Starting phenix.real_space_refine on Mon Sep 23 13:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/09_2024/6xas_22114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/09_2024/6xas_22114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/09_2024/6xas_22114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/09_2024/6xas_22114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/09_2024/6xas_22114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/09_2024/6xas_22114.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 71 5.49 5 Mg 1 5.21 5 S 202 5.16 5 C 29194 2.51 5 N 8310 2.21 5 O 9107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 46887 Number of models: 1 Model: "" Number of chains: 16 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1611 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "W" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "N" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "R" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 386 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 13} Chain breaks: 1 Chain: "K" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2024 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 269} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 10429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10429 Classifications: {'peptide': 1323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1267} Chain breaks: 1 Chain: "J" Number of atoms: 10336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10336 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1273} Chain breaks: 3 Chain: "C" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3058 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 371} Chain: "B" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "F" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2697 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain breaks: 2 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18290 SG CYS J 85 86.910 117.758 45.352 1.00 30.14 S ATOM 18314 SG CYS J 88 90.794 116.449 45.876 1.00 29.38 S ATOM 24002 SG CYS J 814 114.265 51.930 49.122 1.00 18.03 S ATOM 24567 SG CYS J 888 115.264 55.607 50.611 1.00 15.66 S ATOM 24618 SG CYS J 895 112.721 53.333 52.026 1.00 11.14 S ATOM 24639 SG CYS J 898 115.881 51.962 52.768 1.00 9.85 S Time building chain proxies: 19.95, per 1000 atoms: 0.43 Number of scatterers: 46887 At special positions: 0 Unit cell: (211.288, 215.6, 150.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 202 16.00 P 71 15.00 Mg 1 11.99 O 9107 8.00 N 8310 7.00 C 29194 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: 8.83 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 6 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10768 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 71 sheets defined 41.6% alpha, 16.1% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 12.40 Creating SS restraints... Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 21 through 39 Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.971A pdb=" N ALA G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 106 through 133 removed outlier: 3.538A pdb=" N ALA G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 13 removed outlier: 3.833A pdb=" N ILE W 13 " --> pdb=" O ALA W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 32 removed outlier: 3.606A pdb=" N LEU W 21 " --> pdb=" O PHE W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 55 removed outlier: 3.893A pdb=" N GLU W 55 " --> pdb=" O LEU W 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 50 removed outlier: 3.787A pdb=" N ALA K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 86 removed outlier: 3.548A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 158 Processing helix chain 'K' and resid 212 through 229 removed outlier: 3.507A pdb=" N ARG K 219 " --> pdb=" O GLU K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.790A pdb=" N LEU K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.762A pdb=" N LEU K 281 " --> pdb=" O TYR K 277 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG K 284 " --> pdb=" O ASP K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 291 Processing helix chain 'K' and resid 296 through 308 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.699A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.501A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 removed outlier: 3.638A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.588A pdb=" N ASP I 33 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN I 36 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 57 removed outlier: 3.818A pdb=" N PHE I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.683A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 225 removed outlier: 3.715A pdb=" N ASP I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU I 223 " --> pdb=" O GLN I 219 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE I 224 " --> pdb=" O ILE I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.187A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 353 removed outlier: 3.563A pdb=" N VAL I 353 " --> pdb=" O GLU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.421A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER I 383 " --> pdb=" O GLU I 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU I 388 " --> pdb=" O LEU I 384 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 removed outlier: 3.554A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.767A pdb=" N GLN I 463 " --> pdb=" O MET I 459 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.501A pdb=" N PHE I 506 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.910A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 613 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.993A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.538A pdb=" N SER I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 864 removed outlier: 4.174A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 906 removed outlier: 4.281A pdb=" N LYS I 900 " --> pdb=" O THR I 896 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 901 " --> pdb=" O PRO I 897 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 980 removed outlier: 4.388A pdb=" N SER I 973 " --> pdb=" O ALA I 969 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG I 974 " --> pdb=" O GLY I 970 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE I 975 " --> pdb=" O LEU I 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1038 removed outlier: 3.808A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA I1015 " --> pdb=" O LEU I1011 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS I1027 " --> pdb=" O HIS I1023 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS I1028 " --> pdb=" O GLU I1024 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.297A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.777A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.562A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE I1144 " --> pdb=" O LYS I1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1177 through 1179 No H-bonds generated for 'chain 'I' and resid 1177 through 1179' Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.777A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.646A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1293 removed outlier: 3.654A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1309 removed outlier: 3.796A pdb=" N ARG I1301 " --> pdb=" O ASP I1297 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.787A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.757A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.575A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.979A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.528A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR J 218 " --> pdb=" O ARG J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.892A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 337 through 342 Processing helix chain 'J' and resid 370 through 388 Proline residue: J 379 - end of helix Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.316A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL J 415 " --> pdb=" O ILE J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 505 through 514 removed outlier: 3.635A pdb=" N GLY J 509 " --> pdb=" O ASP J 505 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.824A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.687A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 669 removed outlier: 3.865A pdb=" N GLU J 663 " --> pdb=" O ALA J 659 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU J 666 " --> pdb=" O ALA J 662 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE J 668 " --> pdb=" O ILE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.644A pdb=" N ASN J 700 " --> pdb=" O ALA J 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.569A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.028A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 4.382A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 4.155A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1288 Processing helix chain 'J' and resid 1290 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.514A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.502A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.517A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.619A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.745A pdb=" N ASN C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.072A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.544A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.756A pdb=" N LYS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.745A pdb=" N PHE C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.585A pdb=" N SER A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 4.476A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.776A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.585A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.802A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.797A pdb=" N PHE A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.703A pdb=" N SER B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 337 removed outlier: 4.367A pdb=" N GLY B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 404 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.533A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.617A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.300A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 235 through 256 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.526A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.781A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 Processing helix chain 'D' and resid 408 through 417 removed outlier: 3.886A pdb=" N PHE D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.717A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 123 through 129 removed outlier: 4.041A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 4.360A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.516A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.614A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 417 removed outlier: 3.529A pdb=" N PHE E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS E 417 " --> pdb=" O PHE E 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 22 Processing helix chain 'F' and resid 30 through 46 Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.790A pdb=" N ASN F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 166 Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 268 through 278 Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.510A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.549A pdb=" N LYS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.087A pdb=" N ARG G 46 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE G 59 " --> pdb=" O ARG G 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.006A pdb=" N LEU G 63 " --> pdb=" O ILE G 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 138 through 141 removed outlier: 4.137A pdb=" N ILE G 138 " --> pdb=" O GLY G 181 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU G 183 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 198 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER G 185 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG G 187 " --> pdb=" O GLN G 194 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN G 194 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU G 159 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL G 197 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL G 161 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU G 154 " --> pdb=" O ALA G 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 16 through 18 removed outlier: 3.669A pdb=" N LYS K 25 " --> pdb=" O GLU K 17 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET K 205 " --> pdb=" O ALA K 24 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS K 200 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL K 187 " --> pdb=" O LYS K 200 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL K 202 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR K 185 " --> pdb=" O VAL K 202 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU K 204 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE K 183 " --> pdb=" O GLU K 204 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU K 206 " --> pdb=" O GLU K 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 97 through 99 Processing sheet with id=AA6, first strand: chain 'K' and resid 97 through 99 removed outlier: 7.696A pdb=" N SER K 141 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE K 61 " --> pdb=" O SER K 141 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG K 143 " --> pdb=" O VAL K 59 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL K 59 " --> pdb=" O ARG K 143 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS K 145 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA K 55 " --> pdb=" O GLN K 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'K' and resid 108 through 110 Processing sheet with id=AA9, first strand: chain 'K' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'H' and resid 23 through 31 removed outlier: 3.604A pdb=" N MET H 205 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR H 196 " --> pdb=" O ARG H 191 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG H 191 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 142 through 150 removed outlier: 6.513A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.773A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU H 122 " --> pdb=" O ARG H 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.589A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.696A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.249A pdb=" N SER I 66 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N LEU I 102 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N THR I 113 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N ILE I 104 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLU I 111 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU I 106 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.249A pdb=" N SER I 66 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.629A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.552A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.964A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.959A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.895A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.044A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.526A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.124A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 830 through 832 Processing sheet with id=AD3, first strand: chain 'I' and resid 835 through 841 removed outlier: 4.018A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 876 through 877 Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.088A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.830A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1339 removed outlier: 3.605A pdb=" N LYS J 21 " --> pdb=" O GLU I1338 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.489A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE3, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.597A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.554A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.537A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 957 through 961 removed outlier: 6.806A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.965A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 4.372A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1188 through 1190 removed outlier: 3.728A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.892A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP J1305 " --> pdb=" O LYS J1263 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.871A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS C 100 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL C 116 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG C 102 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 114 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.618A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.533A pdb=" N GLY C 174 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 317 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 178 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 226 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.557A pdb=" N GLY A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.663A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 173 through 178 removed outlier: 3.561A pdb=" N GLY A 174 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 317 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.669A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.748A pdb=" N GLU A 342 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 364 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B 96 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 119 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER B 98 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 115 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG B 102 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 113 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 113 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.478A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA B 317 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU B 342 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 364 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'D' and resid 49 through 57 removed outlier: 4.132A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU D 113 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG D 102 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 115 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER D 98 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D 119 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 96 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.621A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 173 through 178 removed outlier: 3.577A pdb=" N LEU D 264 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU D 204 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 341 through 342 removed outlier: 3.831A pdb=" N GLU D 342 " --> pdb=" O GLY D 364 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 364 " --> pdb=" O GLU D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.787A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 113 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.608A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E 226 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.608A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LEU E 343 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 175 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 49 through 57 removed outlier: 4.184A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 113 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS F 100 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER F 98 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.532A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.727A pdb=" N ALA F 178 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU F 343 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) 1904 hydrogen bonds defined for protein. 5412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 24.25 Time building geometry restraints manager: 10.54 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: 14709 1.34 - 1.45: 5653 1.45 - 1.57: 26846 1.57 - 1.69: 139 1.69 - 1.81: 370 Bond restraints: 47717 Sorted by residual: bond pdb=" O3' DC T 8 " pdb=" P DG T 9 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 bond pdb=" N GLY I 482 " pdb=" CA GLY I 482 " ideal model delta sigma weight residual 1.445 1.476 -0.031 1.01e-02 9.80e+03 9.31e+00 bond pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.23e-02 6.61e+03 7.51e+00 bond pdb=" N LEU I 484 " pdb=" CA LEU I 484 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.59e+00 bond pdb=" N ASP I 483 " pdb=" CA ASP I 483 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.26e+00 ... (remaining 47712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 62599 1.24 - 2.47: 1743 2.47 - 3.70: 289 3.70 - 4.94: 41 4.94 - 6.17: 10 Bond angle restraints: 64682 Sorted by residual: angle pdb=" N ILE I 414 " pdb=" CA ILE I 414 " pdb=" C ILE I 414 " ideal model delta sigma weight residual 112.43 108.61 3.82 9.20e-01 1.18e+00 1.72e+01 angle pdb=" C3' C R 2 " pdb=" O3' C R 2 " pdb=" P G R 3 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N THR I 486 " pdb=" CA THR I 486 " pdb=" C THR I 486 " ideal model delta sigma weight residual 113.43 109.18 4.25 1.26e+00 6.30e-01 1.14e+01 angle pdb=" N ILE I1112 " pdb=" CA ILE I1112 " pdb=" C ILE I1112 " ideal model delta sigma weight residual 111.58 108.03 3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" N ILE J1210 " pdb=" CA ILE J1210 " pdb=" C ILE J1210 " ideal model delta sigma weight residual 111.56 108.69 2.87 8.60e-01 1.35e+00 1.11e+01 ... (remaining 64677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 28883 35.37 - 70.74: 406 70.74 - 106.11: 45 106.11 - 141.48: 0 141.48 - 176.85: 1 Dihedral angle restraints: 29335 sinusoidal: 12653 harmonic: 16682 Sorted by residual: dihedral pdb=" CA ASP I1150 " pdb=" C ASP I1150 " pdb=" N LEU I1151 " pdb=" CA LEU I1151 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual 180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C4' C R 2 " pdb=" C3' C R 2 " pdb=" O3' C R 2 " pdb=" P G R 3 " ideal model delta sinusoidal sigma weight residual 250.00 73.15 176.85 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 29332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5662 0.039 - 0.079: 1196 0.079 - 0.118: 526 0.118 - 0.157: 24 0.157 - 0.197: 1 Chirality restraints: 7409 Sorted by residual: chirality pdb=" C3' C R 2 " pdb=" C4' C R 2 " pdb=" O3' C R 2 " pdb=" C2' C R 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE J1190 " pdb=" N ILE J1190 " pdb=" C ILE J1190 " pdb=" CB ILE J1190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE W 13 " pdb=" N ILE W 13 " pdb=" C ILE W 13 " pdb=" CB ILE W 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 7406 not shown) Planarity restraints: 8210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO I 698 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 29 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO K 30 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO K 30 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 30 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS I1022 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LYS I1022 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS I1022 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS I1023 " 0.010 2.00e-02 2.50e+03 ... (remaining 8207 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 211 2.55 - 3.14: 35176 3.14 - 3.72: 69063 3.72 - 4.31: 95977 4.31 - 4.90: 160606 Nonbonded interactions: 361033 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 1.961 2.170 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 2.039 2.170 nonbonded pdb=" O3' A R 60 " pdb="MG MG J1501 " model vdw 2.060 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.105 2.170 nonbonded pdb=" OE1 GLU I 67 " pdb=" OH TYR I 105 " model vdw 2.224 3.040 ... (remaining 361028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 30 through 417) selection = (chain 'C' and resid 30 through 417) selection = (chain 'D' and resid 30 through 417) selection = (chain 'E' and resid 30 through 417) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.060 Extract box with map and model: 2.030 Check model and map are aligned: 0.360 Set scattering table: 0.470 Process input model: 103.830 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 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 : 0.002 0.056 47717 Z= 0.128 Angle : 0.491 6.175 64682 Z= 0.316 Chirality : 0.038 0.197 7409 Planarity : 0.003 0.045 8210 Dihedral : 11.330 176.853 18567 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.80 % Rotamer: Outliers : 1.49 % Allowed : 4.11 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.10), residues: 5764 helix: -0.18 (0.10), residues: 2179 sheet: -2.16 (0.16), residues: 763 loop : -2.00 (0.10), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 409 HIS 0.003 0.000 HIS J 430 PHE 0.008 0.001 PHE A 36 TYR 0.009 0.001 TYR J 631 ARG 0.003 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 851 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 VAL cc_start: 0.5799 (OUTLIER) cc_final: 0.5270 (p) REVERT: G 111 LYS cc_start: 0.7044 (tttp) cc_final: 0.6728 (tppt) REVERT: W 16 ARG cc_start: 0.5139 (ttt90) cc_final: 0.4820 (ttp80) REVERT: K 74 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7648 (p) REVERT: K 156 SER cc_start: 0.7260 (p) cc_final: 0.6836 (t) REVERT: K 226 GLU cc_start: 0.6745 (tt0) cc_final: 0.6444 (tt0) REVERT: H 139 SER cc_start: 0.6159 (t) cc_final: 0.5888 (p) REVERT: H 212 ASP cc_start: 0.7380 (p0) cc_final: 0.7137 (p0) REVERT: I 36 GLN cc_start: 0.8305 (tp40) cc_final: 0.8103 (tp40) REVERT: I 80 PHE cc_start: 0.7657 (m-80) cc_final: 0.7424 (m-80) REVERT: I 369 MET cc_start: 0.5415 (ppp) cc_final: 0.4977 (ttt) REVERT: I 408 SER cc_start: 0.8674 (p) cc_final: 0.8320 (m) REVERT: I 514 PHE cc_start: 0.5371 (OUTLIER) cc_final: 0.4853 (t80) REVERT: I 677 ASN cc_start: 0.7547 (p0) cc_final: 0.6857 (t0) REVERT: I 694 ARG cc_start: 0.6107 (ptt180) cc_final: 0.5823 (ptm160) REVERT: I 850 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7224 (mt) REVERT: I 872 TYR cc_start: 0.8008 (m-80) cc_final: 0.7762 (m-80) REVERT: I 1050 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7872 (t) REVERT: J 219 LYS cc_start: 0.6205 (mmtt) cc_final: 0.5763 (mttm) REVERT: J 325 LYS cc_start: 0.8350 (mmtp) cc_final: 0.7859 (mmtt) REVERT: J 795 TYR cc_start: 0.6260 (m-80) cc_final: 0.5921 (m-80) REVERT: J 872 LEU cc_start: 0.8400 (mt) cc_final: 0.8024 (mp) REVERT: J 1244 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7212 (mm-40) REVERT: D 416 MET cc_start: 0.1188 (mmm) cc_final: 0.0763 (ptm) REVERT: F 21 MET cc_start: -0.1288 (mtp) cc_final: -0.3056 (ptm) outliers start: 73 outliers final: 11 residues processed: 916 average time/residue: 0.5276 time to fit residues: 769.3094 Evaluate side-chains 494 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 478 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 116 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 488 optimal weight: 30.0000 chunk 438 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 234 optimal weight: 0.0770 chunk 453 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 chunk 525 optimal weight: 50.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 GLN G 129 GLN K 93 GLN H 117 HIS H 127 GLN H 132 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN I 673 HIS I 808 ASN I 832 HIS I 834 GLN I1070 HIS I1116 HIS I1299 ASN I1314 GLN J 232 ASN J 593 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 239 HIS B 90 ASN B 295 HIS D 32 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 47717 Z= 0.417 Angle : 0.659 12.299 64682 Z= 0.343 Chirality : 0.047 0.250 7409 Planarity : 0.005 0.080 8210 Dihedral : 11.529 176.357 7198 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 2.26 % Allowed : 9.47 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.11), residues: 5764 helix: 0.53 (0.11), residues: 2219 sheet: -1.57 (0.17), residues: 801 loop : -1.52 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 381 HIS 0.010 0.002 HIS J 104 PHE 0.019 0.002 PHE I 405 TYR 0.024 0.002 TYR J 631 ARG 0.011 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 470 time to evaluate : 4.005 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: W 16 ARG cc_start: 0.5179 (ttt90) cc_final: 0.4747 (ttp80) REVERT: I 445 ILE cc_start: 0.8497 (mt) cc_final: 0.8103 (mm) REVERT: I 514 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5519 (t80) REVERT: I 850 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7318 (mt) REVERT: I 882 ILE cc_start: 0.8092 (mm) cc_final: 0.7368 (mm) REVERT: I 1315 MET cc_start: 0.7444 (ptt) cc_final: 0.7202 (ptt) REVERT: J 325 LYS cc_start: 0.8334 (mmtp) cc_final: 0.8028 (mmtt) REVERT: J 797 THR cc_start: 0.8532 (t) cc_final: 0.7512 (p) REVERT: J 1040 MET cc_start: 0.1261 (mmm) cc_final: -0.1437 (ttt) REVERT: J 1189 MET cc_start: 0.7215 (tpt) cc_final: 0.6415 (tpt) REVERT: C 162 LEU cc_start: 0.6997 (pp) cc_final: 0.6786 (pp) REVERT: B 341 MET cc_start: 0.6967 (tmm) cc_final: 0.6229 (tmm) REVERT: D 405 MET cc_start: 0.1332 (ptt) cc_final: 0.0563 (ptt) REVERT: D 416 MET cc_start: 0.1331 (mmm) cc_final: 0.0612 (ptm) REVERT: F 21 MET cc_start: -0.0994 (mtp) cc_final: -0.2811 (ptm) REVERT: F 245 MET cc_start: -0.1781 (ttt) cc_final: -0.2333 (ttt) outliers start: 111 outliers final: 63 residues processed: 558 average time/residue: 0.4877 time to fit residues: 447.7659 Evaluate side-chains 462 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 397 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 593 ASN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 219 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 292 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 437 optimal weight: 30.0000 chunk 358 optimal weight: 30.0000 chunk 145 optimal weight: 0.6980 chunk 526 optimal weight: 50.0000 chunk 569 optimal weight: 50.0000 chunk 469 optimal weight: 50.0000 chunk 522 optimal weight: 50.0000 chunk 179 optimal weight: 2.9990 chunk 422 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 GLN G 116 GLN K 93 GLN K 147 GLN H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN J 690 ASN J 777 HIS J1235 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN E 239 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.150 47717 Z= 0.694 Angle : 0.800 15.915 64682 Z= 0.415 Chirality : 0.053 0.408 7409 Planarity : 0.006 0.100 8210 Dihedral : 11.804 176.730 7191 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 2.91 % Allowed : 10.44 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 5764 helix: 0.45 (0.11), residues: 2250 sheet: -1.69 (0.17), residues: 763 loop : -1.40 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 381 HIS 0.016 0.002 HIS B 295 PHE 0.027 0.002 PHE H 35 TYR 0.025 0.003 TYR I 47 ARG 0.013 0.001 ARG I 706 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 418 time to evaluate : 4.040 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: W 16 ARG cc_start: 0.5220 (ttt90) cc_final: 0.4773 (ttp80) REVERT: H 103 ASN cc_start: 0.6076 (m-40) cc_final: 0.5871 (m110) REVERT: H 195 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.4968 (mtp180) REVERT: I 445 ILE cc_start: 0.8463 (mt) cc_final: 0.7990 (mm) REVERT: I 514 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.5591 (t80) REVERT: I 538 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8554 (pp) REVERT: I 620 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8377 (p0) REVERT: I 850 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7483 (pp) REVERT: I 876 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: I 882 ILE cc_start: 0.8371 (mm) cc_final: 0.8102 (mp) REVERT: I 1321 GLU cc_start: 0.8123 (tp30) cc_final: 0.7889 (tp30) REVERT: J 325 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7891 (mmtt) REVERT: J 1189 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6629 (tpt) REVERT: A 405 MET cc_start: 0.0949 (ptt) cc_final: 0.0327 (ptt) REVERT: B 21 MET cc_start: -0.2695 (ptt) cc_final: -0.3100 (ptt) REVERT: B 341 MET cc_start: 0.7476 (tmm) cc_final: 0.6768 (tmm) REVERT: D 405 MET cc_start: 0.1330 (ptt) cc_final: 0.1023 (ppp) REVERT: F 21 MET cc_start: -0.0936 (mtp) cc_final: -0.2613 (ptm) REVERT: F 147 MET cc_start: -0.2174 (OUTLIER) cc_final: -0.2455 (mmp) REVERT: F 245 MET cc_start: -0.1736 (ttt) cc_final: -0.2428 (ttt) outliers start: 143 outliers final: 94 residues processed: 539 average time/residue: 0.4859 time to fit residues: 433.0980 Evaluate side-chains 481 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 379 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 147 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 520 optimal weight: 5.9990 chunk 396 optimal weight: 20.0000 chunk 273 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 528 optimal weight: 50.0000 chunk 559 optimal weight: 40.0000 chunk 276 optimal weight: 3.9990 chunk 501 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN K 93 GLN K 147 GLN I 618 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 47717 Z= 0.262 Angle : 0.586 11.844 64682 Z= 0.303 Chirality : 0.043 0.209 7409 Planarity : 0.004 0.062 8210 Dihedral : 11.541 175.553 7188 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.12 % Allowed : 12.13 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5764 helix: 0.87 (0.11), residues: 2245 sheet: -1.32 (0.17), residues: 800 loop : -1.21 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.021 0.001 HIS F 42 PHE 0.015 0.001 PHE J1325 TYR 0.018 0.002 TYR J 631 ARG 0.006 0.000 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 415 time to evaluate : 3.974 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: W 16 ARG cc_start: 0.4970 (ttt90) cc_final: 0.4728 (ttp80) REVERT: H 195 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.4850 (mtp180) REVERT: I 445 ILE cc_start: 0.8460 (mt) cc_final: 0.8122 (mm) REVERT: I 514 PHE cc_start: 0.5826 (OUTLIER) cc_final: 0.5549 (t80) REVERT: I 694 ARG cc_start: 0.6695 (ptt180) cc_final: 0.6091 (ptp-170) REVERT: I 850 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7294 (mm) REVERT: I 1066 MET cc_start: 0.7886 (ttm) cc_final: 0.7629 (mmm) REVERT: I 1157 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: J 325 LYS cc_start: 0.8283 (mmtp) cc_final: 0.7926 (mmtt) REVERT: J 797 THR cc_start: 0.8414 (t) cc_final: 0.7433 (p) REVERT: J 1040 MET cc_start: 0.1324 (mmm) cc_final: -0.0514 (tpt) REVERT: J 1189 MET cc_start: 0.7076 (tpt) cc_final: 0.6539 (tpt) REVERT: C 405 MET cc_start: 0.3884 (ppp) cc_final: 0.3562 (pmm) REVERT: B 21 MET cc_start: -0.2852 (ptt) cc_final: -0.3259 (ptt) REVERT: B 341 MET cc_start: 0.7475 (tmm) cc_final: 0.6764 (tmm) REVERT: D 21 MET cc_start: 0.0431 (ptt) cc_final: -0.0142 (ptt) REVERT: D 405 MET cc_start: 0.1054 (ptt) cc_final: 0.0474 (ppp) REVERT: F 21 MET cc_start: -0.0933 (mtp) cc_final: -0.2799 (ptm) REVERT: F 147 MET cc_start: -0.2275 (mmp) cc_final: -0.2527 (mmp) REVERT: F 245 MET cc_start: -0.2032 (ttt) cc_final: -0.2620 (ttt) outliers start: 104 outliers final: 66 residues processed: 501 average time/residue: 0.4823 time to fit residues: 398.3989 Evaluate side-chains 460 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 390 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 466 optimal weight: 0.9980 chunk 317 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 416 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 477 optimal weight: 30.0000 chunk 386 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 285 optimal weight: 3.9990 chunk 502 optimal weight: 0.0470 chunk 141 optimal weight: 2.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN K 147 GLN H 103 ASN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 47717 Z= 0.366 Angle : 0.613 11.462 64682 Z= 0.318 Chirality : 0.045 0.226 7409 Planarity : 0.005 0.068 8210 Dihedral : 11.539 176.014 7187 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 2.77 % Allowed : 12.15 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5764 helix: 0.90 (0.11), residues: 2249 sheet: -1.21 (0.18), residues: 804 loop : -1.15 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 381 HIS 0.013 0.001 HIS F 42 PHE 0.017 0.001 PHE I 514 TYR 0.025 0.002 TYR E 274 ARG 0.008 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 396 time to evaluate : 3.960 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: W 16 ARG cc_start: 0.5191 (ttt90) cc_final: 0.4738 (ttp80) REVERT: H 195 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.4891 (mtp180) REVERT: I 445 ILE cc_start: 0.8438 (mt) cc_final: 0.8146 (mm) REVERT: I 538 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8575 (pp) REVERT: I 694 ARG cc_start: 0.6738 (ptt180) cc_final: 0.6203 (ptp-170) REVERT: I 850 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7497 (pp) REVERT: I 1033 ARG cc_start: 0.5938 (ttm-80) cc_final: 0.5662 (ttm170) REVERT: J 325 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7950 (mmtt) REVERT: J 797 THR cc_start: 0.8458 (t) cc_final: 0.7503 (p) REVERT: J 1040 MET cc_start: 0.1118 (mmm) cc_final: -0.0524 (tpt) REVERT: J 1189 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6586 (tpt) REVERT: C 245 MET cc_start: 0.7349 (mmm) cc_final: 0.7025 (mmp) REVERT: B 21 MET cc_start: -0.2944 (ptt) cc_final: -0.3351 (ptt) REVERT: B 341 MET cc_start: 0.7579 (tmm) cc_final: 0.6920 (tmm) REVERT: B 413 PHE cc_start: 0.2545 (OUTLIER) cc_final: 0.1154 (m-80) REVERT: D 21 MET cc_start: 0.0150 (ptt) cc_final: -0.0344 (ptt) REVERT: D 405 MET cc_start: 0.0950 (ptt) cc_final: 0.0441 (ppp) REVERT: E 390 MET cc_start: -0.1676 (ptt) cc_final: -0.2161 (ptt) REVERT: F 21 MET cc_start: -0.0947 (mtp) cc_final: -0.2629 (ptm) REVERT: F 147 MET cc_start: -0.2188 (mmp) cc_final: -0.2537 (mmp) REVERT: F 245 MET cc_start: -0.1954 (ttt) cc_final: -0.2412 (ttt) outliers start: 136 outliers final: 97 residues processed: 510 average time/residue: 0.4723 time to fit residues: 399.0421 Evaluate side-chains 482 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 380 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 188 optimal weight: 0.5980 chunk 504 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 328 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 560 optimal weight: 10.0000 chunk 465 optimal weight: 50.0000 chunk 259 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN K 147 GLN I 618 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS D 388 HIS E 172 GLN F 42 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47717 Z= 0.179 Angle : 0.535 11.236 64682 Z= 0.276 Chirality : 0.042 0.204 7409 Planarity : 0.004 0.051 8210 Dihedral : 11.351 175.608 7185 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.10 % Allowed : 13.07 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5764 helix: 1.12 (0.11), residues: 2252 sheet: -1.02 (0.17), residues: 836 loop : -1.03 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 381 HIS 0.008 0.001 HIS D 388 PHE 0.018 0.001 PHE I 514 TYR 0.018 0.001 TYR A 332 ARG 0.010 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 401 time to evaluate : 4.011 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: W 16 ARG cc_start: 0.5141 (ttt90) cc_final: 0.4814 (ttp80) REVERT: H 195 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.4827 (mtp180) REVERT: I 445 ILE cc_start: 0.8437 (mt) cc_final: 0.8169 (mm) REVERT: I 538 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8532 (pp) REVERT: I 694 ARG cc_start: 0.6553 (ptt180) cc_final: 0.6039 (ptp-170) REVERT: I 850 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7254 (mm) REVERT: I 882 ILE cc_start: 0.8114 (mt) cc_final: 0.7892 (mt) REVERT: I 1033 ARG cc_start: 0.5845 (ttm-80) cc_final: 0.5569 (ttm170) REVERT: I 1329 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7180 (mt-10) REVERT: J 653 ILE cc_start: 0.6916 (mt) cc_final: 0.6617 (mm) REVERT: J 797 THR cc_start: 0.8440 (t) cc_final: 0.7399 (p) REVERT: J 1040 MET cc_start: 0.0888 (mmm) cc_final: -0.1331 (ttt) REVERT: J 1189 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6701 (tpt) REVERT: C 245 MET cc_start: 0.7403 (mmm) cc_final: 0.7022 (mmp) REVERT: C 405 MET cc_start: 0.3772 (ppp) cc_final: 0.3387 (pmm) REVERT: A 405 MET cc_start: 0.1438 (ptt) cc_final: -0.0209 (ppp) REVERT: B 21 MET cc_start: -0.3201 (ptt) cc_final: -0.3490 (ptt) REVERT: B 332 TYR cc_start: 0.7608 (t80) cc_final: 0.7375 (t80) REVERT: B 341 MET cc_start: 0.7502 (tmm) cc_final: 0.6882 (tmm) REVERT: B 413 PHE cc_start: 0.2382 (OUTLIER) cc_final: 0.1076 (m-80) REVERT: D 21 MET cc_start: 0.0192 (ptt) cc_final: -0.0211 (ptt) REVERT: D 405 MET cc_start: 0.1009 (ptt) cc_final: 0.0518 (ppp) REVERT: E 390 MET cc_start: -0.1840 (ptt) cc_final: -0.2303 (ptt) REVERT: F 21 MET cc_start: -0.0859 (mtp) cc_final: -0.2736 (ptm) REVERT: F 147 MET cc_start: -0.2165 (mmp) cc_final: -0.2516 (mmp) REVERT: F 245 MET cc_start: -0.2006 (ttt) cc_final: -0.2424 (ttt) outliers start: 103 outliers final: 68 residues processed: 487 average time/residue: 0.4790 time to fit residues: 386.7786 Evaluate side-chains 455 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 382 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 540 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 chunk 316 optimal weight: 40.0000 chunk 471 optimal weight: 8.9990 chunk 312 optimal weight: 30.0000 chunk 558 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 chunk 257 optimal weight: 0.0470 overall best weight: 2.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 147 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS D 42 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 47717 Z= 0.295 Angle : 0.585 11.106 64682 Z= 0.301 Chirality : 0.043 0.215 7409 Planarity : 0.004 0.063 8210 Dihedral : 11.385 175.867 7185 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.70 % Rotamer: Outliers : 2.16 % Allowed : 13.50 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5764 helix: 1.09 (0.11), residues: 2252 sheet: -0.89 (0.18), residues: 816 loop : -1.01 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 381 HIS 0.012 0.001 HIS B 295 PHE 0.024 0.001 PHE I 514 TYR 0.027 0.002 TYR E 274 ARG 0.010 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 390 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 167 MET cc_start: 0.6188 (ppp) cc_final: 0.5868 (tmm) REVERT: W 16 ARG cc_start: 0.5171 (ttt90) cc_final: 0.4822 (ttp80) REVERT: H 195 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.4883 (mtp180) REVERT: I 445 ILE cc_start: 0.8440 (mt) cc_final: 0.8147 (mm) REVERT: I 538 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8553 (pp) REVERT: I 694 ARG cc_start: 0.6754 (ptt180) cc_final: 0.6166 (ptp-170) REVERT: I 850 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7294 (mm) REVERT: I 1033 ARG cc_start: 0.5981 (ttm-80) cc_final: 0.5724 (ttm170) REVERT: J 797 THR cc_start: 0.8473 (t) cc_final: 0.7488 (p) REVERT: J 1040 MET cc_start: 0.1346 (mmm) cc_final: -0.0353 (tpt) REVERT: J 1189 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6727 (tpt) REVERT: C 245 MET cc_start: 0.7475 (mmm) cc_final: 0.7111 (mmp) REVERT: C 380 MET cc_start: 0.5849 (ppp) cc_final: 0.5550 (ppp) REVERT: C 405 MET cc_start: 0.3703 (ppp) cc_final: 0.3329 (pmm) REVERT: A 405 MET cc_start: 0.1610 (ptt) cc_final: 0.0255 (ppp) REVERT: B 21 MET cc_start: -0.3333 (ptt) cc_final: -0.3769 (ptt) REVERT: B 332 TYR cc_start: 0.7633 (t80) cc_final: 0.7379 (t80) REVERT: B 341 MET cc_start: 0.7438 (tmm) cc_final: 0.6947 (tmm) REVERT: B 413 PHE cc_start: 0.2334 (OUTLIER) cc_final: 0.0943 (m-80) REVERT: D 21 MET cc_start: 0.0279 (ptt) cc_final: -0.0055 (ptt) REVERT: D 405 MET cc_start: 0.1038 (ptt) cc_final: 0.0499 (ppp) REVERT: F 21 MET cc_start: -0.0831 (mtp) cc_final: -0.2824 (ptm) REVERT: F 147 MET cc_start: -0.2140 (mmp) cc_final: -0.2502 (mmp) REVERT: F 245 MET cc_start: -0.2022 (ttt) cc_final: -0.2424 (ttt) outliers start: 106 outliers final: 86 residues processed: 479 average time/residue: 0.4754 time to fit residues: 378.9693 Evaluate side-chains 467 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 376 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 326 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 345 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 333 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 354 optimal weight: 9.9990 chunk 380 optimal weight: 7.9990 chunk 275 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 438 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 47717 Z= 0.359 Angle : 0.614 11.199 64682 Z= 0.317 Chirality : 0.045 0.206 7409 Planarity : 0.005 0.068 8210 Dihedral : 11.414 175.841 7185 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.52 % Allowed : 13.50 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5764 helix: 1.06 (0.11), residues: 2245 sheet: -0.90 (0.18), residues: 829 loop : -0.99 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 381 HIS 0.019 0.001 HIS B 295 PHE 0.031 0.001 PHE D 412 TYR 0.030 0.002 TYR E 274 ARG 0.011 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 391 time to evaluate : 4.056 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: G 167 MET cc_start: 0.6105 (ppp) cc_final: 0.5876 (tmm) REVERT: W 16 ARG cc_start: 0.5176 (ttt90) cc_final: 0.4815 (ttp80) REVERT: H 195 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.4875 (mtp180) REVERT: I 445 ILE cc_start: 0.8413 (mt) cc_final: 0.8092 (mm) REVERT: I 538 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8570 (pp) REVERT: I 694 ARG cc_start: 0.6668 (ptt180) cc_final: 0.6181 (ptp-170) REVERT: I 850 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7506 (pp) REVERT: I 1033 ARG cc_start: 0.6042 (ttm-80) cc_final: 0.5795 (ttm170) REVERT: J 797 THR cc_start: 0.8487 (t) cc_final: 0.7526 (p) REVERT: J 1040 MET cc_start: 0.1406 (mmm) cc_final: -0.0258 (tpt) REVERT: J 1189 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6750 (tpt) REVERT: C 245 MET cc_start: 0.7488 (mmm) cc_final: 0.7128 (mmp) REVERT: C 390 MET cc_start: 0.4438 (ppp) cc_final: 0.4198 (ppp) REVERT: C 405 MET cc_start: 0.3868 (ppp) cc_final: 0.3579 (pmm) REVERT: A 380 MET cc_start: 0.4807 (mmm) cc_final: 0.4527 (mmt) REVERT: A 405 MET cc_start: 0.1283 (ptt) cc_final: -0.0085 (ppp) REVERT: B 21 MET cc_start: -0.3350 (ptt) cc_final: -0.3768 (ptt) REVERT: B 186 MET cc_start: 0.4909 (mpp) cc_final: 0.4674 (mtm) REVERT: B 332 TYR cc_start: 0.7693 (t80) cc_final: 0.7473 (t80) REVERT: B 413 PHE cc_start: 0.2320 (OUTLIER) cc_final: 0.1077 (m-80) REVERT: D 21 MET cc_start: 0.0275 (ptt) cc_final: -0.0048 (ptt) REVERT: D 405 MET cc_start: 0.1154 (ptt) cc_final: 0.0730 (ppp) REVERT: F 21 MET cc_start: -0.0637 (mtp) cc_final: -0.2753 (ptm) REVERT: F 147 MET cc_start: -0.2137 (mmp) cc_final: -0.2501 (mmp) REVERT: F 245 MET cc_start: -0.2026 (ttt) cc_final: -0.2420 (ttt) outliers start: 124 outliers final: 105 residues processed: 491 average time/residue: 0.4779 time to fit residues: 391.0608 Evaluate side-chains 490 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 380 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 507 optimal weight: 30.0000 chunk 534 optimal weight: 40.0000 chunk 487 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 313 optimal weight: 0.6980 chunk 226 optimal weight: 4.9990 chunk 408 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 469 optimal weight: 30.0000 chunk 491 optimal weight: 0.9980 chunk 518 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1017 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 47717 Z= 0.427 Angle : 0.656 11.139 64682 Z= 0.339 Chirality : 0.046 0.283 7409 Planarity : 0.005 0.077 8210 Dihedral : 11.494 175.804 7185 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.59 % Allowed : 13.52 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 5764 helix: 0.94 (0.11), residues: 2248 sheet: -0.89 (0.18), residues: 827 loop : -1.02 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 381 HIS 0.007 0.001 HIS I 551 PHE 0.026 0.002 PHE I 514 TYR 0.030 0.002 TYR E 274 ARG 0.012 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 379 time to evaluate : 4.166 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: W 16 ARG cc_start: 0.5253 (ttt90) cc_final: 0.4716 (ttp80) REVERT: K 7 GLU cc_start: 0.5276 (tt0) cc_final: 0.4341 (mt-10) REVERT: H 195 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.4899 (mtp180) REVERT: I 445 ILE cc_start: 0.8441 (mt) cc_final: 0.8119 (mm) REVERT: I 538 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8592 (pp) REVERT: I 647 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7224 (ttp-110) REVERT: I 694 ARG cc_start: 0.6653 (ptt180) cc_final: 0.6248 (ptp-170) REVERT: I 850 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7472 (pp) REVERT: J 256 ASP cc_start: 0.5317 (t0) cc_final: 0.4686 (p0) REVERT: J 797 THR cc_start: 0.8545 (t) cc_final: 0.7653 (p) REVERT: J 1040 MET cc_start: 0.1636 (mmm) cc_final: -0.0543 (tpt) REVERT: J 1189 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6817 (tpt) REVERT: J 1311 LYS cc_start: 0.8360 (tptt) cc_final: 0.8157 (tptt) REVERT: C 245 MET cc_start: 0.7518 (mmm) cc_final: 0.7143 (mmp) REVERT: C 390 MET cc_start: 0.4607 (ppp) cc_final: 0.4362 (ppp) REVERT: C 405 MET cc_start: 0.3940 (ppp) cc_final: 0.3557 (mpp) REVERT: A 380 MET cc_start: 0.4698 (mmm) cc_final: 0.4491 (mmt) REVERT: A 405 MET cc_start: 0.1349 (ptt) cc_final: -0.0004 (ppp) REVERT: B 21 MET cc_start: -0.3285 (ptt) cc_final: -0.3716 (ptt) REVERT: B 341 MET cc_start: 0.7723 (tmm) cc_final: 0.6893 (tmm) REVERT: B 413 PHE cc_start: 0.2379 (OUTLIER) cc_final: 0.0975 (m-80) REVERT: D 405 MET cc_start: 0.1451 (ptt) cc_final: 0.1138 (ppp) REVERT: D 415 MET cc_start: 0.3938 (ppp) cc_final: 0.3639 (ppp) REVERT: E 405 MET cc_start: 0.3323 (ppp) cc_final: 0.1823 (pmm) REVERT: F 21 MET cc_start: -0.0696 (mtp) cc_final: -0.2873 (ptm) REVERT: F 147 MET cc_start: -0.2128 (mmp) cc_final: -0.2485 (mmp) REVERT: F 245 MET cc_start: -0.2035 (ttt) cc_final: -0.2401 (ttt) outliers start: 127 outliers final: 108 residues processed: 482 average time/residue: 0.4832 time to fit residues: 389.5297 Evaluate side-chains 490 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 377 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 326 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 341 optimal weight: 0.5980 chunk 549 optimal weight: 50.0000 chunk 335 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 382 optimal weight: 7.9990 chunk 576 optimal weight: 50.0000 chunk 530 optimal weight: 3.9990 chunk 459 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 354 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 47717 Z= 0.236 Angle : 0.588 13.043 64682 Z= 0.301 Chirality : 0.043 0.241 7409 Planarity : 0.004 0.055 8210 Dihedral : 11.373 175.288 7185 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.89 % Allowed : 14.25 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 5764 helix: 1.09 (0.11), residues: 2250 sheet: -0.74 (0.18), residues: 831 loop : -0.95 (0.12), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 381 HIS 0.006 0.001 HIS J 104 PHE 0.018 0.001 PHE I 514 TYR 0.018 0.002 TYR A 332 ARG 0.013 0.000 ARG A 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 387 time to evaluate : 4.012 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: W 16 ARG cc_start: 0.5202 (ttt90) cc_final: 0.4812 (ttp80) REVERT: K 7 GLU cc_start: 0.5214 (tt0) cc_final: 0.4304 (mt-10) REVERT: H 195 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.4807 (mtp180) REVERT: I 445 ILE cc_start: 0.8415 (mt) cc_final: 0.8126 (mm) REVERT: I 538 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8567 (pp) REVERT: I 647 ARG cc_start: 0.7421 (ttm170) cc_final: 0.7217 (ttp-110) REVERT: I 850 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7269 (mm) REVERT: J 256 ASP cc_start: 0.5736 (t0) cc_final: 0.4613 (p0) REVERT: J 797 THR cc_start: 0.8458 (t) cc_final: 0.7455 (p) REVERT: J 1040 MET cc_start: 0.1662 (mmm) cc_final: -0.0015 (tpt) REVERT: J 1189 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6812 (tpt) REVERT: C 245 MET cc_start: 0.7484 (mmm) cc_final: 0.7078 (mmp) REVERT: C 341 MET cc_start: 0.6168 (ppp) cc_final: 0.5891 (ppp) REVERT: C 405 MET cc_start: 0.3780 (ppp) cc_final: 0.3519 (mpp) REVERT: A 405 MET cc_start: 0.1431 (ptt) cc_final: 0.0050 (ppp) REVERT: A 416 MET cc_start: 0.6508 (mmm) cc_final: 0.5804 (mmp) REVERT: B 21 MET cc_start: -0.3316 (ptt) cc_final: -0.3745 (ptt) REVERT: B 332 TYR cc_start: 0.7597 (t80) cc_final: 0.7369 (t80) REVERT: B 341 MET cc_start: 0.7673 (tmm) cc_final: 0.6663 (tmm) REVERT: B 413 PHE cc_start: 0.2386 (OUTLIER) cc_final: 0.1071 (m-80) REVERT: D 405 MET cc_start: 0.1432 (ptt) cc_final: 0.1118 (ppp) REVERT: D 415 MET cc_start: 0.3791 (ppp) cc_final: 0.3549 (ppp) REVERT: E 396 MET cc_start: 0.2114 (ptm) cc_final: 0.1880 (ppp) REVERT: E 405 MET cc_start: 0.3511 (ppp) cc_final: 0.1992 (pmm) REVERT: F 21 MET cc_start: -0.0747 (mtp) cc_final: -0.2878 (ptm) REVERT: F 147 MET cc_start: -0.2172 (mmp) cc_final: -0.2531 (mmp) REVERT: F 245 MET cc_start: -0.2008 (ttt) cc_final: -0.2333 (ttt) outliers start: 93 outliers final: 78 residues processed: 461 average time/residue: 0.4915 time to fit residues: 378.2722 Evaluate side-chains 458 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 375 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 364 optimal weight: 5.9990 chunk 489 optimal weight: 20.0000 chunk 140 optimal weight: 0.3980 chunk 423 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 127 optimal weight: 0.0000 chunk 460 optimal weight: 6.9990 chunk 192 optimal weight: 0.1980 chunk 472 optimal weight: 50.0000 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 108 GLN G 112 GLN G 116 GLN K 147 GLN H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS D 25 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 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 = 0.4507 r_free = 0.4507 target = 0.211425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.205616 restraints weight = 67777.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.204787 restraints weight = 108012.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.203807 restraints weight = 112154.189| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5228 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 47717 Z= 0.163 Angle : 0.560 12.477 64682 Z= 0.284 Chirality : 0.042 0.296 7409 Planarity : 0.004 0.051 8210 Dihedral : 11.256 175.294 7185 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.65 % Allowed : 14.56 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5764 helix: 1.24 (0.11), residues: 2255 sheet: -0.57 (0.18), residues: 821 loop : -0.88 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 381 HIS 0.006 0.001 HIS J 104 PHE 0.014 0.001 PHE I 514 TYR 0.021 0.001 TYR C 80 ARG 0.013 0.000 ARG A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8046.80 seconds wall clock time: 141 minutes 6.41 seconds (8466.41 seconds total)