Starting phenix.real_space_refine on Fri Mar 6 17:35:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c17_30268/03_2026/7c17_30268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c17_30268/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7c17_30268/03_2026/7c17_30268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c17_30268/03_2026/7c17_30268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c17_30268/03_2026/7c17_30268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c17_30268/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.90, per 1000 atoms: 0.21 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 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: 4.26 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: 8.26 Time building geometry restraints manager: 3.57 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=" 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 bond pdb=" N PRO C 355 " pdb=" CD PRO C 355 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO F 504 " pdb=" CD PRO F 504 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 33758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 45757 3.15 - 6.31: 264 6.31 - 9.46: 35 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: 4786 0.083 - 0.167: 487 0.167 - 0.250: 16 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: 1.830 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 37.440 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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= 0.246 Angle : 0.742 17.846 46075 Z= 0.415 Chirality : 0.048 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 covalent geometry : bond 0.00332 (33763) covalent geometry : angle 0.73036 (46069) hydrogen bonds : bond 0.17886 ( 1327) hydrogen bonds : angle 7.73474 ( 3729) metal coordination : bond 0.37412 ( 6) metal coordination : angle 11.49911 ( 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 : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.5692 (m-30) cc_final: 0.4983 (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: 0.7602 (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: 0.7577 (t80) REVERT: C 555 TYR cc_start: 0.7965 (t80) cc_final: 0.7710 (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: 0.8278 (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: 0.6647 (mt) REVERT: C 1064 ASP cc_start: 0.7891 (t0) cc_final: 0.7551 (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: 0.6584 (mt0) REVERT: C 1281 TYR cc_start: 0.7775 (m-80) cc_final: 0.7349 (m-80) REVERT: D 24 LEU cc_start: 0.7188 (mt) cc_final: 0.6684 (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: 0.7481 (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: 0.7242 (tm-30) REVERT: D 958 ILE cc_start: 0.7660 (mm) cc_final: 0.7431 (mp) REVERT: D 1037 PHE cc_start: 0.2816 (m-10) cc_final: 0.2063 (m-80) REVERT: D 1250 ASP cc_start: 0.7076 (p0) cc_final: 0.6414 (p0) REVERT: D 1350 ASN cc_start: 0.7938 (m-40) cc_final: 0.7546 (t0) REVERT: F 100 MET cc_start: 0.8088 (ptp) cc_final: 0.6466 (ptp) REVERT: F 150 ARG cc_start: 0.5947 (mtt90) cc_final: 0.5351 (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: 0.3168 (ptm) REVERT: F 322 MET cc_start: 0.1819 (pmm) cc_final: 0.0728 (tmm) REVERT: F 393 LYS cc_start: 0.4187 (mttp) cc_final: 0.3650 (tptt) REVERT: F 418 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8361 (tptt) REVERT: F 430 TYR cc_start: 0.6251 (t80) cc_final: 0.5195 (t80) REVERT: F 578 LYS cc_start: 0.8499 (mttt) cc_final: 0.8261 (ttpt) REVERT: G 1 MET cc_start: 0.4992 (mpp) cc_final: 0.4293 (ttp) REVERT: G 50 LEU cc_start: 0.7288 (tp) cc_final: 0.6966 (tp) REVERT: H 58 PHE cc_start: 0.7468 (m-10) cc_final: 0.7251 (m-80) REVERT: H 91 ILE cc_start: 0.7438 (pt) cc_final: 0.7200 (pt) outliers start: 7 outliers final: 3 residues processed: 1002 average time/residue: 0.2627 time to fit residues: 399.2603 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 : 1.205 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 160 HIS B 208 ASN B 227 GLN C 447 HIS C 510 GLN C 554 HIS 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 C1324 ASN D 232 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN D 768 ASN D 777 HIS D 817 HIS D 929 GLN D1010 GLN D1108 GLN D1197 ASN E 15 ASN F 129 GLN F 246 GLN F 258 GLN F 357 GLN F 383 ASN F 400 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN H 71 ASN H 125 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.117186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098905 restraints weight = 105482.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.100192 restraints weight = 67454.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.100751 restraints weight = 44380.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.100847 restraints weight = 40461.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101024 restraints weight = 38739.401| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33769 Z= 0.242 Angle : 0.720 12.349 46075 Z= 0.378 Chirality : 0.044 0.192 5293 Planarity : 0.005 0.085 5664 Dihedral : 15.798 167.254 5475 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % 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: -3.00 (0.12), residues: 3971 helix: -1.30 (0.12), residues: 1589 sheet: -2.56 (0.25), residues: 326 loop : -2.49 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 312 TYR 0.022 0.002 TYR D 609 PHE 0.031 0.002 PHE D 719 TRP 0.020 0.002 TRP D 115 HIS 0.013 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00524 (33763) covalent geometry : angle 0.71815 (46069) hydrogen bonds : bond 0.04542 ( 1327) hydrogen bonds : angle 5.37277 ( 3729) metal coordination : bond 0.00801 ( 6) metal coordination : angle 4.49217 ( 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 704 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 693 time to evaluate : 1.248 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: A 60 GLU cc_start: 0.7615 (tp30) cc_final: 0.7283 (tp30) REVERT: B 46 ILE cc_start: 0.8906 (pt) cc_final: 0.8255 (mm) REVERT: C 149 LEU cc_start: 0.9235 (tp) cc_final: 0.9020 (tp) REVERT: C 182 SER cc_start: 0.8234 (p) cc_final: 0.8033 (p) REVERT: C 204 LEU cc_start: 0.7607 (tp) cc_final: 0.7216 (tt) REVERT: C 367 TYR cc_start: 0.8484 (t80) cc_final: 0.8118 (t80) REVERT: C 369 MET cc_start: 0.7930 (tmm) cc_final: 0.7439 (tmm) REVERT: C 458 GLU cc_start: 0.8013 (tt0) cc_final: 0.7637 (tt0) REVERT: C 503 LYS cc_start: 0.8457 (mtmm) cc_final: 0.7879 (mttt) REVERT: C 555 TYR cc_start: 0.8201 (t80) cc_final: 0.7627 (t80) REVERT: C 688 GLN cc_start: 0.8445 (mt0) cc_final: 0.8009 (mt0) REVERT: C 739 ASP cc_start: 0.7417 (p0) cc_final: 0.6722 (t0) REVERT: C 767 GLN cc_start: 0.8196 (mt0) cc_final: 0.7993 (mt0) REVERT: C 791 LEU cc_start: 0.8918 (tp) cc_final: 0.8661 (tt) REVERT: C 800 MET cc_start: 0.9026 (pmm) cc_final: 0.8760 (pmm) REVERT: C 829 THR cc_start: 0.9047 (p) cc_final: 0.8733 (p) REVERT: C 898 GLU cc_start: 0.9417 (mp0) cc_final: 0.8847 (mp0) REVERT: C 1103 VAL cc_start: 0.8752 (t) cc_final: 0.8347 (t) REVERT: C 1107 MET cc_start: 0.7881 (mmm) cc_final: 0.7510 (mmm) REVERT: C 1117 LEU cc_start: 0.8912 (tt) cc_final: 0.8706 (tt) REVERT: C 1166 ASP cc_start: 0.7084 (t0) cc_final: 0.6841 (t0) REVERT: C 1220 GLN cc_start: 0.7204 (pp30) cc_final: 0.6885 (pp30) REVERT: C 1257 GLN cc_start: 0.7493 (tt0) cc_final: 0.7262 (mt0) REVERT: C 1276 TRP cc_start: 0.8524 (m-10) cc_final: 0.7593 (m-10) REVERT: C 1327 LEU cc_start: 0.9137 (mm) cc_final: 0.8133 (tp) REVERT: C 1328 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8530 (mmtm) REVERT: D 24 LEU cc_start: 0.7950 (mt) cc_final: 0.7005 (mt) REVERT: D 47 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6836 (ptt180) REVERT: D 81 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7394 (mtm180) REVERT: D 106 GLU cc_start: 0.7545 (mp0) cc_final: 0.7040 (mp0) REVERT: D 245 LEU cc_start: 0.8937 (tp) cc_final: 0.8694 (tp) REVERT: D 246 PRO cc_start: 0.9145 (Cg_exo) cc_final: 0.8918 (Cg_endo) REVERT: D 299 LEU cc_start: 0.9356 (tp) cc_final: 0.9132 (tt) REVERT: D 341 ASN cc_start: 0.8349 (m110) cc_final: 0.7955 (m-40) REVERT: D 527 LEU cc_start: 0.8682 (mt) cc_final: 0.8388 (mt) REVERT: D 625 MET cc_start: 0.8658 (ttp) cc_final: 0.8399 (ttp) REVERT: D 681 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8760 (mmtp) REVERT: D 743 MET cc_start: 0.7459 (ppp) cc_final: 0.6994 (ppp) REVERT: D 925 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 958 ILE cc_start: 0.8168 (mm) cc_final: 0.7711 (mp) REVERT: D 983 LYS cc_start: 0.7209 (mtmm) cc_final: 0.7007 (ptpp) REVERT: D 1037 PHE cc_start: 0.3347 (m-10) cc_final: 0.2469 (m-80) REVERT: D 1227 HIS cc_start: 0.7381 (m-70) cc_final: 0.6759 (m-70) REVERT: D 1350 ASN cc_start: 0.8697 (m-40) cc_final: 0.8349 (t0) REVERT: E 17 PHE cc_start: 0.7608 (m-10) cc_final: 0.6871 (m-10) REVERT: E 66 VAL cc_start: 0.8019 (p) cc_final: 0.7795 (p) REVERT: E 70 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: F 100 MET cc_start: 0.8386 (ptp) cc_final: 0.8014 (ptp) REVERT: F 150 ARG cc_start: 0.6175 (mtt90) cc_final: 0.5588 (tmm160) REVERT: F 297 MET cc_start: 0.4507 (ptt) cc_final: 0.3475 (ptm) REVERT: F 378 GLU cc_start: 0.9008 (pt0) cc_final: 0.8032 (pt0) REVERT: F 393 LYS cc_start: 0.5473 (mttp) cc_final: 0.4654 (tptt) REVERT: F 401 PHE cc_start: 0.8503 (t80) cc_final: 0.8302 (t80) REVERT: F 466 ILE cc_start: 0.9185 (mm) cc_final: 0.8982 (mm) REVERT: F 487 MET cc_start: 0.6613 (tpp) cc_final: 0.6321 (tpp) REVERT: F 508 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7731 (pm20) REVERT: F 578 LYS cc_start: 0.8695 (mttt) cc_final: 0.8439 (tmmt) REVERT: G 1 MET cc_start: 0.5721 (mpp) cc_final: 0.5130 (ttm) REVERT: H 91 ILE cc_start: 0.7770 (pt) cc_final: 0.7411 (pt) outliers start: 11 outliers final: 3 residues processed: 702 average time/residue: 0.2146 time to fit residues: 240.1579 Evaluate side-chains 508 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 504 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 374 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 chunk 294 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 86 GLN ** 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** C1038 GLN D 458 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D 929 GLN D 962 ASN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.117922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099764 restraints weight = 104962.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100835 restraints weight = 63751.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.101350 restraints weight = 48116.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.101761 restraints weight = 39194.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101999 restraints weight = 35707.992| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33769 Z= 0.160 Angle : 0.619 10.730 46075 Z= 0.323 Chirality : 0.042 0.177 5293 Planarity : 0.004 0.062 5664 Dihedral : 15.685 163.433 5475 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % 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: -2.43 (0.12), residues: 3971 helix: -0.66 (0.12), residues: 1601 sheet: -2.50 (0.25), residues: 318 loop : -2.28 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 515 TYR 0.019 0.002 TYR D 609 PHE 0.023 0.002 PHE C 405 TRP 0.018 0.001 TRP D 236 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00354 (33763) covalent geometry : angle 0.61737 (46069) hydrogen bonds : bond 0.03992 ( 1327) hydrogen bonds : angle 5.02165 ( 3729) metal coordination : bond 0.00538 ( 6) metal coordination : angle 3.34092 ( 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 682 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 678 time to evaluate : 1.171 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: A 47 LEU cc_start: 0.9234 (tt) cc_final: 0.9034 (tt) REVERT: A 60 GLU cc_start: 0.7633 (tp30) cc_final: 0.7341 (tp30) REVERT: B 46 ILE cc_start: 0.8949 (pt) cc_final: 0.8635 (pt) REVERT: C 136 PHE cc_start: 0.8380 (m-80) cc_final: 0.7987 (m-10) REVERT: C 149 LEU cc_start: 0.9198 (tp) cc_final: 0.8766 (tp) REVERT: C 204 LEU cc_start: 0.7612 (tp) cc_final: 0.7243 (tt) REVERT: C 367 TYR cc_start: 0.8466 (t80) cc_final: 0.8130 (t80) REVERT: C 369 MET cc_start: 0.7759 (tmm) cc_final: 0.7049 (tmm) REVERT: C 458 GLU cc_start: 0.7789 (tt0) cc_final: 0.7441 (tt0) REVERT: C 515 MET cc_start: 0.8699 (ppp) cc_final: 0.8389 (ppp) REVERT: C 516 ASP cc_start: 0.8066 (p0) cc_final: 0.7507 (p0) REVERT: C 555 TYR cc_start: 0.8322 (t80) cc_final: 0.7909 (t80) REVERT: C 600 THR cc_start: 0.6846 (p) cc_final: 0.6447 (p) REVERT: C 688 GLN cc_start: 0.8620 (mt0) cc_final: 0.8204 (mt0) REVERT: C 728 ASP cc_start: 0.7651 (t0) cc_final: 0.7317 (t0) REVERT: C 739 ASP cc_start: 0.7417 (p0) cc_final: 0.6717 (t0) REVERT: C 791 LEU cc_start: 0.9062 (tp) cc_final: 0.8834 (tp) REVERT: C 816 ILE cc_start: 0.9290 (mm) cc_final: 0.9066 (mm) REVERT: C 898 GLU cc_start: 0.9412 (mp0) cc_final: 0.9174 (mp0) REVERT: C 1107 MET cc_start: 0.7920 (mmm) cc_final: 0.7485 (mmm) REVERT: C 1166 ASP cc_start: 0.6998 (t0) cc_final: 0.6754 (t0) REVERT: C 1180 MET cc_start: 0.8438 (tpp) cc_final: 0.8142 (tpp) REVERT: C 1220 GLN cc_start: 0.7165 (pp30) cc_final: 0.6839 (pp30) REVERT: C 1240 ASP cc_start: 0.8082 (m-30) cc_final: 0.7259 (t0) REVERT: C 1257 GLN cc_start: 0.7484 (tt0) cc_final: 0.7220 (mt0) REVERT: C 1276 TRP cc_start: 0.8352 (m-10) cc_final: 0.8080 (m-10) REVERT: C 1286 THR cc_start: 0.8545 (p) cc_final: 0.8226 (p) REVERT: C 1328 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8592 (mmtm) REVERT: D 30 ILE cc_start: 0.9167 (mt) cc_final: 0.8789 (mm) REVERT: D 81 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7391 (mtm180) REVERT: D 96 LYS cc_start: 0.8690 (tttp) cc_final: 0.8477 (tppp) REVERT: D 246 PRO cc_start: 0.9006 (Cg_exo) cc_final: 0.8752 (Cg_endo) REVERT: D 341 ASN cc_start: 0.8075 (m110) cc_final: 0.7483 (m-40) REVERT: D 342 LEU cc_start: 0.9107 (mm) cc_final: 0.8853 (mm) REVERT: D 355 ILE cc_start: 0.9264 (pt) cc_final: 0.9039 (mt) REVERT: D 380 PHE cc_start: 0.8581 (m-80) cc_final: 0.8340 (m-80) REVERT: D 460 ASP cc_start: 0.8214 (p0) cc_final: 0.7990 (p0) REVERT: D 681 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8779 (mmtp) REVERT: D 743 MET cc_start: 0.7585 (ppp) cc_final: 0.7110 (ppp) REVERT: D 958 ILE cc_start: 0.8072 (mm) cc_final: 0.7625 (mp) REVERT: D 983 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6920 (ptpp) REVERT: D 1037 PHE cc_start: 0.3254 (m-10) cc_final: 0.2229 (m-80) REVERT: E 17 PHE cc_start: 0.7321 (m-10) cc_final: 0.6723 (m-10) REVERT: E 72 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5735 (pp30) REVERT: F 150 ARG cc_start: 0.5964 (mtt90) cc_final: 0.5537 (ttp80) REVERT: F 288 MET cc_start: 0.6475 (mtp) cc_final: 0.6275 (mtm) REVERT: F 297 MET cc_start: 0.4213 (ptt) cc_final: 0.3100 (ptm) REVERT: F 403 ASP cc_start: 0.7829 (m-30) cc_final: 0.7461 (m-30) REVERT: F 430 TYR cc_start: 0.6443 (t80) cc_final: 0.6011 (t80) REVERT: F 487 MET cc_start: 0.6529 (tpp) cc_final: 0.6105 (tpp) REVERT: F 489 MET cc_start: 0.6656 (mmm) cc_final: 0.6297 (mmm) REVERT: F 508 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7666 (pm20) REVERT: F 578 LYS cc_start: 0.8590 (mttt) cc_final: 0.8220 (ttmt) REVERT: G 1 MET cc_start: 0.5561 (mpp) cc_final: 0.4950 (ttm) REVERT: H 87 LYS cc_start: 0.6947 (tptm) cc_final: 0.6675 (pttp) REVERT: H 94 HIS cc_start: 0.8243 (m90) cc_final: 0.7977 (m-70) outliers start: 4 outliers final: 2 residues processed: 681 average time/residue: 0.2059 time to fit residues: 226.9878 Evaluate side-chains 514 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 511 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 0.8980 chunk 340 optimal weight: 5.9990 chunk 387 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 289 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 327 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1235 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN F 400 GLN ** F 406 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 = 0.3920 r_free = 0.3920 target = 0.115582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096020 restraints weight = 104820.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097690 restraints weight = 64244.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098827 restraints weight = 44630.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099585 restraints weight = 34414.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099987 restraints weight = 28911.693| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33769 Z= 0.182 Angle : 0.633 13.214 46075 Z= 0.331 Chirality : 0.043 0.249 5293 Planarity : 0.004 0.075 5664 Dihedral : 15.687 168.938 5475 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % 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: -2.13 (0.13), residues: 3971 helix: -0.38 (0.13), residues: 1609 sheet: -2.32 (0.25), residues: 327 loop : -2.15 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 827 TYR 0.019 0.002 TYR D 269 PHE 0.021 0.002 PHE C 405 TRP 0.030 0.002 TRP D 236 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00394 (33763) covalent geometry : angle 0.63184 (46069) hydrogen bonds : bond 0.04025 ( 1327) hydrogen bonds : angle 4.92377 ( 3729) metal coordination : bond 0.00717 ( 6) metal coordination : angle 3.40839 ( 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 641 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 639 time to evaluate : 1.313 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 60 GLU cc_start: 0.7733 (tp30) cc_final: 0.7426 (tp30) REVERT: A 204 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 136 PHE cc_start: 0.8571 (m-80) cc_final: 0.7793 (m-10) REVERT: C 149 LEU cc_start: 0.9236 (tp) cc_final: 0.8823 (tp) REVERT: C 204 LEU cc_start: 0.7771 (tp) cc_final: 0.7420 (tt) REVERT: C 367 TYR cc_start: 0.8351 (t80) cc_final: 0.7944 (t80) REVERT: C 369 MET cc_start: 0.7862 (tmm) cc_final: 0.7128 (tmm) REVERT: C 458 GLU cc_start: 0.8129 (tt0) cc_final: 0.7611 (tt0) REVERT: C 473 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.6990 (tmm160) REVERT: C 516 ASP cc_start: 0.8179 (p0) cc_final: 0.7557 (p0) REVERT: C 555 TYR cc_start: 0.8323 (t80) cc_final: 0.7947 (t80) REVERT: C 688 GLN cc_start: 0.8653 (mt0) cc_final: 0.8341 (mt0) REVERT: C 739 ASP cc_start: 0.7282 (p0) cc_final: 0.6604 (t0) REVERT: C 816 ILE cc_start: 0.9340 (mm) cc_final: 0.9062 (mm) REVERT: C 898 GLU cc_start: 0.9388 (mp0) cc_final: 0.9147 (mp0) REVERT: C 1064 ASP cc_start: 0.8470 (t0) cc_final: 0.7991 (t0) REVERT: C 1107 MET cc_start: 0.7893 (mmm) cc_final: 0.7511 (mmm) REVERT: C 1111 GLN cc_start: 0.7426 (pt0) cc_final: 0.7197 (pt0) REVERT: C 1220 GLN cc_start: 0.7319 (pp30) cc_final: 0.7052 (pp30) REVERT: C 1240 ASP cc_start: 0.8072 (m-30) cc_final: 0.7535 (t0) REVERT: C 1257 GLN cc_start: 0.7658 (tt0) cc_final: 0.7211 (mt0) REVERT: C 1276 TRP cc_start: 0.8657 (m-10) cc_final: 0.7942 (m-10) REVERT: C 1281 TYR cc_start: 0.7499 (m-80) cc_final: 0.6991 (m-10) REVERT: C 1329 GLU cc_start: 0.7851 (tt0) cc_final: 0.7186 (tt0) REVERT: D 30 ILE cc_start: 0.9224 (mt) cc_final: 0.8977 (mm) REVERT: D 47 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6901 (ptt180) REVERT: D 81 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7482 (mtm180) REVERT: D 114 ILE cc_start: 0.9289 (tp) cc_final: 0.9055 (tp) REVERT: D 246 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8798 (Cg_endo) REVERT: D 330 MET cc_start: 0.6602 (ttm) cc_final: 0.6335 (ttm) REVERT: D 341 ASN cc_start: 0.8101 (m110) cc_final: 0.7684 (m-40) REVERT: D 342 LEU cc_start: 0.9085 (mm) cc_final: 0.8774 (mm) REVERT: D 355 ILE cc_start: 0.9320 (pt) cc_final: 0.8844 (mt) REVERT: D 380 PHE cc_start: 0.8572 (m-80) cc_final: 0.8232 (m-80) REVERT: D 450 HIS cc_start: 0.8777 (t70) cc_final: 0.8182 (t70) REVERT: D 484 MET cc_start: 0.7006 (ttp) cc_final: 0.6128 (ptm) REVERT: D 497 GLU cc_start: 0.7220 (mp0) cc_final: 0.6990 (mp0) REVERT: D 503 SER cc_start: 0.8187 (m) cc_final: 0.7941 (m) REVERT: D 821 MET cc_start: 0.7114 (tpp) cc_final: 0.6856 (tpp) REVERT: D 1037 PHE cc_start: 0.3420 (m-10) cc_final: 0.2392 (m-80) REVERT: F 150 ARG cc_start: 0.5814 (mtt90) cc_final: 0.5485 (ttp80) REVERT: F 430 TYR cc_start: 0.6613 (t80) cc_final: 0.6205 (t80) REVERT: F 487 MET cc_start: 0.6640 (tpp) cc_final: 0.6357 (tpt) REVERT: F 489 MET cc_start: 0.6736 (mmm) cc_final: 0.6041 (mmm) REVERT: F 578 LYS cc_start: 0.8519 (mttt) cc_final: 0.8309 (tmmt) REVERT: G 1 MET cc_start: 0.5948 (mpp) cc_final: 0.5497 (ttm) REVERT: H 87 LYS cc_start: 0.7014 (tptm) cc_final: 0.6464 (pttp) REVERT: H 94 HIS cc_start: 0.8215 (m90) cc_final: 0.7992 (m-70) outliers start: 2 outliers final: 1 residues processed: 641 average time/residue: 0.2076 time to fit residues: 218.1175 Evaluate side-chains 488 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 201 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 chunk 358 optimal weight: 9.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 419 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN F 258 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN H 125 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088002 restraints weight = 107079.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089652 restraints weight = 67995.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090006 restraints weight = 47394.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090566 restraints weight = 39067.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090643 restraints weight = 34860.034| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 33769 Z= 0.330 Angle : 0.812 14.009 46075 Z= 0.425 Chirality : 0.047 0.250 5293 Planarity : 0.005 0.078 5664 Dihedral : 16.065 166.771 5475 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.18 % Favored : 91.79 % Rotamer: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.40 (0.12), residues: 3971 helix: -0.63 (0.12), residues: 1624 sheet: -2.66 (0.25), residues: 329 loop : -2.24 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 538 TYR 0.034 0.003 TYR G 20 PHE 0.026 0.003 PHE H 58 TRP 0.035 0.002 TRP D 236 HIS 0.024 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00709 (33763) covalent geometry : angle 0.80998 (46069) hydrogen bonds : bond 0.05045 ( 1327) hydrogen bonds : angle 5.43409 ( 3729) metal coordination : bond 0.01375 ( 6) metal coordination : angle 5.64974 ( 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 589 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 587 time to evaluate : 1.264 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: A 204 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 229 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6788 (tm-30) REVERT: B 185 TYR cc_start: 0.8667 (p90) cc_final: 0.8442 (p90) REVERT: C 53 PHE cc_start: 0.7449 (m-10) cc_final: 0.7242 (m-10) REVERT: C 90 VAL cc_start: 0.8454 (t) cc_final: 0.8234 (t) REVERT: C 136 PHE cc_start: 0.8666 (m-80) cc_final: 0.8060 (m-10) REVERT: C 149 LEU cc_start: 0.9339 (tp) cc_final: 0.9015 (tp) REVERT: C 347 ILE cc_start: 0.9248 (mm) cc_final: 0.8865 (mm) REVERT: C 349 GLU cc_start: 0.7910 (pt0) cc_final: 0.7549 (pt0) REVERT: C 369 MET cc_start: 0.7932 (tmm) cc_final: 0.7160 (tmm) REVERT: C 473 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7098 (tmm160) REVERT: C 515 MET cc_start: 0.8693 (ppp) cc_final: 0.8448 (ppp) REVERT: C 516 ASP cc_start: 0.8463 (p0) cc_final: 0.7860 (p0) REVERT: C 674 ASP cc_start: 0.8130 (t0) cc_final: 0.7861 (t0) REVERT: C 739 ASP cc_start: 0.7500 (p0) cc_final: 0.7048 (t0) REVERT: C 741 MET cc_start: 0.8714 (mtt) cc_final: 0.8509 (mtt) REVERT: C 816 ILE cc_start: 0.9453 (mm) cc_final: 0.9186 (mm) REVERT: C 829 THR cc_start: 0.9389 (p) cc_final: 0.8925 (p) REVERT: C 898 GLU cc_start: 0.9383 (mp0) cc_final: 0.9170 (mp0) REVERT: C 952 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8197 (tp-100) REVERT: C 1066 MET cc_start: 0.8534 (tmm) cc_final: 0.8154 (tmm) REVERT: C 1107 MET cc_start: 0.8403 (mmm) cc_final: 0.7966 (mmm) REVERT: C 1257 GLN cc_start: 0.7990 (tt0) cc_final: 0.7722 (tt0) REVERT: C 1276 TRP cc_start: 0.8891 (m-10) cc_final: 0.8687 (m-10) REVERT: C 1281 TYR cc_start: 0.7797 (m-80) cc_final: 0.7315 (m-10) REVERT: D 47 ARG cc_start: 0.7305 (mtm110) cc_final: 0.7077 (ptt180) REVERT: D 81 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7685 (mtm180) REVERT: D 140 TYR cc_start: 0.5970 (m-80) cc_final: 0.5085 (m-80) REVERT: D 300 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8262 (tm-30) REVERT: D 484 MET cc_start: 0.7359 (ttp) cc_final: 0.6522 (ptm) REVERT: D 644 MET cc_start: 0.6567 (ttm) cc_final: 0.6065 (mtp) REVERT: D 925 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7727 (tm-30) REVERT: D 1037 PHE cc_start: 0.4275 (m-10) cc_final: 0.3056 (m-80) REVERT: D 1313 SER cc_start: 0.9474 (m) cc_final: 0.9089 (t) REVERT: E 17 PHE cc_start: 0.8348 (m-10) cc_final: 0.7838 (m-10) REVERT: F 150 ARG cc_start: 0.5449 (mtt90) cc_final: 0.5192 (ttp80) REVERT: F 466 ILE cc_start: 0.9271 (mm) cc_final: 0.8983 (mm) REVERT: F 487 MET cc_start: 0.6917 (tpp) cc_final: 0.6635 (tpp) REVERT: F 489 MET cc_start: 0.7125 (mmm) cc_final: 0.6709 (mmm) REVERT: H 91 ILE cc_start: 0.7765 (pt) cc_final: 0.7508 (pt) REVERT: H 94 HIS cc_start: 0.8318 (m90) cc_final: 0.8073 (m-70) outliers start: 2 outliers final: 2 residues processed: 589 average time/residue: 0.1983 time to fit residues: 192.8470 Evaluate side-chains 448 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 446 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 0.8980 chunk 154 optimal weight: 8.9990 chunk 384 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS B 18 GLN B 132 HIS C 273 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 808 ASN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3885 r_free = 0.3885 target = 0.113149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093008 restraints weight = 104649.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094626 restraints weight = 63780.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.095773 restraints weight = 44715.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.096465 restraints weight = 34591.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096978 restraints weight = 29280.716| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33769 Z= 0.152 Angle : 0.649 12.563 46075 Z= 0.337 Chirality : 0.043 0.175 5293 Planarity : 0.004 0.061 5664 Dihedral : 15.827 167.057 5475 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % 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: -2.05 (0.13), residues: 3971 helix: -0.34 (0.13), residues: 1614 sheet: -2.59 (0.25), residues: 334 loop : -2.01 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 182 TYR 0.025 0.002 TYR D 140 PHE 0.023 0.002 PHE C 35 TRP 0.026 0.002 TRP D 236 HIS 0.014 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00343 (33763) covalent geometry : angle 0.64827 (46069) hydrogen bonds : bond 0.04008 ( 1327) hydrogen bonds : angle 5.03170 ( 3729) metal coordination : bond 0.00346 ( 6) metal coordination : angle 2.66313 ( 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 635 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 634 time to evaluate : 1.227 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: A 75 GLN cc_start: 0.7392 (tt0) cc_final: 0.6898 (tm-30) REVERT: A 229 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6481 (tm-30) REVERT: C 53 PHE cc_start: 0.7303 (m-10) cc_final: 0.7068 (m-10) REVERT: C 130 MET cc_start: 0.8599 (tpt) cc_final: 0.7938 (mmm) REVERT: C 136 PHE cc_start: 0.8463 (m-80) cc_final: 0.7358 (m-10) REVERT: C 149 LEU cc_start: 0.9283 (tp) cc_final: 0.8875 (tp) REVERT: C 349 GLU cc_start: 0.7789 (pt0) cc_final: 0.7449 (pt0) REVERT: C 367 TYR cc_start: 0.7903 (t80) cc_final: 0.6650 (t80) REVERT: C 369 MET cc_start: 0.7806 (tmm) cc_final: 0.7261 (tmm) REVERT: C 458 GLU cc_start: 0.8259 (tt0) cc_final: 0.7876 (tt0) REVERT: C 473 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7031 (tmm160) REVERT: C 511 LEU cc_start: 0.8786 (mm) cc_final: 0.8537 (mm) REVERT: C 516 ASP cc_start: 0.8462 (p0) cc_final: 0.7785 (p0) REVERT: C 688 GLN cc_start: 0.8647 (mt0) cc_final: 0.8204 (mt0) REVERT: C 728 ASP cc_start: 0.8020 (t0) cc_final: 0.7671 (t0) REVERT: C 739 ASP cc_start: 0.7445 (p0) cc_final: 0.6836 (t0) REVERT: C 741 MET cc_start: 0.8724 (mtt) cc_final: 0.8481 (mtt) REVERT: C 761 GLN cc_start: 0.8524 (mp10) cc_final: 0.8245 (mp10) REVERT: C 800 MET cc_start: 0.9026 (pmm) cc_final: 0.8653 (pmm) REVERT: C 816 ILE cc_start: 0.9327 (mm) cc_final: 0.9040 (mm) REVERT: C 829 THR cc_start: 0.9178 (p) cc_final: 0.8933 (p) REVERT: C 952 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8186 (tp-100) REVERT: C 1066 MET cc_start: 0.8464 (tmm) cc_final: 0.8219 (tmm) REVERT: C 1107 MET cc_start: 0.8007 (mmm) cc_final: 0.7599 (mmm) REVERT: C 1203 ASP cc_start: 0.7748 (t0) cc_final: 0.7503 (t0) REVERT: C 1240 ASP cc_start: 0.8146 (m-30) cc_final: 0.7378 (t0) REVERT: C 1276 TRP cc_start: 0.8557 (m-10) cc_final: 0.7748 (m-10) REVERT: C 1279 GLU cc_start: 0.8487 (tt0) cc_final: 0.8243 (tt0) REVERT: D 39 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8304 (mmtt) REVERT: D 47 ARG cc_start: 0.7285 (mtm110) cc_final: 0.6929 (ptt180) REVERT: D 81 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7585 (mtm180) REVERT: D 106 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7133 (mp0) REVERT: D 117 LEU cc_start: 0.9066 (mm) cc_final: 0.8684 (tt) REVERT: D 268 LEU cc_start: 0.9273 (mp) cc_final: 0.9046 (mt) REVERT: D 283 LEU cc_start: 0.8688 (mt) cc_final: 0.8216 (tt) REVERT: D 289 ASP cc_start: 0.7821 (p0) cc_final: 0.7612 (p0) REVERT: D 293 ARG cc_start: 0.8459 (ptp-110) cc_final: 0.7691 (ptp-110) REVERT: D 342 LEU cc_start: 0.9073 (mm) cc_final: 0.8699 (mm) REVERT: D 435 GLN cc_start: 0.8280 (pm20) cc_final: 0.7835 (pm20) REVERT: D 443 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7983 (tp30) REVERT: D 499 ILE cc_start: 0.7658 (tt) cc_final: 0.7405 (mt) REVERT: D 644 MET cc_start: 0.5843 (ttm) cc_final: 0.5163 (mtp) REVERT: D 821 MET cc_start: 0.7661 (tpp) cc_final: 0.7176 (tpp) REVERT: D 913 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7707 (tp30) REVERT: D 925 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 1037 PHE cc_start: 0.3667 (m-10) cc_final: 0.3034 (m-80) REVERT: D 1313 SER cc_start: 0.9407 (m) cc_final: 0.9004 (t) REVERT: D 1329 THR cc_start: 0.8725 (p) cc_final: 0.8453 (p) REVERT: D 1357 ILE cc_start: 0.9346 (pt) cc_final: 0.9080 (pt) REVERT: E 17 PHE cc_start: 0.7511 (m-10) cc_final: 0.6992 (m-10) REVERT: F 150 ARG cc_start: 0.5746 (mtt90) cc_final: 0.5143 (mtp-110) REVERT: F 288 MET cc_start: 0.5939 (mtp) cc_final: 0.5721 (mtp) REVERT: F 430 TYR cc_start: 0.6935 (t80) cc_final: 0.6560 (t80) REVERT: F 466 ILE cc_start: 0.9249 (mm) cc_final: 0.9031 (mm) REVERT: G 1 MET cc_start: 0.6570 (mtm) cc_final: 0.5880 (ttm) REVERT: G 30 MET cc_start: 0.3224 (ttt) cc_final: 0.2699 (tpt) REVERT: H 91 ILE cc_start: 0.7756 (pt) cc_final: 0.7510 (pt) REVERT: H 94 HIS cc_start: 0.8284 (m90) cc_final: 0.7966 (m-70) outliers start: 1 outliers final: 1 residues processed: 635 average time/residue: 0.2071 time to fit residues: 217.1846 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 : 1.137 ------------------------------------------------------------------------------- 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: 0.8980 chunk 330 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 279 optimal weight: 0.0270 chunk 202 optimal weight: 0.0030 chunk 49 optimal weight: 0.9990 chunk 270 optimal weight: 0.0040 chunk 273 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN C1236 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D 157 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.115471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096478 restraints weight = 104711.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098081 restraints weight = 66817.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.098510 restraints weight = 44490.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098850 restraints weight = 36839.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099093 restraints weight = 35134.526| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33769 Z= 0.133 Angle : 0.645 12.385 46075 Z= 0.333 Chirality : 0.043 0.257 5293 Planarity : 0.004 0.077 5664 Dihedral : 15.588 165.763 5475 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % 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: -1.85 (0.13), residues: 3971 helix: -0.22 (0.13), residues: 1603 sheet: -2.40 (0.26), residues: 316 loop : -1.88 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 838 TYR 0.042 0.002 TYR G 20 PHE 0.032 0.002 PHE D1274 TRP 0.051 0.002 TRP D 236 HIS 0.023 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00299 (33763) covalent geometry : angle 0.64444 (46069) hydrogen bonds : bond 0.03824 ( 1327) hydrogen bonds : angle 4.89170 ( 3729) metal coordination : bond 0.00185 ( 6) metal coordination : angle 2.25185 ( 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 621 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 620 time to evaluate : 1.333 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 75 GLN cc_start: 0.7215 (tt0) cc_final: 0.6766 (tm-30) REVERT: A 147 GLN cc_start: 0.7829 (tp40) cc_final: 0.7627 (tp40) REVERT: A 204 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 229 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6604 (tm-30) REVERT: B 85 LEU cc_start: 0.9280 (mt) cc_final: 0.8954 (tt) REVERT: B 174 ASP cc_start: 0.4918 (m-30) cc_final: 0.4718 (m-30) REVERT: C 136 PHE cc_start: 0.8431 (m-80) cc_final: 0.7776 (m-10) REVERT: C 204 LEU cc_start: 0.7545 (tp) cc_final: 0.7242 (tt) REVERT: C 347 ILE cc_start: 0.9207 (mm) cc_final: 0.8811 (mm) REVERT: C 349 GLU cc_start: 0.7881 (pt0) cc_final: 0.7511 (pt0) REVERT: C 367 TYR cc_start: 0.8033 (t80) cc_final: 0.7537 (t80) REVERT: C 369 MET cc_start: 0.7764 (tmm) cc_final: 0.7182 (tmm) REVERT: C 458 GLU cc_start: 0.8227 (tt0) cc_final: 0.7762 (tt0) REVERT: C 473 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7024 (tmm160) REVERT: C 516 ASP cc_start: 0.8355 (p0) cc_final: 0.7941 (p0) REVERT: C 687 ARG cc_start: 0.8440 (ttp-110) cc_final: 0.8147 (ttp-110) REVERT: C 728 ASP cc_start: 0.8034 (t0) cc_final: 0.7683 (t0) REVERT: C 739 ASP cc_start: 0.7469 (p0) cc_final: 0.6783 (t0) REVERT: C 767 GLN cc_start: 0.8540 (mt0) cc_final: 0.8272 (mp10) REVERT: C 800 MET cc_start: 0.8930 (pmm) cc_final: 0.8515 (pmm) REVERT: C 816 ILE cc_start: 0.9272 (mm) cc_final: 0.8936 (mm) REVERT: C 829 THR cc_start: 0.9130 (p) cc_final: 0.8870 (p) REVERT: C 952 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8207 (tp-100) REVERT: C 1007 LYS cc_start: 0.8179 (mptt) cc_final: 0.7974 (pttp) REVERT: C 1070 HIS cc_start: 0.8071 (m170) cc_final: 0.7706 (m170) REVERT: C 1107 MET cc_start: 0.7877 (mmm) cc_final: 0.7605 (mmm) REVERT: C 1203 ASP cc_start: 0.7770 (t0) cc_final: 0.7563 (t0) REVERT: C 1240 ASP cc_start: 0.8084 (m-30) cc_final: 0.7284 (t0) REVERT: C 1276 TRP cc_start: 0.8516 (m-10) cc_final: 0.7621 (m-10) REVERT: C 1279 GLU cc_start: 0.8414 (tt0) cc_final: 0.8213 (tt0) REVERT: C 1315 MET cc_start: 0.4548 (tpt) cc_final: 0.4065 (tpt) REVERT: D 39 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8226 (mmtt) REVERT: D 47 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6834 (ptt180) REVERT: D 81 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7594 (mtm180) REVERT: D 106 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7172 (mp0) REVERT: D 114 ILE cc_start: 0.9178 (tp) cc_final: 0.8807 (tt) REVERT: D 266 ASN cc_start: 0.9182 (m-40) cc_final: 0.8929 (t0) REVERT: D 268 LEU cc_start: 0.9182 (mp) cc_final: 0.8969 (mt) REVERT: D 289 ASP cc_start: 0.7773 (p0) cc_final: 0.7572 (p0) REVERT: D 293 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.7600 (ptp-110) REVERT: D 299 LEU cc_start: 0.9487 (tt) cc_final: 0.9186 (tp) REVERT: D 300 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8424 (tm-30) REVERT: D 342 LEU cc_start: 0.9060 (mm) cc_final: 0.8752 (mm) REVERT: D 435 GLN cc_start: 0.7680 (pm20) cc_final: 0.7451 (pm20) REVERT: D 443 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7834 (tp30) REVERT: D 503 SER cc_start: 0.8088 (m) cc_final: 0.7838 (m) REVERT: D 644 MET cc_start: 0.5776 (ttm) cc_final: 0.5346 (mtp) REVERT: D 783 LEU cc_start: 0.9571 (mm) cc_final: 0.9264 (tp) REVERT: D 913 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7758 (tp30) REVERT: D 983 LYS cc_start: 0.7455 (ptpp) cc_final: 0.7068 (pttm) REVERT: D 1037 PHE cc_start: 0.3414 (m-10) cc_final: 0.2673 (m-80) REVERT: D 1313 SER cc_start: 0.9326 (m) cc_final: 0.8961 (t) REVERT: E 17 PHE cc_start: 0.7041 (m-10) cc_final: 0.6834 (m-10) REVERT: F 150 ARG cc_start: 0.5742 (mtt90) cc_final: 0.5083 (mtp-110) REVERT: F 288 MET cc_start: 0.6150 (mtp) cc_final: 0.5919 (mtp) REVERT: F 430 TYR cc_start: 0.7030 (t80) cc_final: 0.6671 (t80) REVERT: F 466 ILE cc_start: 0.9241 (mm) cc_final: 0.9035 (mm) REVERT: F 487 MET cc_start: 0.6742 (tpp) cc_final: 0.6540 (tpp) REVERT: F 489 MET cc_start: 0.6972 (mmm) cc_final: 0.6699 (mmm) REVERT: G 1 MET cc_start: 0.6800 (mtm) cc_final: 0.6017 (ttm) REVERT: H 91 ILE cc_start: 0.7708 (pt) cc_final: 0.7430 (pt) outliers start: 1 outliers final: 1 residues processed: 621 average time/residue: 0.1983 time to fit residues: 204.3906 Evaluate side-chains 489 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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: 8.9990 chunk 189 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 311 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 288 optimal weight: 30.0000 chunk 347 optimal weight: 6.9990 chunk 156 optimal weight: 0.0870 chunk 315 optimal weight: 0.8980 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 760 ASN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.112200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092174 restraints weight = 104337.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093887 restraints weight = 63548.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095048 restraints weight = 43947.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095783 restraints weight = 33779.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096176 restraints weight = 28276.495| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33769 Z= 0.197 Angle : 0.688 11.700 46075 Z= 0.356 Chirality : 0.044 0.197 5293 Planarity : 0.005 0.063 5664 Dihedral : 15.668 165.845 5475 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.03 % Allowed : 1.21 % Favored : 98.76 % 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: -1.86 (0.13), residues: 3971 helix: -0.22 (0.13), residues: 1603 sheet: -2.37 (0.26), residues: 329 loop : -1.89 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 312 TYR 0.026 0.002 TYR C 73 PHE 0.020 0.002 PHE C 35 TRP 0.030 0.002 TRP D 236 HIS 0.024 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00436 (33763) covalent geometry : angle 0.68712 (46069) hydrogen bonds : bond 0.04113 ( 1327) hydrogen bonds : angle 4.98215 ( 3729) metal coordination : bond 0.00735 ( 6) metal coordination : angle 2.71083 ( 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 587 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 586 time to evaluate : 1.225 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: A 47 LEU cc_start: 0.9223 (tt) cc_final: 0.8693 (tt) REVERT: A 75 GLN cc_start: 0.7299 (tt0) cc_final: 0.6791 (tm-30) REVERT: A 147 GLN cc_start: 0.7937 (tp40) cc_final: 0.7713 (tp40) REVERT: A 203 ILE cc_start: 0.9043 (mp) cc_final: 0.8813 (mt) REVERT: A 204 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 229 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6751 (tm-30) REVERT: B 85 LEU cc_start: 0.9249 (mt) cc_final: 0.8983 (tt) REVERT: C 136 PHE cc_start: 0.8660 (m-80) cc_final: 0.7830 (m-10) REVERT: C 347 ILE cc_start: 0.9018 (mm) cc_final: 0.8756 (mm) REVERT: C 349 GLU cc_start: 0.7754 (pt0) cc_final: 0.7394 (pt0) REVERT: C 367 TYR cc_start: 0.7931 (t80) cc_final: 0.7608 (t80) REVERT: C 369 MET cc_start: 0.7741 (tmm) cc_final: 0.7203 (tmm) REVERT: C 458 GLU cc_start: 0.8229 (tt0) cc_final: 0.7758 (tt0) REVERT: C 515 MET cc_start: 0.8697 (ppp) cc_final: 0.8472 (ppp) REVERT: C 516 ASP cc_start: 0.8530 (p0) cc_final: 0.7989 (p0) REVERT: C 739 ASP cc_start: 0.7407 (p0) cc_final: 0.6848 (t0) REVERT: C 800 MET cc_start: 0.9128 (pmm) cc_final: 0.8765 (pmm) REVERT: C 829 THR cc_start: 0.9229 (p) cc_final: 0.8934 (p) REVERT: C 1007 LYS cc_start: 0.8120 (mptt) cc_final: 0.7888 (pttp) REVERT: C 1064 ASP cc_start: 0.8253 (t0) cc_final: 0.7940 (t0) REVERT: C 1107 MET cc_start: 0.8057 (mmm) cc_final: 0.7601 (mmm) REVERT: C 1203 ASP cc_start: 0.7721 (t0) cc_final: 0.7510 (t0) REVERT: C 1240 ASP cc_start: 0.8168 (m-30) cc_final: 0.7334 (t0) REVERT: C 1276 TRP cc_start: 0.8588 (m-10) cc_final: 0.7754 (m-10) REVERT: D 47 ARG cc_start: 0.7090 (mtm110) cc_final: 0.6814 (ptt180) REVERT: D 81 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7552 (mtm180) REVERT: D 114 ILE cc_start: 0.9400 (tp) cc_final: 0.9050 (tt) REVERT: D 283 LEU cc_start: 0.8621 (mt) cc_final: 0.8097 (tt) REVERT: D 293 ARG cc_start: 0.8527 (ptp-110) cc_final: 0.8193 (ptp-110) REVERT: D 300 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8603 (tm-30) REVERT: D 342 LEU cc_start: 0.9112 (mm) cc_final: 0.8837 (mm) REVERT: D 435 GLN cc_start: 0.8281 (pm20) cc_final: 0.7881 (pm20) REVERT: D 591 ILE cc_start: 0.7891 (tp) cc_final: 0.7584 (tp) REVERT: D 644 MET cc_start: 0.6062 (ttm) cc_final: 0.5540 (mtp) REVERT: D 760 THR cc_start: 0.8712 (p) cc_final: 0.8458 (p) REVERT: D 913 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7883 (tp30) REVERT: D 925 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 983 LYS cc_start: 0.7513 (ptpp) cc_final: 0.6795 (pttm) REVERT: D 1037 PHE cc_start: 0.3498 (m-10) cc_final: 0.2903 (m-80) REVERT: D 1313 SER cc_start: 0.9332 (m) cc_final: 0.8983 (t) REVERT: E 17 PHE cc_start: 0.7361 (m-10) cc_final: 0.6919 (m-10) REVERT: F 378 GLU cc_start: 0.8540 (pt0) cc_final: 0.8174 (pt0) REVERT: G 1 MET cc_start: 0.7038 (mtm) cc_final: 0.6469 (ttm) REVERT: G 17 ILE cc_start: 0.8676 (pt) cc_final: 0.8352 (pt) REVERT: H 91 ILE cc_start: 0.7640 (pt) cc_final: 0.7379 (pt) outliers start: 1 outliers final: 1 residues processed: 587 average time/residue: 0.2007 time to fit residues: 196.6800 Evaluate side-chains 462 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 461 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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: 0.7980 chunk 282 optimal weight: 5.9990 chunk 321 optimal weight: 0.7980 chunk 389 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 364 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 280 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1010 GLN C1157 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS D 458 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** 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 = 0.3909 r_free = 0.3909 target = 0.114441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095153 restraints weight = 104321.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096895 restraints weight = 64713.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097119 restraints weight = 46301.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.097774 restraints weight = 38558.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097981 restraints weight = 31905.020| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33769 Z= 0.149 Angle : 0.667 12.708 46075 Z= 0.344 Chirality : 0.044 0.246 5293 Planarity : 0.004 0.055 5664 Dihedral : 15.556 165.473 5475 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.03 % Allowed : 1.00 % Favored : 98.97 % 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: -1.77 (0.13), residues: 3971 helix: -0.16 (0.13), residues: 1608 sheet: -2.33 (0.27), residues: 325 loop : -1.82 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 293 TYR 0.023 0.002 TYR G 20 PHE 0.039 0.002 PHE H 58 TRP 0.056 0.002 TRP D 236 HIS 0.023 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00332 (33763) covalent geometry : angle 0.66657 (46069) hydrogen bonds : bond 0.03940 ( 1327) hydrogen bonds : angle 4.92632 ( 3729) metal coordination : bond 0.00368 ( 6) metal coordination : angle 2.17128 ( 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 594 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 593 time to evaluate : 1.406 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: A 47 LEU cc_start: 0.9175 (tt) cc_final: 0.8617 (tt) REVERT: A 75 GLN cc_start: 0.7178 (tt0) cc_final: 0.6738 (tm-30) REVERT: A 204 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 136 PHE cc_start: 0.8592 (m-80) cc_final: 0.8015 (m-10) REVERT: C 204 LEU cc_start: 0.7513 (tp) cc_final: 0.7254 (tt) REVERT: C 347 ILE cc_start: 0.9147 (mm) cc_final: 0.8773 (mm) REVERT: C 349 GLU cc_start: 0.7939 (pt0) cc_final: 0.7528 (pt0) REVERT: C 367 TYR cc_start: 0.8037 (t80) cc_final: 0.7667 (t80) REVERT: C 369 MET cc_start: 0.7759 (tmm) cc_final: 0.7180 (tmm) REVERT: C 458 GLU cc_start: 0.8238 (tt0) cc_final: 0.7755 (tt0) REVERT: C 473 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7212 (tmm160) REVERT: C 516 ASP cc_start: 0.8444 (p0) cc_final: 0.7921 (p0) REVERT: C 685 MET cc_start: 0.7588 (mtt) cc_final: 0.7193 (mtt) REVERT: C 686 GLN cc_start: 0.8433 (mt0) cc_final: 0.8154 (mt0) REVERT: C 688 GLN cc_start: 0.8663 (tt0) cc_final: 0.8071 (tt0) REVERT: C 728 ASP cc_start: 0.7955 (t0) cc_final: 0.7422 (t0) REVERT: C 739 ASP cc_start: 0.7452 (p0) cc_final: 0.6922 (t0) REVERT: C 767 GLN cc_start: 0.8570 (mt0) cc_final: 0.7469 (mp10) REVERT: C 800 MET cc_start: 0.9048 (pmm) cc_final: 0.8537 (pmm) REVERT: C 829 THR cc_start: 0.9107 (p) cc_final: 0.8849 (p) REVERT: C 1007 LYS cc_start: 0.8234 (mptt) cc_final: 0.7972 (pttp) REVERT: C 1064 ASP cc_start: 0.8147 (t0) cc_final: 0.7819 (t0) REVERT: C 1107 MET cc_start: 0.7909 (mmm) cc_final: 0.7554 (mmm) REVERT: C 1188 ASP cc_start: 0.5990 (m-30) cc_final: 0.5612 (m-30) REVERT: C 1240 ASP cc_start: 0.8094 (m-30) cc_final: 0.7197 (t0) REVERT: C 1276 TRP cc_start: 0.8669 (m-10) cc_final: 0.7812 (m-10) REVERT: C 1315 MET cc_start: 0.4880 (tpt) cc_final: 0.4465 (tpt) REVERT: C 1329 GLU cc_start: 0.8169 (tt0) cc_final: 0.7123 (tt0) REVERT: D 47 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6855 (ptt180) REVERT: D 81 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7556 (mtm180) REVERT: D 114 ILE cc_start: 0.9332 (tp) cc_final: 0.8971 (tt) REVERT: D 117 LEU cc_start: 0.9104 (mm) cc_final: 0.8896 (mm) REVERT: D 133 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8353 (ptm-80) REVERT: D 237 MET cc_start: 0.7778 (tmm) cc_final: 0.7560 (tpp) REVERT: D 283 LEU cc_start: 0.8620 (mt) cc_final: 0.8081 (tt) REVERT: D 293 ARG cc_start: 0.8231 (ptp-110) cc_final: 0.7451 (ptp-110) REVERT: D 300 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8657 (tm-30) REVERT: D 342 LEU cc_start: 0.9156 (mm) cc_final: 0.8815 (mm) REVERT: D 435 GLN cc_start: 0.8151 (pm20) cc_final: 0.7431 (pm20) REVERT: D 443 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7663 (tp30) REVERT: D 644 MET cc_start: 0.6034 (ttm) cc_final: 0.5308 (mtp) REVERT: D 760 THR cc_start: 0.8639 (p) cc_final: 0.8418 (p) REVERT: D 913 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7822 (tp30) REVERT: D 983 LYS cc_start: 0.7587 (ptpp) cc_final: 0.7172 (pttm) REVERT: D 1037 PHE cc_start: 0.3537 (m-10) cc_final: 0.2801 (m-80) REVERT: D 1313 SER cc_start: 0.9310 (m) cc_final: 0.9007 (t) REVERT: E 17 PHE cc_start: 0.7318 (m-10) cc_final: 0.6911 (m-10) REVERT: E 71 GLU cc_start: 0.8554 (mp0) cc_final: 0.8314 (mp0) REVERT: F 378 GLU cc_start: 0.8398 (pt0) cc_final: 0.8198 (pt0) REVERT: F 430 TYR cc_start: 0.7165 (t80) cc_final: 0.6797 (t80) REVERT: F 466 ILE cc_start: 0.9229 (mm) cc_final: 0.8998 (mm) REVERT: F 487 MET cc_start: 0.6661 (tpp) cc_final: 0.6430 (tpp) REVERT: F 489 MET cc_start: 0.6999 (mmm) cc_final: 0.6723 (mmm) REVERT: G 1 MET cc_start: 0.6830 (mtm) cc_final: 0.6216 (ttm) REVERT: H 1 MET cc_start: 0.1879 (ptm) cc_final: 0.1493 (ptm) REVERT: H 94 HIS cc_start: 0.7972 (m-70) cc_final: 0.7760 (m-70) outliers start: 1 outliers final: 1 residues processed: 594 average time/residue: 0.1993 time to fit residues: 196.9512 Evaluate side-chains 482 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 4.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 229 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.109999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089994 restraints weight = 105951.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091647 restraints weight = 64545.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092733 restraints weight = 44712.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093352 restraints weight = 34658.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093869 restraints weight = 29544.523| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33769 Z= 0.237 Angle : 0.743 12.114 46075 Z= 0.386 Chirality : 0.046 0.204 5293 Planarity : 0.005 0.059 5664 Dihedral : 15.741 165.627 5475 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % 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: -1.87 (0.13), residues: 3971 helix: -0.21 (0.13), residues: 1598 sheet: -2.34 (0.26), residues: 342 loop : -1.91 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 156 TYR 0.024 0.002 TYR G 20 PHE 0.019 0.002 PHE C 812 TRP 0.051 0.002 TRP D 236 HIS 0.023 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00521 (33763) covalent geometry : angle 0.74222 (46069) hydrogen bonds : bond 0.04456 ( 1327) hydrogen bonds : angle 5.14756 ( 3729) metal coordination : bond 0.01419 ( 6) metal coordination : angle 3.84367 ( 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 563 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 562 time to evaluate : 1.198 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 147 GLN cc_start: 0.8023 (tp40) cc_final: 0.7803 (tp40) REVERT: A 204 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7324 (tm-30) REVERT: B 85 LEU cc_start: 0.9218 (mt) cc_final: 0.8951 (tt) REVERT: B 176 CYS cc_start: 0.8098 (m) cc_final: 0.7777 (m) REVERT: B 186 ASN cc_start: 0.8360 (p0) cc_final: 0.7881 (p0) REVERT: C 136 PHE cc_start: 0.8603 (m-80) cc_final: 0.8095 (m-10) REVERT: C 211 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7484 (mmm160) REVERT: C 347 ILE cc_start: 0.9238 (mm) cc_final: 0.8841 (mm) REVERT: C 349 GLU cc_start: 0.7819 (pt0) cc_final: 0.7394 (pt0) REVERT: C 367 TYR cc_start: 0.7948 (t80) cc_final: 0.7658 (t80) REVERT: C 369 MET cc_start: 0.7765 (tmm) cc_final: 0.7186 (tmm) REVERT: C 458 GLU cc_start: 0.8324 (tt0) cc_final: 0.7809 (tt0) REVERT: C 515 MET cc_start: 0.8730 (ppp) cc_final: 0.8402 (ppp) REVERT: C 516 ASP cc_start: 0.8410 (p0) cc_final: 0.8016 (p0) REVERT: C 739 ASP cc_start: 0.7293 (p0) cc_final: 0.6851 (t0) REVERT: C 829 THR cc_start: 0.9237 (p) cc_final: 0.9005 (p) REVERT: C 1007 LYS cc_start: 0.8164 (mptt) cc_final: 0.7916 (pttp) REVERT: C 1064 ASP cc_start: 0.8441 (t0) cc_final: 0.8009 (t0) REVERT: C 1240 ASP cc_start: 0.8263 (m-30) cc_final: 0.7435 (t0) REVERT: C 1244 HIS cc_start: 0.7889 (t-170) cc_final: 0.7556 (t-170) REVERT: C 1272 GLU cc_start: 0.7292 (pp20) cc_final: 0.7082 (pp20) REVERT: C 1276 TRP cc_start: 0.8521 (m-10) cc_final: 0.8259 (m-10) REVERT: D 29 MET cc_start: 0.7412 (ptp) cc_final: 0.6766 (ptp) REVERT: D 47 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6968 (ptt180) REVERT: D 81 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7623 (mtm180) REVERT: D 114 ILE cc_start: 0.9412 (tp) cc_final: 0.9064 (tt) REVERT: D 133 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8388 (ptm-80) REVERT: D 283 LEU cc_start: 0.8835 (mt) cc_final: 0.8178 (tt) REVERT: D 293 ARG cc_start: 0.8625 (ptp-110) cc_final: 0.8015 (ptp-110) REVERT: D 300 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8588 (tm-30) REVERT: D 330 MET cc_start: 0.7320 (ttm) cc_final: 0.7024 (ttm) REVERT: D 342 LEU cc_start: 0.9007 (mm) cc_final: 0.8789 (mm) REVERT: D 435 GLN cc_start: 0.8479 (pm20) cc_final: 0.8232 (pm20) REVERT: D 591 ILE cc_start: 0.7987 (tp) cc_final: 0.7723 (tp) REVERT: D 644 MET cc_start: 0.6737 (ttm) cc_final: 0.6172 (mtp) REVERT: D 913 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7900 (mm-30) REVERT: D 925 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7627 (tm-30) REVERT: D 983 LYS cc_start: 0.7386 (ptpp) cc_final: 0.6957 (pttm) REVERT: D 1037 PHE cc_start: 0.3810 (m-10) cc_final: 0.3231 (m-80) REVERT: D 1313 SER cc_start: 0.9373 (m) cc_final: 0.9075 (t) REVERT: E 17 PHE cc_start: 0.7924 (m-10) cc_final: 0.7344 (m-10) REVERT: F 100 MET cc_start: 0.7068 (ptt) cc_final: 0.6702 (ptt) REVERT: F 378 GLU cc_start: 0.8399 (pt0) cc_final: 0.8114 (pt0) REVERT: F 487 MET cc_start: 0.6429 (tpp) cc_final: 0.6217 (tpp) REVERT: F 489 MET cc_start: 0.6960 (mmm) cc_final: 0.6633 (mmm) REVERT: G 1 MET cc_start: 0.7224 (mtm) cc_final: 0.6629 (ttm) REVERT: G 17 ILE cc_start: 0.8692 (pt) cc_final: 0.8391 (pt) REVERT: G 30 MET cc_start: 0.2421 (ttp) cc_final: 0.1666 (tpt) REVERT: H 1 MET cc_start: 0.1863 (ptm) cc_final: 0.1533 (ptm) REVERT: H 91 ILE cc_start: 0.7767 (pt) cc_final: 0.7519 (pt) REVERT: H 94 HIS cc_start: 0.8052 (m-70) cc_final: 0.7845 (m-70) outliers start: 1 outliers final: 1 residues processed: 563 average time/residue: 0.2024 time to fit residues: 190.1553 Evaluate side-chains 446 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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: 6.9990 chunk 109 optimal weight: 0.7980 chunk 278 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 357 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 390 optimal weight: 3.9990 chunk 378 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 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 = 0.3845 r_free = 0.3845 target = 0.110583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090587 restraints weight = 104384.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092235 restraints weight = 63751.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093368 restraints weight = 44225.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094094 restraints weight = 34146.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094515 restraints weight = 28673.665| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33769 Z= 0.205 Angle : 0.730 12.509 46075 Z= 0.377 Chirality : 0.045 0.273 5293 Planarity : 0.005 0.059 5664 Dihedral : 15.707 165.381 5475 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % 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: -1.92 (0.13), residues: 3971 helix: -0.29 (0.13), residues: 1611 sheet: -2.52 (0.26), residues: 347 loop : -1.87 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 150 TYR 0.026 0.002 TYR B 185 PHE 0.024 0.002 PHE H 58 TRP 0.058 0.002 TRP D 236 HIS 0.023 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00457 (33763) covalent geometry : angle 0.72909 (46069) hydrogen bonds : bond 0.04345 ( 1327) hydrogen bonds : angle 5.16640 ( 3729) metal coordination : bond 0.01045 ( 6) metal coordination : angle 3.01217 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.34 seconds wall clock time: 106 minutes 27.23 seconds (6387.23 seconds total)