3929 r_free = 0.3929 target = 0.116192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097351 restraints weight = 105728.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.098887 restraints weight = 68040.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099453 restraints weight = 44176.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.099849 restraints weight = 37621.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099937 restraints weight = 33998.099| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33769 Z= 0.216 Angle : 0.691 10.007 46075 Z= 0.361 Chirality : 0.045 0.333 5293 Planarity : 0.005 0.089 5664 Dihedral : 15.873 161.917 5475 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3971 helix: -0.44 (0.13), residues: 1614 sheet: -2.04 (0.27), residues: 300 loop : -2.31 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 182 TYR 0.024 0.002 TYR C1281 PHE 0.024 0.002 PHE C 405 TRP 0.026 0.002 TRP D 236 HIS 0.016 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (33763) covalent geometry : angle 0.68966 / 0.36 (46069) hydrogen bonds : bond 0.04465 / 3.22 ( 1327) hydrogen bonds : angle 5.11095 / 3.51 ( 3729) metal coordination : bond 0.00889 / 0.48 ( 6) metal coordination : angle 3.78875 / 2.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 619 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8796 (mt) cc_final: 0.8588 (mt) REVERT: C 136 PHE cc_start: 0.8526 (m-80) cc_final: 0.8044 (m-10) REVERT: C 149 LEU cc_start: 0.9281 (tp) cc_final: 0.8818 (tp) REVERT: C 458 GLU cc_start: 0.7870 (tt0) cc_final: 0.7628 (tt0) REVERT: C 473 ARG cc_start: 0.7664 (tmm160) cc_final: 0.7262 (ttp80) REVERT: C 674 ASP cc_start: 0.7673 (t0) cc_final: 0.7411 (t0) REVERT: C 728 ASP cc_start: 0.8306 (t70) cc_final: 0.8029 (t0) REVERT: C 739 ASP cc_start: 0.7473 (p0) cc_final: 0.6724 (t0) REVERT: C 741 MET cc_start: 0.8386 (mtt) cc_final: 0.7512 (mtt) REVERT: C 898 GLU cc_start: 0.9469 (mp0) cc_final: 0.9194 (mp0) REVERT: C 1080 ASN cc_start: 0.8944 (t0) cc_final: 0.8562 (t0) REVERT: C 1220 GLN cc_start: 0.7526 (pp30) cc_final: 0.7249 (pp30) REVERT: C 1243 MET cc_start: 0.8387 (tmm) cc_final: 0.8156 (tmm) REVERT: C 1257 GLN cc_start: 0.7744 (tt0) cc_final: 0.7476 (tt0) REVERT: C 1276 TRP cc_start: 0.8613 (m-10) cc_final: 0.8404 (m-10) REVERT: D 117 LEU cc_start: 0.9185 (mm) cc_final: 0.8670 (tp) REVERT: D 133 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8189 (mpt-90) REVERT: D 341 ASN cc_start: 0.8191 (m110) cc_final: 0.7967 (m-40) REVERT: D 355 ILE cc_start: 0.9417 (pt) cc_final: 0.8929 (mt) REVERT: D 625 MET cc_start: 0.8581 (ttp) cc_final: 0.8353 (ttp) REVERT: D 644 MET cc_start: 0.6515 (ttm) cc_final: 0.5731 (mtp) REVERT: D 681 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8753 (mmtp) REVERT: D 743 MET cc_start: 0.7689 (ppp) cc_final: 0.7200 (ppp) REVERT: D 800 LEU cc_start: 0.8848 (mt) cc_final: 0.8571 (mt) REVERT: D 925 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7445 (tm-30) REVERT: D 958 ILE cc_start: 0.8107 (mm) cc_final: 0.7702 (mp) REVERT: D 1037 PHE cc_start: 0.3313 (m-10) cc_final: 0.2301 (m-80) REVERT: D 1095 MET cc_start: 0.6756 (tmm) cc_final: 0.6171 (tmm) REVERT: D 1256 ILE cc_start: 0.9213 (mm) cc_final: 0.8873 (mm) REVERT: D 1329 THR cc_start: 0.8695 (p) cc_final: 0.8277 (p) REVERT: E 19 LEU cc_start: 0.7144 (tt) cc_final: 0.6721 (tp) REVERT: F 150 ARG cc_start: 0.5891 (mtt90) cc_final: 0.5496 (ttp80) REVERT: F 320 ILE cc_start: 0.4852 (mm) cc_final: 0.4427 (mm) REVERT: F 322 MET cc_start: 0.2001 (pmm) cc_final: 0.1617 (tmm) REVERT: F 508 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7764 (pm20) REVERT: G 1 MET cc_start: 0.5837 (mpp) cc_final: 0.5309 (ttm) REVERT: G 59 ASN cc_start: 0.8266 (p0) cc_final: 0.8049 (p0) REVERT: G 88 VAL cc_start: 0.7781 (p) cc_final: 0.7472 (m) REVERT: H 1 MET cc_start: 0.3371 (mtp) cc_final: 0.2726 (ppp) REVERT: H 91 ILE cc_start: 0.7771 (pt) cc_final: 0.7536 (pt) REVERT: H 94 HIS cc_start: 0.8211 (m90) cc_final: 0.7935 (m-70) outliers start: 1 outliers final: 1 residues processed: 620 average time/residue: 0.1950 time to fit residues: 199.3934 Evaluate side-chains 480 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 205 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 384 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 67 optimal weight: 0.0770 chunk 170 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1038 GLN D 157 GLN D 419 HIS D 458 ASN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN D 962 ASN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.118615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100176 restraints weight = 104849.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101971 restraints weight = 63142.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.102755 restraints weight = 40203.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103064 restraints weight = 36363.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103166 restraints weight = 31118.078| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33769 Z= 0.137 Angle : 0.635 11.044 46075 Z= 0.332 Chirality : 0.044 0.331 5293 Planarity : 0.005 0.109 5664 Dihedral : 15.799 159.592 5475 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3971 helix: -0.32 (0.13), residues: 1604 sheet: -2.07 (0.27), residues: 302 loop : -2.12 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 102 TYR 0.024 0.002 TYR C 73 PHE 0.018 0.002 PHE C1187 TRP 0.021 0.001 TRP D 236 HIS 0.020 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (33763) covalent geometry : angle 0.63454 / 0.33 (46069) hydrogen bonds : bond 0.04120 / 2.99 ( 1327) hydrogen bonds : angle 4.97820 / 3.43 ( 3729) metal coordination : bond 0.00279 / 0.16 ( 6) metal coordination : angle 2.80991 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 634 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8688 (mt) cc_final: 0.8488 (mt) REVERT: A 206 GLU cc_start: 0.6436 (tp30) cc_final: 0.5592 (tp30) REVERT: C 30 ILE cc_start: 0.8831 (pt) cc_final: 0.8627 (pt) REVERT: C 136 PHE cc_start: 0.8372 (m-80) cc_final: 0.7905 (m-10) REVERT: C 171 LEU cc_start: 0.5992 (mm) cc_final: 0.5549 (mt) REVERT: C 182 SER cc_start: 0.8290 (p) cc_final: 0.8083 (p) REVERT: C 458 GLU cc_start: 0.7946 (tt0) cc_final: 0.7633 (tt0) REVERT: C 478 ARG cc_start: 0.7018 (ttt-90) cc_final: 0.6816 (ttt-90) REVERT: C 503 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8060 (mttt) REVERT: C 739 ASP cc_start: 0.7499 (p0) cc_final: 0.6698 (t0) REVERT: C 761 GLN cc_start: 0.8399 (mp10) cc_final: 0.8191 (mp10) REVERT: C 898 GLU cc_start: 0.9448 (mp0) cc_final: 0.9160 (mp0) REVERT: C 1064 ASP cc_start: 0.8039 (t0) cc_final: 0.7775 (t0) REVERT: C 1080 ASN cc_start: 0.8825 (t0) cc_final: 0.8453 (t0) REVERT: C 1180 MET cc_start: 0.8477 (tpp) cc_final: 0.7931 (tpp) REVERT: C 1220 GLN cc_start: 0.7429 (pp30) cc_final: 0.7121 (pp30) REVERT: C 1240 ASP cc_start: 0.7891 (m-30) cc_final: 0.7373 (t0) REVERT: C 1257 GLN cc_start: 0.7647 (tt0) cc_final: 0.7381 (tt0) REVERT: C 1262 LYS cc_start: 0.7230 (ttmm) cc_final: 0.7020 (ttpt) REVERT: C 1329 GLU cc_start: 0.7827 (tt0) cc_final: 0.7622 (tt0) REVERT: D 100 GLU cc_start: 0.7869 (pt0) cc_final: 0.7659 (pt0) REVERT: D 117 LEU cc_start: 0.9048 (mm) cc_final: 0.8618 (tp) REVERT: D 133 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8154 (mpt-90) REVERT: D 341 ASN cc_start: 0.8009 (m110) cc_final: 0.7761 (m-40) REVERT: D 355 ILE cc_start: 0.9321 (pt) cc_final: 0.8915 (mt) REVERT: D 644 MET cc_start: 0.5935 (ttm) cc_final: 0.5289 (mtp) REVERT: D 681 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8745 (mmtp) REVERT: D 743 MET cc_start: 0.7677 (ppp) cc_final: 0.7167 (ppp) REVERT: D 958 ILE cc_start: 0.7886 (mm) cc_final: 0.7539 (mt) REVERT: D 1037 PHE cc_start: 0.3371 (m-10) cc_final: 0.2352 (m-80) REVERT: D 1256 ILE cc_start: 0.9166 (mm) cc_final: 0.8853 (mm) REVERT: E 19 LEU cc_start: 0.7058 (tt) cc_final: 0.6512 (tp) REVERT: E 21 LEU cc_start: 0.8668 (mm) cc_final: 0.8423 (mt) REVERT: F 150 ARG cc_start: 0.5898 (mtt90) cc_final: 0.5506 (ttp80) REVERT: F 288 MET cc_start: 0.6448 (mtp) cc_final: 0.6200 (mtp) REVERT: F 320 ILE cc_start: 0.4764 (mm) cc_final: 0.4325 (mm) REVERT: F 322 MET cc_start: 0.1936 (pmm) cc_final: 0.1630 (tmm) REVERT: F 378 GLU cc_start: 0.8691 (pt0) cc_final: 0.7775 (pt0) REVERT: F 430 TYR cc_start: 0.6431 (t80) cc_final: 0.6050 (t80) REVERT: F 487 MET cc_start: 0.6545 (tpp) cc_final: 0.5998 (tpp) REVERT: G 1 MET cc_start: 0.5796 (mpp) cc_final: 0.5296 (ttm) REVERT: H 87 LYS cc_start: 0.6932 (tptm) cc_final: 0.6652 (pttp) REVERT: H 94 HIS cc_start: 0.8193 (m90) cc_final: 0.7933 (m-70) outliers start: 3 outliers final: 2 residues processed: 637 average time/residue: 0.1946 time to fit residues: 203.3562 Evaluate side-chains 484 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 482 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 209 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 23 optimal weight: 0.2980 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 447 HIS ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 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 = 0.3909 r_free = 0.3909 target = 0.114797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095194 restraints weight = 106137.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097004 restraints weight = 67514.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098348 restraints weight = 44808.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098459 restraints weight = 32251.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098559 restraints weight = 31593.119| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 33769 Z= 0.228 Angle : 0.718 10.006 46075 Z= 0.375 Chirality : 0.046 0.356 5293 Planarity : 0.005 0.107 5664 Dihedral : 15.865 159.181 5475 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3971 helix: -0.30 (0.13), residues: 1619 sheet: -2.04 (0.26), residues: 317 loop : -2.17 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 374 TYR 0.033 0.002 TYR D 140 PHE 0.036 0.002 PHE C 53 TRP 0.028 0.002 TRP C1276 HIS 0.016 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (33763) covalent geometry : angle 0.71697 / 0.38 (46069) hydrogen bonds : bond 0.04503 / 3.23 ( 1327) hydrogen bonds : angle 5.10246 / 3.51 ( 3729) metal coordination : bond 0.01050 / 0.58 ( 6) metal coordination : angle 3.41089 / 1.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 595 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: A 204 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 136 PHE cc_start: 0.8469 (m-80) cc_final: 0.7907 (m-10) REVERT: C 149 LEU cc_start: 0.9186 (tp) cc_final: 0.8937 (tt) REVERT: C 195 PHE cc_start: 0.7189 (m-10) cc_final: 0.6618 (m-10) REVERT: C 349 GLU cc_start: 0.7458 (pt0) cc_final: 0.7140 (pt0) REVERT: C 473 ARG cc_start: 0.7889 (tmm160) cc_final: 0.7422 (ttp80) REVERT: C 739 ASP cc_start: 0.7483 (p0) cc_final: 0.6769 (t0) REVERT: C 741 MET cc_start: 0.8508 (mtt) cc_final: 0.7715 (mtt) REVERT: C 800 MET cc_start: 0.9289 (pmm) cc_final: 0.8992 (pmm) REVERT: C 898 GLU cc_start: 0.9421 (mp0) cc_final: 0.9146 (mp0) REVERT: C 1066 MET cc_start: 0.8470 (tmm) cc_final: 0.7757 (ppp) REVERT: C 1080 ASN cc_start: 0.8941 (t0) cc_final: 0.8690 (t0) REVERT: C 1107 MET cc_start: 0.7661 (mmt) cc_final: 0.7115 (mmp) REVERT: C 1262 LYS cc_start: 0.7522 (ttmm) cc_final: 0.6787 (ttmm) REVERT: C 1274 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7190 (mt-10) REVERT: C 1285 TYR cc_start: 0.7504 (m-80) cc_final: 0.7179 (m-80) REVERT: D 114 ILE cc_start: 0.9323 (tp) cc_final: 0.8969 (tt) REVERT: D 299 LEU cc_start: 0.9452 (tp) cc_final: 0.9188 (tt) REVERT: D 355 ILE cc_start: 0.9429 (pt) cc_final: 0.8953 (mt) REVERT: D 431 ARG cc_start: 0.7387 (ttt180) cc_final: 0.7073 (ttt180) REVERT: D 644 MET cc_start: 0.6114 (ttm) cc_final: 0.5519 (mtp) REVERT: D 743 MET cc_start: 0.7818 (ppp) cc_final: 0.7325 (ppp) REVERT: D 796 LEU cc_start: 0.9234 (tp) cc_final: 0.8991 (tt) REVERT: D 925 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 958 ILE cc_start: 0.8050 (mm) cc_final: 0.7583 (mp) REVERT: D 1037 PHE cc_start: 0.3517 (m-10) cc_final: 0.3124 (m-80) REVERT: F 150 ARG cc_start: 0.5822 (mtt90) cc_final: 0.5492 (ttp80) REVERT: F 288 MET cc_start: 0.6398 (mtp) cc_final: 0.6192 (mtp) REVERT: F 378 GLU cc_start: 0.8307 (pt0) cc_final: 0.8094 (pt0) REVERT: F 430 TYR cc_start: 0.6714 (t80) cc_final: 0.6324 (t80) REVERT: G 1 MET cc_start: 0.6109 (mpp) cc_final: 0.5633 (ttm) REVERT: H 1 MET cc_start: 0.3195 (mtp) cc_final: 0.2891 (ttp) REVERT: H 87 LYS cc_start: 0.6977 (tptm) cc_final: 0.6692 (pttp) REVERT: H 94 HIS cc_start: 0.8196 (m90) cc_final: 0.7940 (m-70) outliers start: 2 outliers final: 1 residues processed: 597 average time/residue: 0.1851 time to fit residues: 184.0275 Evaluate side-chains 460 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 3 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 373 optimal weight: 30.0000 chunk 311 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 326 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 347 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 315 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 490 GLN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 929 GLN D1108 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093422 restraints weight = 105583.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095240 restraints weight = 69454.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096204 restraints weight = 45482.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096353 restraints weight = 35529.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096460 restraints weight = 35178.229| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33769 Z= 0.236 Angle : 0.737 11.211 46075 Z= 0.385 Chirality : 0.047 0.346 5293 Planarity : 0.005 0.107 5664 Dihedral : 15.928 156.798 5475 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3971 helix: -0.37 (0.12), residues: 1627 sheet: -2.08 (0.27), residues: 309 loop : -2.19 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 54 TYR 0.024 0.002 TYR D 140 PHE 0.024 0.002 PHE F 401 TRP 0.046 0.002 TRP C1276 HIS 0.025 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (33763) covalent geometry : angle 0.73563 / 0.38 (46069) hydrogen bonds : bond 0.04545 / 3.25 ( 1327) hydrogen bonds : angle 5.21169 / 3.60 ( 3729) metal coordination : bond 0.00973 / 0.53 ( 6) metal coordination : angle 3.78280 / 1.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 229 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6822 (tm-30) REVERT: C 136 PHE cc_start: 0.8471 (m-80) cc_final: 0.7830 (m-10) REVERT: C 189 ASP cc_start: 0.6359 (m-30) cc_final: 0.5980 (m-30) REVERT: C 349 GLU cc_start: 0.7367 (pt0) cc_final: 0.6797 (pt0) REVERT: C 407 ARG cc_start: 0.8521 (tpt90) cc_final: 0.8272 (tpp80) REVERT: C 458 GLU cc_start: 0.8121 (tt0) cc_final: 0.7755 (tt0) REVERT: C 739 ASP cc_start: 0.7448 (p0) cc_final: 0.6807 (t0) REVERT: C 800 MET cc_start: 0.9223 (pmm) cc_final: 0.8990 (pmm) REVERT: C 898 GLU cc_start: 0.9401 (mp0) cc_final: 0.9133 (mp0) REVERT: C 1080 ASN cc_start: 0.8913 (t0) cc_final: 0.8622 (t0) REVERT: C 1111 GLN cc_start: 0.7665 (pt0) cc_final: 0.7373 (pt0) REVERT: C 1274 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7169 (mt-10) REVERT: C 1285 TYR cc_start: 0.7726 (m-80) cc_final: 0.6945 (m-80) REVERT: D 431 ARG cc_start: 0.7213 (ttt180) cc_final: 0.7008 (ttt180) REVERT: D 644 MET cc_start: 0.6209 (ttm) cc_final: 0.5638 (mtp) REVERT: D 743 MET cc_start: 0.7887 (ppp) cc_final: 0.7376 (ppp) REVERT: D 821 MET cc_start: 0.7433 (tpp) cc_final: 0.6836 (tpp) REVERT: D 925 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 958 ILE cc_start: 0.8064 (mm) cc_final: 0.7586 (mp) REVERT: D 1037 PHE cc_start: 0.3713 (m-10) cc_final: 0.2623 (m-80) REVERT: F 150 ARG cc_start: 0.5697 (mtt90) cc_final: 0.5456 (ttp80) REVERT: F 288 MET cc_start: 0.6359 (mtp) cc_final: 0.6152 (mtp) REVERT: F 322 MET cc_start: 0.2214 (pmm) cc_final: 0.1807 (tmm) REVERT: F 489 MET cc_start: 0.7594 (mmt) cc_final: 0.7270 (mmm) REVERT: F 508 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7990 (pm20) REVERT: G 1 MET cc_start: 0.6156 (mpp) cc_final: 0.5686 (ttm) REVERT: H 1 MET cc_start: 0.3312 (mtp) cc_final: 0.2983 (ttp) REVERT: H 91 ILE cc_start: 0.7791 (pt) cc_final: 0.7549 (pt) REVERT: H 94 HIS cc_start: 0.8121 (m90) cc_final: 0.7894 (m-70) outliers start: 1 outliers final: 1 residues processed: 581 average time/residue: 0.1968 time to fit residues: 190.3935 Evaluate side-chains 441 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 290 optimal weight: 8.9990 chunk 282 optimal weight: 0.6980 chunk 321 optimal weight: 0.0570 chunk 389 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 364 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 760 ASN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.115655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096945 restraints weight = 104233.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.098655 restraints weight = 64404.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099255 restraints weight = 43085.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099753 restraints weight = 33321.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099859 restraints weight = 32299.885| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33769 Z= 0.155 Angle : 0.704 15.280 46075 Z= 0.364 Chirality : 0.045 0.335 5293 Planarity : 0.005 0.100 5664 Dihedral : 15.859 155.212 5475 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 0.91 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 3971 helix: -0.31 (0.13), residues: 1615 sheet: -2.24 (0.27), residues: 317 loop : -2.08 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 54 TYR 0.033 0.002 TYR C 73 PHE 0.033 0.002 PHE C 53 TRP 0.070 0.003 TRP D 236 HIS 0.017 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (33763) covalent geometry : angle 0.70300 / 0.36 (46069) hydrogen bonds : bond 0.04184 / 3.04 ( 1327) hydrogen bonds : angle 5.10203 / 3.53 ( 3729) metal coordination : bond 0.00278 / 0.16 ( 6) metal coordination : angle 2.77408 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 590 time to evaluate : 1.242 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: A 47 LEU cc_start: 0.9159 (tt) cc_final: 0.8357 (tt) REVERT: A 206 GLU cc_start: 0.7058 (tp30) cc_final: 0.5925 (tp30) REVERT: B 85 LEU cc_start: 0.9277 (mt) cc_final: 0.8940 (tt) REVERT: C 136 PHE cc_start: 0.8339 (m-80) cc_final: 0.7796 (m-10) REVERT: C 149 LEU cc_start: 0.9246 (tp) cc_final: 0.8904 (tt) REVERT: C 189 ASP cc_start: 0.6269 (m-30) cc_final: 0.5814 (m-30) REVERT: C 349 GLU cc_start: 0.7528 (pt0) cc_final: 0.7049 (pt0) REVERT: C 369 MET cc_start: 0.7277 (ttp) cc_final: 0.7066 (ttp) REVERT: C 458 GLU cc_start: 0.7995 (tt0) cc_final: 0.7659 (tt0) REVERT: C 473 ARG cc_start: 0.7866 (tmm160) cc_final: 0.7444 (ttp80) REVERT: C 688 GLN cc_start: 0.8558 (mt0) cc_final: 0.8290 (mt0) REVERT: C 739 ASP cc_start: 0.7426 (p0) cc_final: 0.6743 (t0) REVERT: C 800 MET cc_start: 0.8991 (pmm) cc_final: 0.8776 (pmm) REVERT: C 898 GLU cc_start: 0.9370 (mp0) cc_final: 0.9133 (mp0) REVERT: C 1007 LYS cc_start: 0.7990 (mptt) cc_final: 0.7763 (pttp) REVERT: C 1064 ASP cc_start: 0.8198 (t0) cc_final: 0.7934 (t0) REVERT: C 1080 ASN cc_start: 0.8845 (t0) cc_final: 0.8473 (t0) REVERT: C 1107 MET cc_start: 0.7654 (mmt) cc_final: 0.5864 (mmm) REVERT: C 1111 GLN cc_start: 0.7529 (pt0) cc_final: 0.7122 (pt0) REVERT: C 1187 PHE cc_start: 0.7617 (m-10) cc_final: 0.6493 (m-10) REVERT: C 1240 ASP cc_start: 0.7959 (m-30) cc_final: 0.7523 (t0) REVERT: C 1274 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7047 (mt-10) REVERT: C 1279 GLU cc_start: 0.8636 (tt0) cc_final: 0.7954 (tp30) REVERT: C 1285 TYR cc_start: 0.7586 (m-80) cc_final: 0.6984 (m-80) REVERT: C 1315 MET cc_start: 0.4657 (tpt) cc_final: 0.4238 (tpt) REVERT: D 100 GLU cc_start: 0.7836 (pt0) cc_final: 0.7607 (pt0) REVERT: D 117 LEU cc_start: 0.9109 (mm) cc_final: 0.8817 (mm) REVERT: D 237 MET cc_start: 0.7609 (ttt) cc_final: 0.7404 (tmm) REVERT: D 299 LEU cc_start: 0.9469 (tp) cc_final: 0.9254 (tt) REVERT: D 341 ASN cc_start: 0.8241 (m-40) cc_final: 0.7901 (m-40) REVERT: D 466 MET cc_start: 0.8757 (tpp) cc_final: 0.8553 (tpp) REVERT: D 497 GLU cc_start: 0.6944 (mp0) cc_final: 0.6669 (mp0) REVERT: D 644 MET cc_start: 0.5946 (ttm) cc_final: 0.5352 (mtp) REVERT: D 743 MET cc_start: 0.7890 (ppp) cc_final: 0.7276 (ppp) REVERT: D 821 MET cc_start: 0.7287 (tpp) cc_final: 0.6902 (tpp) REVERT: D 958 ILE cc_start: 0.7994 (mm) cc_final: 0.7534 (mp) REVERT: D 1037 PHE cc_start: 0.3460 (m-10) cc_final: 0.3020 (m-80) REVERT: E 70 GLN cc_start: 0.8765 (pt0) cc_final: 0.8431 (mt0) REVERT: E 71 GLU cc_start: 0.8439 (mp0) cc_final: 0.7954 (mp0) REVERT: F 150 ARG cc_start: 0.5765 (mtt90) cc_final: 0.5382 (ttp80) REVERT: F 288 MET cc_start: 0.6296 (mtp) cc_final: 0.6043 (mtp) REVERT: F 322 MET cc_start: 0.2183 (pmm) cc_final: 0.1852 (tmm) REVERT: F 404 LEU cc_start: 0.8831 (mt) cc_final: 0.8615 (mt) REVERT: F 430 TYR cc_start: 0.6848 (t80) cc_final: 0.6431 (t80) REVERT: F 487 MET cc_start: 0.6405 (tpp) cc_final: 0.5710 (tpp) REVERT: F 489 MET cc_start: 0.7597 (mmt) cc_final: 0.7259 (mmm) REVERT: G 1 MET cc_start: 0.5913 (mpp) cc_final: 0.5490 (ttm) REVERT: G 88 VAL cc_start: 0.7644 (p) cc_final: 0.7190 (m) REVERT: H 1 MET cc_start: 0.2940 (mtp) cc_final: 0.2697 (ttp) REVERT: H 91 ILE cc_start: 0.7816 (pt) cc_final: 0.7538 (pt) REVERT: H 94 HIS cc_start: 0.8125 (m90) cc_final: 0.7909 (m-70) outliers start: 1 outliers final: 1 residues processed: 591 average time/residue: 0.1897 time to fit residues: 189.0199 Evaluate side-chains 471 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 403 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS B 18 GLN B 132 HIS C 219 GLN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 760 ASN C 808 ASN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 929 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.111958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092073 restraints weight = 106156.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093738 restraints weight = 64912.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094841 restraints weight = 44929.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095569 restraints weight = 34635.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.095945 restraints weight = 29054.648| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33769 Z= 0.250 Angle : 0.783 11.715 46075 Z= 0.405 Chirality : 0.048 0.362 5293 Planarity : 0.005 0.106 5664 Dihedral : 15.945 153.732 5475 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.09 % Allowed : 0.42 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.13), residues: 3971 helix: -0.44 (0.12), residues: 1624 sheet: -1.99 (0.27), residues: 310 loop : -2.17 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 538 TYR 0.038 0.002 TYR C 73 PHE 0.030 0.002 PHE C 53 TRP 0.087 0.003 TRP C1276 HIS 0.026 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (33763) covalent geometry : angle 0.78185 / 0.41 (46069) hydrogen bonds : bond 0.04651 / 3.34 ( 1327) hydrogen bonds : angle 5.25004 / 3.64 ( 3729) metal coordination : bond 0.01149 / 0.63 ( 6) metal coordination : angle 3.46881 / 1.83 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 554 time to evaluate : 1.118 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: A 199 ASP cc_start: 0.6184 (m-30) cc_final: 0.5955 (m-30) REVERT: A 204 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 229 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6607 (tm-30) REVERT: C 136 PHE cc_start: 0.8491 (m-80) cc_final: 0.7943 (m-10) REVERT: C 182 SER cc_start: 0.8560 (p) cc_final: 0.8068 (m) REVERT: C 189 ASP cc_start: 0.6652 (m-30) cc_final: 0.6309 (m-30) REVERT: C 349 GLU cc_start: 0.7245 (pt0) cc_final: 0.6753 (pt0) REVERT: C 407 ARG cc_start: 0.8477 (tpt90) cc_final: 0.8219 (tpp80) REVERT: C 458 GLU cc_start: 0.8123 (tt0) cc_final: 0.7744 (tt0) REVERT: C 688 GLN cc_start: 0.8614 (mt0) cc_final: 0.8328 (mt0) REVERT: C 739 ASP cc_start: 0.7364 (p0) cc_final: 0.6803 (t0) REVERT: C 800 MET cc_start: 0.9141 (pmm) cc_final: 0.8940 (pmm) REVERT: C 812 PHE cc_start: 0.8551 (t80) cc_final: 0.8141 (t80) REVERT: C 898 GLU cc_start: 0.9390 (mp0) cc_final: 0.9140 (mp0) REVERT: C 1007 LYS cc_start: 0.8042 (mptt) cc_final: 0.7816 (pttp) REVERT: C 1064 ASP cc_start: 0.8259 (t0) cc_final: 0.8014 (t0) REVERT: C 1080 ASN cc_start: 0.8927 (t0) cc_final: 0.8678 (t0) REVERT: C 1111 GLN cc_start: 0.7770 (pt0) cc_final: 0.7367 (pt0) REVERT: C 1276 TRP cc_start: 0.8759 (m-10) cc_final: 0.8399 (m-10) REVERT: C 1279 GLU cc_start: 0.8642 (tt0) cc_final: 0.7981 (tp30) REVERT: C 1315 MET cc_start: 0.5054 (tpt) cc_final: 0.4670 (tpt) REVERT: D 644 MET cc_start: 0.6475 (ttm) cc_final: 0.5873 (mtp) REVERT: D 743 MET cc_start: 0.7935 (ppp) cc_final: 0.7433 (ppp) REVERT: D 821 MET cc_start: 0.7471 (tpp) cc_final: 0.7069 (tpp) REVERT: D 925 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7942 (tm-30) REVERT: D 958 ILE cc_start: 0.8106 (mm) cc_final: 0.7602 (mp) REVERT: D 983 LYS cc_start: 0.7367 (ptpp) cc_final: 0.6978 (pttm) REVERT: D 1037 PHE cc_start: 0.3276 (m-10) cc_final: 0.2676 (m-80) REVERT: D 1111 ASP cc_start: 0.7112 (m-30) cc_final: 0.6720 (m-30) REVERT: E 70 GLN cc_start: 0.8870 (pt0) cc_final: 0.8544 (mt0) REVERT: E 71 GLU cc_start: 0.8609 (mp0) cc_final: 0.8062 (mp0) REVERT: F 150 ARG cc_start: 0.5760 (mtt90) cc_final: 0.5450 (ttp80) REVERT: F 288 MET cc_start: 0.6138 (mtp) cc_final: 0.5919 (mtp) REVERT: F 487 MET cc_start: 0.6359 (tpp) cc_final: 0.5881 (tpp) REVERT: F 489 MET cc_start: 0.7565 (mmt) cc_final: 0.7267 (mmm) REVERT: G 1 MET cc_start: 0.6316 (mpp) cc_final: 0.5844 (ttm) REVERT: H 1 MET cc_start: 0.2973 (mtp) cc_final: 0.2673 (ttp) REVERT: H 91 ILE cc_start: 0.7753 (pt) cc_final: 0.7484 (pt) REVERT: H 94 HIS cc_start: 0.8130 (m90) cc_final: 0.7882 (m-70) outliers start: 3 outliers final: 2 residues processed: 557 average time/residue: 0.1938 time to fit residues: 180.6399 Evaluate side-chains 433 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 431 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 276 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 357 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 237 optimal weight: 0.9980 chunk 390 optimal weight: 9.9990 chunk 378 optimal weight: 40.0000 chunk 228 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.114117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094465 restraints weight = 104301.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096127 restraints weight = 63762.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097274 restraints weight = 44224.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097977 restraints weight = 34032.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.098475 restraints weight = 28648.587| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33769 Z= 0.162 Angle : 0.707 14.944 46075 Z= 0.367 Chirality : 0.046 0.337 5293 Planarity : 0.005 0.076 5664 Dihedral : 15.867 155.146 5475 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 3971 helix: -0.30 (0.13), residues: 1613 sheet: -2.12 (0.27), residues: 306 loop : -2.05 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 293 TYR 0.029 0.002 TYR C 73 PHE 0.027 0.002 PHE C 53 TRP 0.072 0.003 TRP C1276 HIS 0.009 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (33763) covalent geometry : angle 0.70622 / 0.37 (46069) hydrogen bonds : bond 0.04216 / 3.05 ( 1327) hydrogen bonds : angle 5.12318 / 3.55 ( 3729) metal coordination : bond 0.00400 / 0.22 ( 6) metal coordination : angle 2.71824 / 1.47 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5750.49 seconds wall clock time: 100 minutes 14.33 seconds (6014.33 seconds total)