Starting phenix.real_space_refine on Tue Sep 15 13:11:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k1n_22626/09_2026/7k1n_22626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1n_22626/09_2026/7k1n_22626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k1n_22626/09_2026/7k1n_22626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1n_22626/09_2026/7k1n_22626.map" model { file = "/net/cci-nas-00/data/ceres_data/7k1n_22626/09_2026/7k1n_22626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1n_22626/09_2026/7k1n_22626.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 71 5.49 5 S 230 5.16 5 C 25099 2.51 5 N 6709 2.21 5 O 7412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39521 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 28808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3634, 28808 Classifications: {'peptide': 3634} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 1, 'PTRANS': 153, 'TRANS': 3479} Chain breaks: 19 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 30, 'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'TYR:plan': 3, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 208 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3954 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5251 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 7.98, per 1000 atoms: 0.20 Number of scatterers: 39521 At special positions: 0 Unit cell: (134.56, 178.64, 235.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 71 15.00 O 7412 8.00 N 6709 7.00 C 25099 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9166 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 12 sheets defined 58.0% alpha, 4.1% beta 36 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 25 through 42 Processing helix chain 'A' and resid 47 through 58 removed outlier: 3.895A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.712A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.733A pdb=" N ASP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.905A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.222A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.557A pdb=" N PHE A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.526A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.667A pdb=" N LEU A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 4.158A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.698A pdb=" N ARG A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.629A pdb=" N PHE A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.552A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.695A pdb=" N VAL A 375 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.733A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 4.267A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.049A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 478 through 491 removed outlier: 4.010A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 534 removed outlier: 4.206A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.997A pdb=" N MET A 540 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 removed outlier: 3.959A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.525A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.815A pdb=" N ALA A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.083A pdb=" N SER A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.846A pdb=" N TYR A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 749 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 752 through 758 removed outlier: 3.732A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.044A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.716A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.885A pdb=" N LYS A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 Processing helix chain 'A' and resid 847 through 862 removed outlier: 3.991A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 878 through 882 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.872A pdb=" N VAL A 914 " --> pdb=" O PHE A 910 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 3.888A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.425A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 974 Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 984 through 996 removed outlier: 3.883A pdb=" N ILE A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS A 993 " --> pdb=" O MET A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 removed outlier: 3.715A pdb=" N PHE A1001 " --> pdb=" O ASN A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 4.057A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1008 " --> pdb=" O GLN A1004 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1043 removed outlier: 4.316A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A1043 " --> pdb=" O TRP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1072 through 1086 removed outlier: 4.168A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 removed outlier: 6.394A pdb=" N VAL A1105 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1142 removed outlier: 3.694A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A1139 " --> pdb=" O CYS A1135 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 removed outlier: 3.686A pdb=" N VAL A1169 " --> pdb=" O LEU A1165 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1170 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1193 removed outlier: 3.829A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1198 removed outlier: 3.909A pdb=" N LEU A1197 " --> pdb=" O PHE A1194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A1198 " --> pdb=" O VAL A1195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1194 through 1198' Processing helix chain 'A' and resid 1203 through 1213 removed outlier: 4.465A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1226 removed outlier: 3.807A pdb=" N THR A1223 " --> pdb=" O PHE A1219 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1250 through 1271 removed outlier: 4.293A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A1270 " --> pdb=" O CYS A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 removed outlier: 3.812A pdb=" N ALA A1295 " --> pdb=" O LEU A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1350 removed outlier: 3.762A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A1349 " --> pdb=" O THR A1345 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A1350 " --> pdb=" O THR A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.423A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1408 Proline residue: A1396 - end of helix removed outlier: 4.399A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1420 Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1442 through 1462 removed outlier: 4.159A pdb=" N VAL A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1491 removed outlier: 3.986A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1518 Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1556 through 1564 removed outlier: 4.085A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1572 Processing helix chain 'A' and resid 1578 through 1585 removed outlier: 3.897A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.685A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1624 removed outlier: 3.581A pdb=" N LYS A1617 " --> pdb=" O HIS A1613 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A1619 " --> pdb=" O GLY A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1629 Processing helix chain 'A' and resid 1640 through 1656 removed outlier: 3.535A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1681 removed outlier: 4.846A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A1679 " --> pdb=" O TYR A1675 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1689 removed outlier: 3.519A pdb=" N LYS A1689 " --> pdb=" O LEU A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1722 removed outlier: 4.375A pdb=" N GLU A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1753 removed outlier: 4.127A pdb=" N LYS A1745 " --> pdb=" O ASP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.606A pdb=" N LEU A1759 " --> pdb=" O SER A1755 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 Processing helix chain 'A' and resid 1793 through 1807 removed outlier: 3.607A pdb=" N LYS A1807 " --> pdb=" O GLU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.857A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1831 removed outlier: 3.859A pdb=" N CYS A1831 " --> pdb=" O LEU A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 3.594A pdb=" N ALA A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 3.505A pdb=" N PHE A1863 " --> pdb=" O ASN A1859 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1909 through 1922 removed outlier: 3.813A pdb=" N LYS A1913 " --> pdb=" O ASN A1909 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1953 Processing helix chain 'A' and resid 1960 through 1965 Processing helix chain 'A' and resid 1970 through 1974 Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.704A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2037 through 2046 removed outlier: 4.498A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP A2044 " --> pdb=" O MET A2040 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A2046 " --> pdb=" O GLN A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2126 through 2135 removed outlier: 4.191A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2146 removed outlier: 3.512A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2146 through 2151 removed outlier: 4.177A pdb=" N VAL A2150 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.841A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2174 removed outlier: 3.546A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2195 Processing helix chain 'A' and resid 2207 through 2222 removed outlier: 3.971A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 3.886A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A2232 " --> pdb=" O ARG A2228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS A2233 " --> pdb=" O ALA A2229 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A2246 " --> pdb=" O VAL A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2284 removed outlier: 3.703A pdb=" N ILE A2274 " --> pdb=" O ASN A2270 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A2284 " --> pdb=" O VAL A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 3.874A pdb=" N TYR A2299 " --> pdb=" O GLN A2295 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 3.746A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A2317 " --> pdb=" O LYS A2313 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2351 removed outlier: 3.761A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2403 removed outlier: 4.244A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS A2403 " --> pdb=" O GLU A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2423 Processing helix chain 'A' and resid 2429 through 2442 removed outlier: 4.075A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A2439 " --> pdb=" O CYS A2435 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A2441 " --> pdb=" O ASP A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 4.007A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2464 removed outlier: 4.014A pdb=" N SER A2463 " --> pdb=" O GLU A2460 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A2464 " --> pdb=" O PHE A2461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2460 through 2464' Processing helix chain 'A' and resid 2466 through 2484 removed outlier: 3.778A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A2482 " --> pdb=" O MET A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2507 removed outlier: 3.984A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A2506 " --> pdb=" O ALA A2502 " (cutoff:3.500A) Processing helix chain 'A' and resid 2517 through 2526 removed outlier: 3.844A pdb=" N ILE A2521 " --> pdb=" O LEU A2517 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2542 Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.376A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2566 through 2569 Processing helix chain 'A' and resid 2787 through 2799 removed outlier: 3.774A pdb=" N ILE A2791 " --> pdb=" O HIS A2787 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A2792 " --> pdb=" O SER A2788 " (cutoff:3.500A) Proline residue: A2793 - end of helix removed outlier: 3.664A pdb=" N ALA A2798 " --> pdb=" O LEU A2794 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.986A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 4.086A pdb=" N LYS A2829 " --> pdb=" O THR A2825 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2862 removed outlier: 4.130A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) Processing helix chain 'A' and resid 2863 through 2865 No H-bonds generated for 'chain 'A' and resid 2863 through 2865' Processing helix chain 'A' and resid 2866 through 2870 removed outlier: 3.997A pdb=" N LEU A2869 " --> pdb=" O ALA A2866 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2866 through 2870' Processing helix chain 'A' and resid 2875 through 2884 removed outlier: 4.071A pdb=" N ALA A2882 " --> pdb=" O ALA A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.914A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2931 removed outlier: 4.977A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2941 Processing helix chain 'A' and resid 2952 through 2962 removed outlier: 4.075A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2972 through 2977 Processing helix chain 'A' and resid 2992 through 3004 Processing helix chain 'A' and resid 3008 through 3017 removed outlier: 3.567A pdb=" N GLU A3012 " --> pdb=" O TRP A3008 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3027 through 3032 removed outlier: 3.835A pdb=" N TRP A3031 " --> pdb=" O LEU A3027 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.734A pdb=" N THR A3039 " --> pdb=" O PHE A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3053 removed outlier: 3.833A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.567A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3094 Processing helix chain 'A' and resid 3095 through 3115 Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3146 Processing helix chain 'A' and resid 3148 through 3153 removed outlier: 3.648A pdb=" N LEU A3151 " --> pdb=" O GLN A3148 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A3153 " --> pdb=" O ASN A3150 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3167 removed outlier: 3.611A pdb=" N ARG A3167 " --> pdb=" O THR A3163 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.638A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3229 through 3249 removed outlier: 3.957A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3252 through 3263 removed outlier: 3.840A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A3258 " --> pdb=" O LEU A3254 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3287 Processing helix chain 'A' and resid 3292 through 3306 removed outlier: 4.486A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A3304 " --> pdb=" O VAL A3300 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3307 through 3309 No H-bonds generated for 'chain 'A' and resid 3307 through 3309' Processing helix chain 'A' and resid 3320 through 3341 removed outlier: 3.671A pdb=" N ARG A3324 " --> pdb=" O ILE A3320 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A3325 " --> pdb=" O LEU A3321 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A3341 " --> pdb=" O ILE A3337 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3362 removed outlier: 3.527A pdb=" N LEU A3362 " --> pdb=" O ARG A3358 " (cutoff:3.500A) Processing helix chain 'A' and resid 3373 through 3391 removed outlier: 4.127A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A3390 " --> pdb=" O SER A3386 " (cutoff:3.500A) Processing helix chain 'A' and resid 3408 through 3428 removed outlier: 3.659A pdb=" N ALA A3412 " --> pdb=" O GLY A3408 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3442 through 3455 removed outlier: 3.731A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 removed outlier: 3.748A pdb=" N LEU A3463 " --> pdb=" O ASN A3459 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.772A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3511 through 3514 Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3529 through 3537 removed outlier: 4.280A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3548 Processing helix chain 'A' and resid 3549 through 3562 removed outlier: 3.961A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3579 removed outlier: 3.911A pdb=" N SER A3579 " --> pdb=" O LEU A3575 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3596 removed outlier: 3.675A pdb=" N LYS A3586 " --> pdb=" O GLU A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3617 removed outlier: 4.924A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3643 through 3650 removed outlier: 3.698A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3651 through 3654 removed outlier: 3.937A pdb=" N MET A3654 " --> pdb=" O LEU A3651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3651 through 3654' Processing helix chain 'A' and resid 3660 through 3668 removed outlier: 3.575A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3673 removed outlier: 4.067A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A3673 " --> pdb=" O LYS A3669 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3668 through 3673' Processing helix chain 'A' and resid 3680 through 3684 removed outlier: 4.084A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) Processing helix chain 'A' and resid 3760 through 3775 Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.685A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3848 Processing helix chain 'A' and resid 3853 through 3859 removed outlier: 3.784A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 4.187A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3890 removed outlier: 3.863A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.855A pdb=" N LEU A3898 " --> pdb=" O PRO A3894 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A3904 " --> pdb=" O LEU A3900 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3965 through 3970 Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4012 through 4021 Processing helix chain 'A' and resid 4041 through 4052 Processing helix chain 'A' and resid 4057 through 4066 Processing helix chain 'A' and resid 4073 through 4081 removed outlier: 3.511A pdb=" N TYR A4077 " --> pdb=" O ALA A4073 " (cutoff:3.500A) Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.545A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.560A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4119 removed outlier: 3.853A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 4.042A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.746A pdb=" N ASP B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.778A pdb=" N GLY B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 377 through 393 removed outlier: 3.997A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.870A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 492 Processing helix chain 'B' and resid 510 through 519 removed outlier: 4.443A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 530 removed outlier: 4.286A pdb=" N VAL B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 48 removed outlier: 3.836A pdb=" N GLN C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 removed outlier: 4.054A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 4.127A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.710A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 595 through 599 removed outlier: 3.978A pdb=" N ARG C 599 " --> pdb=" O GLU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.660A pdb=" N ILE C 617 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN C 618 " --> pdb=" O ASN C 614 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 622 " --> pdb=" O ASN C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 631 through 640 removed outlier: 4.194A pdb=" N SER C 635 " --> pdb=" O TYR C 631 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 636 " --> pdb=" O PHE C 632 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP C 637 " --> pdb=" O MET C 633 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 removed outlier: 3.543A pdb=" N ASN C 656 " --> pdb=" O GLU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 668 removed outlier: 3.756A pdb=" N LYS C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 680 removed outlier: 4.019A pdb=" N ILE C 677 " --> pdb=" O HIS C 673 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 726 through 732 removed outlier: 3.748A pdb=" N ASP C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET C 731 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 732' Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 894 Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 4.042A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.567A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.446A pdb=" N ASP B 36 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ALA B 84 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 38 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 88 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 42 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 removed outlier: 4.182A pdb=" N LEU B 366 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 434 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 349 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA8, first strand: chain 'B' and resid 299 through 303 Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.688A pdb=" N ARG B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 250 removed outlier: 3.679A pdb=" N ALA C 366 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR C 264 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL C 364 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA C 366 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLU C 417 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS C 339 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 464 through 465 1638 hydrogen bonds defined for protein. 4803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 15.45 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9751 1.33 - 1.45: 8075 1.45 - 1.57: 22134 1.57 - 1.70: 142 1.70 - 1.82: 363 Bond restraints: 40465 Sorted by residual: bond pdb=" CA ALA A 610 " pdb=" C ALA A 610 " ideal model delta sigma weight residual 1.522 1.586 -0.064 1.72e-02 3.38e+03 1.39e+01 bond pdb=" C3' DG D 13 " pdb=" O3' DG D 13 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DG F 24 " pdb=" O3' DG F 24 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C3' DA G 29 " pdb=" C2' DA G 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 bond pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.87e+00 ... (remaining 40460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 54541 4.49 - 8.99: 412 8.99 - 13.48: 37 13.48 - 17.98: 4 17.98 - 22.47: 2 Bond angle restraints: 54996 Sorted by residual: angle pdb=" C GLU A 214 " pdb=" N PRO A 215 " pdb=" CA PRO A 215 " ideal model delta sigma weight residual 119.84 134.39 -14.55 1.25e+00 6.40e-01 1.36e+02 angle pdb=" C PRO A2887 " pdb=" CA PRO A2887 " pdb=" CB PRO A2887 " ideal model delta sigma weight residual 112.62 131.41 -18.79 1.65e+00 3.67e-01 1.30e+02 angle pdb=" N ASN A3311 " pdb=" CA ASN A3311 " pdb=" C ASN A3311 " ideal model delta sigma weight residual 110.80 88.33 22.47 2.13e+00 2.20e-01 1.11e+02 angle pdb=" N ASN A 739 " pdb=" CA ASN A 739 " pdb=" C ASN A 739 " ideal model delta sigma weight residual 113.72 101.29 12.43 1.30e+00 5.92e-01 9.14e+01 angle pdb=" O LEU A1475 " pdb=" C LEU A1475 " pdb=" N HIS A1476 " ideal model delta sigma weight residual 122.07 129.70 -7.63 1.03e+00 9.43e-01 5.49e+01 ... (remaining 54991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 21019 17.79 - 35.57: 2622 35.57 - 53.36: 676 53.36 - 71.14: 160 71.14 - 88.93: 28 Dihedral angle restraints: 24505 sinusoidal: 10452 harmonic: 14053 Sorted by residual: dihedral pdb=" C PRO A2887 " pdb=" N PRO A2887 " pdb=" CA PRO A2887 " pdb=" CB PRO A2887 " ideal model delta harmonic sigma weight residual -120.70 -145.77 25.07 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" N PRO A2887 " pdb=" C PRO A2887 " pdb=" CA PRO A2887 " pdb=" CB PRO A2887 " ideal model delta harmonic sigma weight residual 115.10 133.00 -17.90 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" CA LEU B 243 " pdb=" C LEU B 243 " pdb=" N ARG B 244 " pdb=" CA ARG B 244 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 24502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 6227 0.201 - 0.402: 24 0.402 - 0.604: 4 0.604 - 0.805: 0 0.805 - 1.006: 1 Chirality restraints: 6256 Sorted by residual: chirality pdb=" CA PRO A2887 " pdb=" N PRO A2887 " pdb=" C PRO A2887 " pdb=" CB PRO A2887 " both_signs ideal model delta sigma weight residual False 2.72 1.71 1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" CA ASN A3311 " pdb=" N ASN A3311 " pdb=" C ASN A3311 " pdb=" CB ASN A3311 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CB ILE A2336 " pdb=" CA ILE A2336 " pdb=" CG1 ILE A2336 " pdb=" CG2 ILE A2336 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 6253 not shown) Planarity restraints: 6740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2182 " -0.027 2.00e-02 2.50e+03 5.66e-02 3.21e+01 pdb=" C ILE A2182 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE A2182 " -0.038 2.00e-02 2.50e+03 pdb=" N HIS A2183 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 244 " -0.022 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C ARG B 244 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG B 244 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS B 245 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 215 " -0.022 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C LEU B 215 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU B 215 " -0.032 2.00e-02 2.50e+03 pdb=" N PHE B 216 " -0.026 2.00e-02 2.50e+03 ... (remaining 6737 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2476 2.72 - 3.27: 37987 3.27 - 3.81: 61888 3.81 - 4.36: 71776 4.36 - 4.90: 120489 Nonbonded interactions: 294616 Sorted by model distance: nonbonded pdb=" N ASN A3311 " pdb=" N VAL A3312 " model vdw 2.179 2.560 nonbonded pdb=" OG SER A 60 " pdb=" O PHE A 63 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR C 198 " pdb=" OE1 GLN C 201 " model vdw 2.261 3.040 nonbonded pdb=" O VAL A 646 " pdb=" OG SER A 650 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A1250 " pdb=" OG1 THR A1253 " model vdw 2.276 3.040 ... (remaining 294611 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 'D' and resid 4 through 24) selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 47.390 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.007 0.100 40465 Z= 0.346 Angle : 1.068 22.471 54996 Z= 0.605 Chirality : 0.061 1.006 6256 Planarity : 0.008 0.074 6740 Dihedral : 17.013 88.928 15339 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.23 % Favored : 86.37 % Rotamer: Outliers : 0.78 % Allowed : 10.80 % Favored : 88.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.09), residues: 4725 helix: -2.87 (0.07), residues: 2591 sheet: -1.94 (0.34), residues: 213 loop : -4.00 (0.11), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2377 TYR 0.032 0.003 TYR A2316 PHE 0.044 0.003 PHE A2260 TRP 0.027 0.003 TRP B 148 HIS 0.008 0.001 HIS A3643 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.35 (40465) covalent geometry : angle 1.06789 / 0.61 (54996) hydrogen bonds : bond 0.11322 / 7.79 ( 1728) hydrogen bonds : angle 6.04008 / 4.16 ( 4983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 529 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7021 (pttt) cc_final: 0.6700 (pttp) REVERT: A 520 LYS cc_start: 0.5992 (mmtp) cc_final: 0.5163 (mmtm) REVERT: A 1061 LYS cc_start: 0.8145 (mttp) cc_final: 0.7708 (mptt) REVERT: A 1361 LYS cc_start: 0.8225 (mmmm) cc_final: 0.7660 (mmtm) REVERT: A 1592 MET cc_start: 0.9043 (mmm) cc_final: 0.8563 (tpp) REVERT: A 1860 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 2189 ILE cc_start: 0.8986 (mt) cc_final: 0.8463 (pt) REVERT: A 2568 MET cc_start: 0.7519 (mpp) cc_final: 0.7175 (tpp) REVERT: A 2820 MET cc_start: 0.8727 (ptm) cc_final: 0.8524 (ttp) REVERT: A 3067 LYS cc_start: 0.7527 (mttp) cc_final: 0.6825 (tppt) REVERT: A 3577 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8137 (mp10) REVERT: A 3808 ASN cc_start: 0.8732 (t0) cc_final: 0.8222 (p0) REVERT: A 3895 GLU cc_start: 0.8417 (tp30) cc_final: 0.8133 (tp30) REVERT: A 3929 MET cc_start: 0.8324 (mtp) cc_final: 0.8059 (mtp) REVERT: A 3959 MET cc_start: 0.9323 (pmm) cc_final: 0.9023 (pmm) REVERT: A 3974 MET cc_start: 0.8175 (mpp) cc_final: 0.7848 (mpp) REVERT: B 135 MET cc_start: 0.7903 (ptp) cc_final: 0.7529 (ptp) REVERT: B 217 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5707 (m-10) REVERT: B 468 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7452 (ptpt) REVERT: B 497 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7750 (pt) REVERT: B 514 MET cc_start: 0.6581 (mtt) cc_final: 0.5885 (ptm) REVERT: C 234 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8287 (pp) outliers start: 33 outliers final: 13 residues processed: 559 average time/residue: 0.2529 time to fit residues: 232.0012 Evaluate side-chains 376 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 360 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 647 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 442 GLN A 485 GLN A 656 GLN A 720 GLN A 833 HIS A 935 HIS A1048 GLN A1098 GLN A1115 HIS ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 HIS A1350 ASN A1598 ASN A1610 ASN A1624 GLN A1770 GLN A1866 GLN A2103 HIS A2135 ASN A2222 HIS A2270 ASN A2283 ASN A2301 GLN A2305 ASN A2365 ASN A2432 GLN A2496 GLN A2885 GLN A3122 HIS A3251 ASN A3524 ASN A3643 HIS A3760 GLN A4015 ASN B 52 GLN B 152 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 360 HIS B 515 ASN C 256 ASN C 269 GLN C 411 HIS ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN C 619 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099613 restraints weight = 102490.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098923 restraints weight = 86426.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099311 restraints weight = 76853.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099658 restraints weight = 64888.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099995 restraints weight = 58106.133| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40465 Z= 0.188 Angle : 0.752 11.204 54996 Z= 0.392 Chirality : 0.045 0.239 6256 Planarity : 0.005 0.062 6740 Dihedral : 13.835 76.378 5936 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.95 % Favored : 86.96 % Rotamer: Outliers : 2.50 % Allowed : 14.96 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.11), residues: 4725 helix: -1.64 (0.09), residues: 2632 sheet: -1.85 (0.32), residues: 221 loop : -3.75 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 290 TYR 0.028 0.002 TYR A1940 PHE 0.026 0.002 PHE A2260 TRP 0.016 0.002 TRP A2196 HIS 0.006 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (40465) covalent geometry : angle 0.75164 / 0.39 (54996) hydrogen bonds : bond 0.04833 / 3.17 ( 1728) hydrogen bonds : angle 5.10793 / 3.50 ( 4983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 383 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.4855 (mtp) cc_final: 0.4177 (ttt) REVERT: A 384 MET cc_start: 0.8314 (mtm) cc_final: 0.8104 (mtp) REVERT: A 520 LYS cc_start: 0.5846 (mmtp) cc_final: 0.5143 (mmtm) REVERT: A 1061 LYS cc_start: 0.8267 (mttp) cc_final: 0.7800 (mptt) REVERT: A 1361 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7628 (mmtm) REVERT: A 1592 MET cc_start: 0.9122 (mmm) cc_final: 0.8696 (tpp) REVERT: A 1752 LEU cc_start: 0.8269 (pt) cc_final: 0.7831 (pt) REVERT: A 1860 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 2301 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: A 2305 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7775 (m110) REVERT: A 2545 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8585 (pp) REVERT: A 2568 MET cc_start: 0.7783 (mpp) cc_final: 0.7410 (tpp) REVERT: A 2812 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8564 (tt) REVERT: A 3067 LYS cc_start: 0.7502 (mttp) cc_final: 0.6884 (tppt) REVERT: A 3577 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8182 (mp10) REVERT: A 3808 ASN cc_start: 0.8739 (t0) cc_final: 0.8416 (t0) REVERT: A 3820 MET cc_start: 0.8345 (mtt) cc_final: 0.7978 (mmm) REVERT: A 3895 GLU cc_start: 0.8588 (tp30) cc_final: 0.8226 (tp30) REVERT: A 3929 MET cc_start: 0.8053 (mtp) cc_final: 0.7753 (mtp) REVERT: A 3974 MET cc_start: 0.8129 (mpp) cc_final: 0.7825 (mpp) REVERT: B 217 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5261 (m-10) REVERT: B 497 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 514 MET cc_start: 0.6474 (mtt) cc_final: 0.6080 (ptm) REVERT: C 234 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8160 (pp) REVERT: C 515 MET cc_start: 0.8098 (ttm) cc_final: 0.7879 (ttp) outliers start: 105 outliers final: 63 residues processed: 467 average time/residue: 0.2322 time to fit residues: 184.6543 Evaluate side-chains 412 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 342 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1207 TRP Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2305 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2480 ILE Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2812 LEU Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3724 GLU Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 647 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 409 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 472 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 276 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN A1866 GLN A2301 GLN A2305 ASN A3510 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.121842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100127 restraints weight = 102952.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099637 restraints weight = 81573.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099866 restraints weight = 83831.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100199 restraints weight = 70476.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100613 restraints weight = 59390.888| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40465 Z= 0.162 Angle : 0.698 10.767 54996 Z= 0.362 Chirality : 0.043 0.213 6256 Planarity : 0.005 0.059 6740 Dihedral : 13.623 74.649 5933 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.42 % Favored : 87.49 % Rotamer: Outliers : 2.85 % Allowed : 16.77 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.11), residues: 4725 helix: -1.15 (0.10), residues: 2633 sheet: -1.61 (0.33), residues: 221 loop : -3.64 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1837 TYR 0.025 0.001 TYR A1940 PHE 0.024 0.001 PHE A2260 TRP 0.014 0.001 TRP B 148 HIS 0.005 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (40465) covalent geometry : angle 0.69796 / 0.36 (54996) hydrogen bonds : bond 0.04405 / 2.89 ( 1728) hydrogen bonds : angle 4.89753 / 3.37 ( 4983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 372 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7825 (pp) REVERT: A 238 MET cc_start: 0.4499 (mtp) cc_final: 0.4009 (ttt) REVERT: A 520 LYS cc_start: 0.5750 (mmtp) cc_final: 0.5066 (mmtm) REVERT: A 1061 LYS cc_start: 0.8264 (mttp) cc_final: 0.7757 (mptt) REVERT: A 1361 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7605 (mmtm) REVERT: A 1507 CYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 1553 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8288 (p90) REVERT: A 1592 MET cc_start: 0.9087 (mmm) cc_final: 0.8847 (tpp) REVERT: A 1770 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7262 (pp30) REVERT: A 1933 LEU cc_start: 0.8539 (mm) cc_final: 0.8326 (mp) REVERT: A 2325 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7303 (mm) REVERT: A 2545 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8597 (pp) REVERT: A 2568 MET cc_start: 0.7690 (mpp) cc_final: 0.7409 (tpp) REVERT: A 2812 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 3067 LYS cc_start: 0.7497 (mttp) cc_final: 0.6885 (tppt) REVERT: A 3510 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: A 3577 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8216 (mp10) REVERT: A 3808 ASN cc_start: 0.8689 (t0) cc_final: 0.8381 (t0) REVERT: A 3820 MET cc_start: 0.8334 (mtt) cc_final: 0.7956 (mmm) REVERT: A 3895 GLU cc_start: 0.8615 (tp30) cc_final: 0.8289 (tp30) REVERT: A 3913 ILE cc_start: 0.7770 (tp) cc_final: 0.7494 (tt) REVERT: A 3929 MET cc_start: 0.7978 (mtp) cc_final: 0.7676 (mtp) REVERT: A 3932 MET cc_start: 0.8555 (mmm) cc_final: 0.8261 (mmm) REVERT: A 3974 MET cc_start: 0.8090 (mpp) cc_final: 0.7757 (mpp) REVERT: B 217 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5255 (m-10) REVERT: B 496 ASP cc_start: 0.8461 (m-30) cc_final: 0.8064 (m-30) REVERT: B 497 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8058 (pt) REVERT: B 514 MET cc_start: 0.6447 (mtt) cc_final: 0.6056 (ptm) REVERT: C 234 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8121 (pp) outliers start: 120 outliers final: 66 residues processed: 470 average time/residue: 0.2168 time to fit residues: 175.5098 Evaluate side-chains 421 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 344 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1207 TRP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1553 PHE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1770 GLN Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2480 ILE Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2812 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3724 GLU Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3793 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 647 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 335 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 344 optimal weight: 1.9990 chunk 314 optimal weight: 9.9990 chunk 465 optimal weight: 3.9990 chunk 431 optimal weight: 5.9990 chunk 367 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2177 ASN A2305 ASN A3028 ASN A3986 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098873 restraints weight = 104063.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098362 restraints weight = 86847.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098565 restraints weight = 80648.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099085 restraints weight = 65351.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099233 restraints weight = 57799.329| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40465 Z= 0.196 Angle : 0.719 12.155 54996 Z= 0.370 Chirality : 0.044 0.260 6256 Planarity : 0.005 0.059 6740 Dihedral : 13.558 75.687 5931 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.08 % Favored : 86.86 % Rotamer: Outliers : 3.42 % Allowed : 18.12 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.12), residues: 4725 helix: -0.90 (0.10), residues: 2624 sheet: -1.56 (0.34), residues: 222 loop : -3.56 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3653 TYR 0.030 0.002 TYR A3036 PHE 0.040 0.002 PHE A1814 TRP 0.015 0.002 TRP B 148 HIS 0.008 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (40465) covalent geometry : angle 0.71942 / 0.37 (54996) hydrogen bonds : bond 0.04451 / 2.92 ( 1728) hydrogen bonds : angle 4.90043 / 3.37 ( 4983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 347 time to evaluate : 1.537 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: A 73 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7937 (pp) REVERT: A 96 MET cc_start: 0.7402 (mpp) cc_final: 0.7183 (mpp) REVERT: A 396 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6158 (p90) REVERT: A 520 LYS cc_start: 0.5729 (mmtp) cc_final: 0.5038 (mmtm) REVERT: A 541 MET cc_start: 0.7861 (mmm) cc_final: 0.7608 (mmm) REVERT: A 785 MET cc_start: 0.8110 (tpt) cc_final: 0.7830 (tpp) REVERT: A 1018 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8376 (m) REVERT: A 1061 LYS cc_start: 0.8392 (mttp) cc_final: 0.7906 (mptt) REVERT: A 1361 LYS cc_start: 0.8350 (mmmm) cc_final: 0.7683 (mmtm) REVERT: A 1507 CYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 1592 MET cc_start: 0.9127 (mmm) cc_final: 0.8920 (tpp) REVERT: A 1927 MET cc_start: 0.8560 (mtt) cc_final: 0.8255 (mtt) REVERT: A 2325 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7406 (mm) REVERT: A 2545 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 2568 MET cc_start: 0.7897 (mpp) cc_final: 0.7427 (tpp) REVERT: A 2812 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 3067 LYS cc_start: 0.7505 (mttp) cc_final: 0.6853 (tppt) REVERT: A 3577 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8270 (mp10) REVERT: A 3718 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7822 (mtt90) REVERT: A 3808 ASN cc_start: 0.8735 (t0) cc_final: 0.8427 (t0) REVERT: A 3895 GLU cc_start: 0.8735 (tp30) cc_final: 0.8370 (tp30) REVERT: A 3913 ILE cc_start: 0.7822 (tp) cc_final: 0.7510 (tt) REVERT: A 3929 MET cc_start: 0.8083 (mtp) cc_final: 0.7734 (mtp) REVERT: A 3932 MET cc_start: 0.8569 (mmm) cc_final: 0.8240 (mmm) REVERT: B 217 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.5133 (m-10) REVERT: B 496 ASP cc_start: 0.8440 (m-30) cc_final: 0.8029 (m-30) REVERT: B 497 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8110 (pt) REVERT: B 514 MET cc_start: 0.6546 (mtt) cc_final: 0.6142 (ptm) REVERT: C 234 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8118 (pp) outliers start: 144 outliers final: 96 residues processed: 467 average time/residue: 0.2202 time to fit residues: 178.2768 Evaluate side-chains 438 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 332 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1207 TRP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1639 LEU Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2480 ILE Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2812 LEU Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3724 GLU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3788 LEU Chi-restraints excluded: chain A residue 3793 VAL Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4011 PHE Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 179 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 403 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 407 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 366 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN C 269 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100476 restraints weight = 103567.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099674 restraints weight = 95737.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100119 restraints weight = 79955.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100685 restraints weight = 64387.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100807 restraints weight = 56573.966| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40465 Z= 0.137 Angle : 0.677 14.527 54996 Z= 0.345 Chirality : 0.042 0.270 6256 Planarity : 0.004 0.056 6740 Dihedral : 13.396 76.563 5931 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.00 % Favored : 87.94 % Rotamer: Outliers : 3.19 % Allowed : 19.17 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.12), residues: 4725 helix: -0.66 (0.10), residues: 2630 sheet: -1.41 (0.34), residues: 223 loop : -3.52 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1837 TYR 0.025 0.001 TYR A3036 PHE 0.027 0.001 PHE A3236 TRP 0.017 0.001 TRP B 148 HIS 0.007 0.001 HIS A1687 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (40465) covalent geometry : angle 0.67689 / 0.35 (54996) hydrogen bonds : bond 0.04010 / 2.63 ( 1728) hydrogen bonds : angle 4.71389 / 3.25 ( 4983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 368 time to evaluate : 1.213 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: A 73 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7982 (pp) REVERT: A 96 MET cc_start: 0.7276 (mpp) cc_final: 0.7043 (mpp) REVERT: A 396 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6246 (p90) REVERT: A 541 MET cc_start: 0.7940 (mmm) cc_final: 0.7683 (mmm) REVERT: A 785 MET cc_start: 0.7963 (tpt) cc_final: 0.7662 (tpp) REVERT: A 966 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8418 (m-10) REVERT: A 1061 LYS cc_start: 0.8340 (mttp) cc_final: 0.7888 (mptt) REVERT: A 1361 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7629 (mmtm) REVERT: A 1507 CYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 1592 MET cc_start: 0.9120 (mmm) cc_final: 0.8432 (tpp) REVERT: A 2325 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7400 (mm) REVERT: A 2545 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 2568 MET cc_start: 0.7801 (mpp) cc_final: 0.7339 (tpp) REVERT: A 2812 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8573 (tt) REVERT: A 3067 LYS cc_start: 0.7526 (mttp) cc_final: 0.6827 (tppt) REVERT: A 3577 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8249 (mp10) REVERT: A 3595 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 3808 ASN cc_start: 0.8718 (t0) cc_final: 0.8364 (t0) REVERT: A 3820 MET cc_start: 0.8358 (mtt) cc_final: 0.7991 (mmm) REVERT: A 3895 GLU cc_start: 0.8656 (tp30) cc_final: 0.8346 (tp30) REVERT: A 3929 MET cc_start: 0.8087 (mtp) cc_final: 0.7743 (mtp) REVERT: A 3932 MET cc_start: 0.8591 (mmm) cc_final: 0.8235 (mmm) REVERT: A 4017 GLU cc_start: 0.7870 (pt0) cc_final: 0.7647 (mt-10) REVERT: B 137 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6592 (p-80) REVERT: B 217 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5039 (m-10) REVERT: B 496 ASP cc_start: 0.8410 (m-30) cc_final: 0.7863 (m-30) REVERT: B 497 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8093 (pt) REVERT: B 514 MET cc_start: 0.6548 (mtt) cc_final: 0.6086 (ptm) REVERT: C 234 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8071 (pp) outliers start: 134 outliers final: 83 residues processed: 481 average time/residue: 0.2154 time to fit residues: 178.9920 Evaluate side-chains 431 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 337 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1207 TRP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2812 LEU Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3724 GLU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3793 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 226 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 371 optimal weight: 6.9990 chunk 438 optimal weight: 10.0000 chunk 364 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 0.0170 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN ** A1941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2553 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN C 382 HIS ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099381 restraints weight = 105490.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098954 restraints weight = 91207.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099441 restraints weight = 90717.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099610 restraints weight = 72546.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100020 restraints weight = 60944.789| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40465 Z= 0.187 Angle : 0.708 15.018 54996 Z= 0.361 Chirality : 0.044 0.163 6256 Planarity : 0.005 0.054 6740 Dihedral : 13.390 78.029 5931 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.74 % Favored : 87.20 % Rotamer: Outliers : 3.78 % Allowed : 19.69 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.12), residues: 4725 helix: -0.58 (0.10), residues: 2621 sheet: -1.41 (0.34), residues: 222 loop : -3.50 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3653 TYR 0.024 0.002 TYR A1940 PHE 0.041 0.002 PHE A1814 TRP 0.015 0.002 TRP B 148 HIS 0.005 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (40465) covalent geometry : angle 0.70848 / 0.36 (54996) hydrogen bonds : bond 0.04205 / 2.77 ( 1728) hydrogen bonds : angle 4.80535 / 3.32 ( 4983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 338 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 316 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7190 (tp) REVERT: A 396 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6281 (p90) REVERT: A 520 LYS cc_start: 0.5568 (mmtp) cc_final: 0.4887 (mmtm) REVERT: A 541 MET cc_start: 0.7896 (mmm) cc_final: 0.7661 (mmm) REVERT: A 966 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: A 1018 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 1061 LYS cc_start: 0.8350 (mttp) cc_final: 0.7856 (mptt) REVERT: A 1361 LYS cc_start: 0.8334 (mmmm) cc_final: 0.7663 (mmtm) REVERT: A 1507 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 1524 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 1592 MET cc_start: 0.9098 (mmm) cc_final: 0.8515 (tpp) REVERT: A 2094 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.5950 (mtm) REVERT: A 2325 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 2545 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8778 (pp) REVERT: A 2565 MET cc_start: 0.8537 (ptp) cc_final: 0.8267 (ptp) REVERT: A 2568 MET cc_start: 0.7816 (mpp) cc_final: 0.7359 (tpp) REVERT: A 2812 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 3067 LYS cc_start: 0.7541 (mttp) cc_final: 0.6859 (tppt) REVERT: A 3577 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8269 (mp10) REVERT: A 3595 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 3806 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7516 (mp) REVERT: A 3808 ASN cc_start: 0.8725 (t0) cc_final: 0.8408 (t0) REVERT: A 3895 GLU cc_start: 0.8710 (tp30) cc_final: 0.8323 (tp30) REVERT: A 3913 ILE cc_start: 0.7682 (tp) cc_final: 0.7384 (tt) REVERT: A 3929 MET cc_start: 0.8244 (mtp) cc_final: 0.7900 (mtp) REVERT: B 137 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6433 (p-80) REVERT: B 217 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5090 (m-10) REVERT: B 496 ASP cc_start: 0.8405 (m-30) cc_final: 0.7886 (m-30) REVERT: B 497 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8135 (pt) REVERT: C 234 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8123 (pp) outliers start: 159 outliers final: 111 residues processed: 470 average time/residue: 0.2206 time to fit residues: 181.0547 Evaluate side-chains 456 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 329 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1207 TRP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1335 CYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1981 LEU Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2469 CYS Chi-restraints excluded: chain A residue 2480 ILE Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2812 LEU Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 3061 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3724 GLU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3788 LEU Chi-restraints excluded: chain A residue 3793 VAL Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4011 PHE Chi-restraints excluded: chain A residue 4030 GLU Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 180 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.0040 chunk 347 optimal weight: 3.9990 chunk 447 optimal weight: 10.0000 chunk 120 optimal weight: 0.0870 chunk 258 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 HIS ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN A1941 HIS ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN C 488 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101285 restraints weight = 104051.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100673 restraints weight = 76351.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101224 restraints weight = 71156.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101723 restraints weight = 55322.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101756 restraints weight = 50306.111| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40465 Z= 0.120 Angle : 0.655 13.732 54996 Z= 0.332 Chirality : 0.041 0.175 6256 Planarity : 0.004 0.075 6740 Dihedral : 13.186 78.502 5931 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.60 % Favored : 89.33 % Rotamer: Outliers : 2.66 % Allowed : 21.05 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.12), residues: 4725 helix: -0.31 (0.11), residues: 2617 sheet: -1.09 (0.35), residues: 219 loop : -3.39 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 9 TYR 0.030 0.001 TYR C 416 PHE 0.023 0.001 PHE A1297 TRP 0.014 0.001 TRP A1256 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (40465) covalent geometry : angle 0.65531 / 0.33 (54996) hydrogen bonds : bond 0.03540 / 2.31 ( 1728) hydrogen bonds : angle 4.50852 / 3.12 ( 4983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 391 time to evaluate : 1.486 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: A 73 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7908 (pp) REVERT: A 96 MET cc_start: 0.7528 (mpp) cc_final: 0.7003 (ptp) REVERT: A 396 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6095 (p90) REVERT: A 541 MET cc_start: 0.7839 (mmm) cc_final: 0.7569 (mmm) REVERT: A 966 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8505 (m-10) REVERT: A 1043 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7093 (mp10) REVERT: A 1061 LYS cc_start: 0.8303 (mttp) cc_final: 0.7788 (mptt) REVERT: A 1163 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5678 (tt) REVERT: A 1361 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7622 (mmtm) REVERT: A 1507 CYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8367 (p) REVERT: A 1524 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7533 (tt) REVERT: A 1592 MET cc_start: 0.9069 (mmm) cc_final: 0.8829 (tpp) REVERT: A 2443 MET cc_start: 0.8157 (ttp) cc_final: 0.7656 (ttp) REVERT: A 2568 MET cc_start: 0.7937 (mpp) cc_final: 0.7451 (tpp) REVERT: A 3067 LYS cc_start: 0.7515 (mttp) cc_final: 0.6826 (tppt) REVERT: A 3087 SER cc_start: 0.9042 (m) cc_final: 0.8711 (p) REVERT: A 3272 TRP cc_start: 0.7735 (m-10) cc_final: 0.7162 (m100) REVERT: A 3351 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 3577 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8313 (mp10) REVERT: A 3595 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 3767 LEU cc_start: 0.8597 (mt) cc_final: 0.8375 (tp) REVERT: A 3888 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 3895 GLU cc_start: 0.8627 (tp30) cc_final: 0.8318 (tp30) REVERT: A 3929 MET cc_start: 0.8055 (mtp) cc_final: 0.7772 (mtp) REVERT: A 4014 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8348 (mtmm) REVERT: B 137 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6174 (p-80) REVERT: B 217 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.4792 (m-10) REVERT: B 496 ASP cc_start: 0.8351 (m-30) cc_final: 0.7800 (m-30) REVERT: B 497 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8093 (pt) REVERT: C 234 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7993 (pp) outliers start: 112 outliers final: 67 residues processed: 482 average time/residue: 0.2267 time to fit residues: 188.6571 Evaluate side-chains 429 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 350 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 3061 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 309 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 320 optimal weight: 0.4980 chunk 118 optimal weight: 0.3980 chunk 355 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 GLN A 982 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 HIS A1721 HIS A1770 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3590 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 269 GLN ** C 511 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 = 0.3821 r_free = 0.3821 target = 0.122307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101060 restraints weight = 104787.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100930 restraints weight = 85908.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101313 restraints weight = 93062.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101603 restraints weight = 67092.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102074 restraints weight = 59057.184| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40465 Z= 0.150 Angle : 0.682 11.526 54996 Z= 0.345 Chirality : 0.043 0.309 6256 Planarity : 0.004 0.075 6740 Dihedral : 13.191 78.853 5931 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.60 % Favored : 88.34 % Rotamer: Outliers : 3.04 % Allowed : 21.31 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4725 helix: -0.25 (0.11), residues: 2613 sheet: -1.11 (0.35), residues: 219 loop : -3.37 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 290 TYR 0.031 0.001 TYR C 416 PHE 0.043 0.001 PHE A1814 TRP 0.015 0.001 TRP A2981 HIS 0.004 0.001 HIS A1941 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (40465) covalent geometry : angle 0.68241 / 0.34 (54996) hydrogen bonds : bond 0.03722 / 2.44 ( 1728) hydrogen bonds : angle 4.58281 / 3.17 ( 4983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 350 time to evaluate : 1.472 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: A 73 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7872 (pp) REVERT: A 96 MET cc_start: 0.7667 (mpp) cc_final: 0.6544 (ptp) REVERT: A 274 LEU cc_start: 0.9141 (tp) cc_final: 0.8934 (tt) REVERT: A 396 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6243 (p90) REVERT: A 541 MET cc_start: 0.7871 (mmm) cc_final: 0.7669 (mmm) REVERT: A 966 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8396 (m-10) REVERT: A 1061 LYS cc_start: 0.8253 (mttp) cc_final: 0.7770 (mptt) REVERT: A 1163 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5636 (tt) REVERT: A 1361 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7523 (mmtm) REVERT: A 1507 CYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 1524 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7507 (tt) REVERT: A 1592 MET cc_start: 0.9024 (mmm) cc_final: 0.8773 (tpp) REVERT: A 2325 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7388 (mm) REVERT: A 2568 MET cc_start: 0.7886 (mpp) cc_final: 0.7431 (tpp) REVERT: A 3067 LYS cc_start: 0.7452 (mttp) cc_final: 0.6918 (tppt) REVERT: A 3087 SER cc_start: 0.9083 (m) cc_final: 0.8759 (p) REVERT: A 3272 TRP cc_start: 0.7723 (m-10) cc_final: 0.7355 (m100) REVERT: A 3352 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6636 (pm20) REVERT: A 3577 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8250 (mp10) REVERT: A 3595 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 3808 ASN cc_start: 0.8712 (t0) cc_final: 0.8265 (t0) REVERT: A 3888 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 3895 GLU cc_start: 0.8641 (tp30) cc_final: 0.8193 (tp30) REVERT: A 3929 MET cc_start: 0.8202 (mtp) cc_final: 0.7909 (mtp) REVERT: B 137 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6262 (p-80) REVERT: B 217 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.4814 (m-10) REVERT: B 496 ASP cc_start: 0.8244 (m-30) cc_final: 0.7753 (m-30) REVERT: B 497 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8104 (pt) REVERT: C 234 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8149 (pp) outliers start: 128 outliers final: 91 residues processed: 456 average time/residue: 0.2213 time to fit residues: 174.1027 Evaluate side-chains 444 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 340 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1770 GLN Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1863 PHE Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 3061 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3352 GLU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3724 GLU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3788 LEU Chi-restraints excluded: chain A residue 3793 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 246 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 123 optimal weight: 0.0170 chunk 216 optimal weight: 0.5980 chunk 338 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101301 restraints weight = 105126.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100658 restraints weight = 77687.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101254 restraints weight = 72105.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101730 restraints weight = 56334.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101775 restraints weight = 51412.231| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 40465 Z= 0.123 Angle : 0.667 11.610 54996 Z= 0.337 Chirality : 0.042 0.478 6256 Planarity : 0.004 0.075 6740 Dihedral : 13.114 78.760 5931 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.67 % Favored : 89.27 % Rotamer: Outliers : 2.69 % Allowed : 21.45 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.12), residues: 4725 helix: -0.14 (0.11), residues: 2601 sheet: -0.99 (0.35), residues: 219 loop : -3.32 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 290 TYR 0.028 0.001 TYR C 416 PHE 0.026 0.001 PHE A2371 TRP 0.030 0.001 TRP A4013 HIS 0.005 0.001 HIS A1941 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (40465) covalent geometry : angle 0.66726 / 0.34 (54996) hydrogen bonds : bond 0.03496 / 2.29 ( 1728) hydrogen bonds : angle 4.47225 / 3.09 ( 4983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 359 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7854 (pp) REVERT: A 96 MET cc_start: 0.7577 (mpp) cc_final: 0.6621 (ptp) REVERT: A 396 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6093 (p90) REVERT: A 541 MET cc_start: 0.7772 (mmm) cc_final: 0.7499 (mmm) REVERT: A 966 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: A 1043 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7073 (mp10) REVERT: A 1061 LYS cc_start: 0.8277 (mttp) cc_final: 0.7838 (mptt) REVERT: A 1163 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5819 (tt) REVERT: A 1361 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7627 (mmtm) REVERT: A 1507 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 1524 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7508 (tt) REVERT: A 1592 MET cc_start: 0.9067 (mmm) cc_final: 0.8823 (tpp) REVERT: A 2220 MET cc_start: 0.8421 (ttp) cc_final: 0.8214 (ttm) REVERT: A 2325 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7488 (mm) REVERT: A 2568 MET cc_start: 0.7946 (mpp) cc_final: 0.7479 (tpp) REVERT: A 3067 LYS cc_start: 0.7502 (mttp) cc_final: 0.6820 (tppt) REVERT: A 3087 SER cc_start: 0.8992 (m) cc_final: 0.8678 (p) REVERT: A 3272 TRP cc_start: 0.7769 (m-10) cc_final: 0.7306 (m100) REVERT: A 3352 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: A 3577 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8336 (mp10) REVERT: A 3595 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 3888 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8801 (p) REVERT: A 3929 MET cc_start: 0.8030 (mtp) cc_final: 0.7750 (mtp) REVERT: B 137 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6114 (p-80) REVERT: B 217 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.4604 (m-10) REVERT: B 496 ASP cc_start: 0.8250 (m-30) cc_final: 0.7637 (m-30) REVERT: B 497 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8228 (pt) REVERT: C 234 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8197 (pp) REVERT: C 427 MET cc_start: 0.6992 (ppp) cc_final: 0.6683 (ppp) outliers start: 113 outliers final: 82 residues processed: 453 average time/residue: 0.2205 time to fit residues: 172.2017 Evaluate side-chains 443 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 348 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1863 PHE Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2256 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2480 ILE Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 3061 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3352 GLU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3788 LEU Chi-restraints excluded: chain A residue 3793 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 87 optimal weight: 0.0980 chunk 53 optimal weight: 0.0670 chunk 464 optimal weight: 0.0970 chunk 65 optimal weight: 0.4980 chunk 163 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 374 optimal weight: 0.3980 chunk 253 optimal weight: 0.9980 chunk 407 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 461 optimal weight: 0.7980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 ASN A1048 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 ASN A3590 ASN A3605 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102579 restraints weight = 104250.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102041 restraints weight = 74845.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102621 restraints weight = 67772.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103009 restraints weight = 55502.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103140 restraints weight = 50021.281| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40465 Z= 0.120 Angle : 0.662 12.074 54996 Z= 0.334 Chirality : 0.042 0.452 6256 Planarity : 0.004 0.075 6740 Dihedral : 13.003 77.740 5929 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.39 % Favored : 89.57 % Rotamer: Outliers : 2.24 % Allowed : 21.88 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.12), residues: 4725 helix: -0.03 (0.11), residues: 2611 sheet: -0.77 (0.36), residues: 214 loop : -3.28 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 290 TYR 0.028 0.001 TYR B 473 PHE 0.028 0.001 PHE A2577 TRP 0.027 0.001 TRP A4013 HIS 0.004 0.001 HIS A1941 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (40465) covalent geometry : angle 0.66194 / 0.33 (54996) hydrogen bonds : bond 0.03223 / 2.10 ( 1728) hydrogen bonds : angle 4.35235 / 3.03 ( 4983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9450 Ramachandran restraints generated. 4725 Oldfield, 0 Emsley, 4725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 390 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7640 (mpp) cc_final: 0.6689 (ptp) REVERT: A 396 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6136 (p90) REVERT: A 541 MET cc_start: 0.7695 (mmm) cc_final: 0.7435 (mmm) REVERT: A 633 ILE cc_start: 0.9144 (mm) cc_final: 0.8921 (mm) REVERT: A 966 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: A 1061 LYS cc_start: 0.8211 (mttp) cc_final: 0.7738 (mptt) REVERT: A 1163 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5514 (tt) REVERT: A 1190 LEU cc_start: 0.7852 (mt) cc_final: 0.7646 (mt) REVERT: A 1361 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7536 (mmtm) REVERT: A 1524 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 1592 MET cc_start: 0.8946 (mmm) cc_final: 0.8689 (tpp) REVERT: A 1639 LEU cc_start: 0.8404 (pt) cc_final: 0.7966 (tt) REVERT: A 1779 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: A 1827 LEU cc_start: 0.8033 (mp) cc_final: 0.7784 (mp) REVERT: A 1987 ARG cc_start: 0.7098 (mmp-170) cc_final: 0.6552 (mmm160) REVERT: A 2325 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7374 (mm) REVERT: A 2443 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: A 2568 MET cc_start: 0.7782 (mpp) cc_final: 0.7465 (tpp) REVERT: A 3067 LYS cc_start: 0.7544 (mttp) cc_final: 0.6892 (tppt) REVERT: A 3087 SER cc_start: 0.8957 (m) cc_final: 0.8667 (p) REVERT: A 3272 TRP cc_start: 0.7710 (m-10) cc_final: 0.7251 (m100) REVERT: A 3352 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: A 3577 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8290 (mp10) REVERT: A 3595 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 3638 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7581 (mmtm) REVERT: A 3888 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8804 (p) REVERT: B 137 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6094 (p-80) REVERT: B 320 GLN cc_start: 0.7884 (mt0) cc_final: 0.7507 (mt0) REVERT: B 496 ASP cc_start: 0.8011 (m-30) cc_final: 0.7573 (m-30) REVERT: B 497 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8180 (pp) REVERT: C 74 TYR cc_start: 0.5071 (m-80) cc_final: 0.4743 (m-80) REVERT: C 84 MET cc_start: 0.7357 (tpp) cc_final: 0.7130 (mpp) REVERT: C 115 MET cc_start: 0.7099 (tpt) cc_final: 0.6710 (mtp) REVERT: C 234 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8144 (pp) outliers start: 94 outliers final: 75 residues processed: 465 average time/residue: 0.2235 time to fit residues: 178.8609 Evaluate side-chains 446 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 359 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1553 PHE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1684 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1863 PHE Chi-restraints excluded: chain A residue 1900 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2036 LEU Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 3061 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3240 MET Chi-restraints excluded: chain A residue 3352 GLU Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4044 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 638 CYS Chi-restraints excluded: chain C residue 684 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 254 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 308 optimal weight: 6.9990 chunk 469 optimal weight: 9.9990 chunk 442 optimal weight: 4.9990 chunk 149 optimal weight: 0.0040 chunk 56 optimal weight: 0.8980 chunk 326 optimal weight: 0.9980 chunk 450 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 394 optimal weight: 0.1980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2514 ASN ** A3074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102637 restraints weight = 104371.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102260 restraints weight = 78309.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102827 restraints weight = 67952.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103176 restraints weight = 56960.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103292 restraints weight = 51590.455| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40465 Z= 0.118 Angle : 0.673 16.248 54996 Z= 0.336 Chirality : 0.042 0.456 6256 Planarity : 0.004 0.070 6740 Dihedral : 12.965 76.976 5924 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.24 % Favored : 89.71 % Rotamer: Outliers : 2.26 % Allowed : 22.24 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.12), residues: 4725 helix: 0.02 (0.11), residues: 2610 sheet: -0.72 (0.36), residues: 214 loop : -3.24 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 290 TYR 0.029 0.001 TYR A3036 PHE 0.028 0.001 PHE A2577 TRP 0.026 0.001 TRP A4013 HIS 0.005 0.001 HIS A3850 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (40465) covalent geometry : angle 0.67298 / 0.34 (54996) hydrogen bonds : bond 0.03195 / 2.09 ( 1728) hydrogen bonds : angle 4.31325 / 3.01 ( 4983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6097.33 seconds wall clock time: 106 minutes 43.53 seconds (6403.53 seconds total)