Starting phenix.real_space_refine on Tue May 27 07:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qn8_18511/05_2025/8qn8_18511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qn8_18511/05_2025/8qn8_18511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qn8_18511/05_2025/8qn8_18511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qn8_18511/05_2025/8qn8_18511.map" model { file = "/net/cci-nas-00/data/ceres_data/8qn8_18511/05_2025/8qn8_18511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qn8_18511/05_2025/8qn8_18511.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 102 5.16 5 C 18406 2.51 5 N 5232 2.21 5 O 5667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 1.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29410 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1771 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Chain: "C" Number of atoms: 8431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8431 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1030} Chain breaks: 1 Chain: "D" Number of atoms: 9983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9983 Classifications: {'peptide': 1278} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1220} Chain: "E" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 70} Chain breaks: 1 Chain: "F" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1237 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain breaks: 1 Chain: "H" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5532 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 36, 'TRANS': 673} Chain breaks: 1 Chain: "J" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18950 SG CYS D 890 34.771 59.586 87.557 1.00 29.22 S ATOM 19512 SG CYS D 967 37.707 61.794 88.598 1.00 23.79 S ATOM 19554 SG CYS D 974 35.305 60.693 90.977 1.00 21.59 S ATOM 19573 SG CYS D 977 37.531 58.214 89.677 1.00 19.91 S ATOM 12377 SG CYS D 60 30.164 124.015 101.942 1.00100.68 S ATOM 12395 SG CYS D 62 29.618 127.517 100.754 1.00106.01 S ATOM 12504 SG CYS D 75 26.957 124.921 99.799 1.00 95.46 S ATOM 12530 SG CYS D 78 30.158 125.237 98.066 1.00 99.45 S Time building chain proxies: 16.66, per 1000 atoms: 0.57 Number of scatterers: 29410 At special positions: 0 Unit cell: (132.32, 160.438, 183.594, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 102 16.00 Mg 1 11.99 O 5667 8.00 N 5232 7.00 C 18406 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: 7.10 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7004 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 46 sheets defined 46.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.128A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.642A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.588A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.862A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.505A pdb=" N THR C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.727A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.259A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 325 through 342 Processing helix chain 'C' and resid 371 through 395 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.924A pdb=" N ARG C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 removed outlier: 4.261A pdb=" N MET C 577 " --> pdb=" O PRO C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.585A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.774A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.783A pdb=" N ASP C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 725 " --> pdb=" O TYR C 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 725' Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 909 through 918 removed outlier: 3.792A pdb=" N GLY C 912 " --> pdb=" O ASN C 909 " (cutoff:3.500A) Proline residue: C 914 - end of helix removed outlier: 3.834A pdb=" N MET C 917 " --> pdb=" O PRO C 914 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN C 918 " --> pdb=" O ARG C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1060 through 1071 Processing helix chain 'C' and resid 1072 through 1082 Processing helix chain 'C' and resid 1086 through 1099 Processing helix chain 'C' and resid 1109 through 1122 removed outlier: 3.604A pdb=" N LEU C1115 " --> pdb=" O SER C1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.781A pdb=" N LYS D 40 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.516A pdb=" N PHE D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 143 through 186 removed outlier: 3.545A pdb=" N GLU D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 removed outlier: 3.791A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.937A pdb=" N ARG D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.579A pdb=" N SER D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 306 removed outlier: 3.965A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.596A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 340 through 360 removed outlier: 4.242A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 408 removed outlier: 3.616A pdb=" N LEU D 405 " --> pdb=" O SER D 401 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.267A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.613A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 removed outlier: 3.545A pdb=" N LEU D 745 " --> pdb=" O LYS D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.664A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 Processing helix chain 'D' and resid 844 through 881 removed outlier: 3.974A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 859 " --> pdb=" O ALA D 855 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 860 " --> pdb=" O ARG D 856 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA D 867 " --> pdb=" O ALA D 863 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 944 through 955 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1020 through 1024 removed outlier: 3.677A pdb=" N ASP D1024 " --> pdb=" O GLY D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1127 Processing helix chain 'D' and resid 1127 through 1146 Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 4.028A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1194 Processing helix chain 'D' and resid 1195 through 1198 Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1228 removed outlier: 3.586A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1249 through 1256 removed outlier: 3.836A pdb=" N VAL D1253 " --> pdb=" O LEU D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1283 removed outlier: 3.531A pdb=" N ALA D1282 " --> pdb=" O GLU D1278 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.576A pdb=" N ARG E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 67 Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.848A pdb=" N ALA F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 180 through 201 removed outlier: 4.143A pdb=" N ALA F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 246 removed outlier: 3.629A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP F 227 " --> pdb=" O CYS F 223 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ARG F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 254 through 272 removed outlier: 4.242A pdb=" N GLU F 271 " --> pdb=" O ILE F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 280 through 298 Processing helix chain 'H' and resid 3 through 42 removed outlier: 3.576A pdb=" N HIS H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 67 Processing helix chain 'H' and resid 106 through 109 Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 175 through 189 Processing helix chain 'H' and resid 204 through 220 Processing helix chain 'H' and resid 220 through 225 Processing helix chain 'H' and resid 236 through 246 Processing helix chain 'H' and resid 246 through 251 Processing helix chain 'H' and resid 258 through 262 removed outlier: 4.089A pdb=" N PHE H 262 " --> pdb=" O PRO H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 281 Processing helix chain 'H' and resid 282 through 284 No H-bonds generated for 'chain 'H' and resid 282 through 284' Processing helix chain 'H' and resid 285 through 296 Processing helix chain 'H' and resid 316 through 331 removed outlier: 3.640A pdb=" N GLY H 331 " --> pdb=" O ALA H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 358 removed outlier: 4.568A pdb=" N ALA H 339 " --> pdb=" O ASN H 335 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 382 Processing helix chain 'H' and resid 384 through 394 Processing helix chain 'H' and resid 399 through 411 removed outlier: 3.714A pdb=" N GLN H 406 " --> pdb=" O ASP H 402 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS H 411 " --> pdb=" O LEU H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 418 Processing helix chain 'H' and resid 420 through 424 removed outlier: 3.779A pdb=" N LEU H 423 " --> pdb=" O PRO H 420 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP H 424 " --> pdb=" O GLU H 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 420 through 424' Processing helix chain 'H' and resid 434 through 447 removed outlier: 4.339A pdb=" N LEU H 438 " --> pdb=" O SER H 434 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 473 Processing helix chain 'H' and resid 488 through 493 removed outlier: 3.811A pdb=" N LEU H 492 " --> pdb=" O LEU H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 502 removed outlier: 3.682A pdb=" N PHE H 502 " --> pdb=" O LEU H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 514 Processing helix chain 'H' and resid 529 through 533 Processing helix chain 'H' and resid 534 through 545 Processing helix chain 'H' and resid 555 through 559 Processing helix chain 'H' and resid 567 through 573 Processing helix chain 'H' and resid 592 through 604 removed outlier: 3.551A pdb=" N VAL H 598 " --> pdb=" O GLU H 594 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA H 601 " --> pdb=" O ALA H 597 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 607 No H-bonds generated for 'chain 'H' and resid 605 through 607' Processing helix chain 'H' and resid 632 through 646 removed outlier: 4.180A pdb=" N GLY H 646 " --> pdb=" O SER H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 687 removed outlier: 3.760A pdb=" N ILE H 684 " --> pdb=" O GLU H 680 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 686 " --> pdb=" O GLU H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 700 Processing helix chain 'H' and resid 716 through 721 removed outlier: 3.512A pdb=" N ALA H 719 " --> pdb=" O GLN H 716 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY H 720 " --> pdb=" O ALA H 717 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU H 721 " --> pdb=" O LEU H 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 716 through 721' Processing helix chain 'J' and resid 83 through 89 Processing helix chain 'J' and resid 90 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.277A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.981A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.761A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.342A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.552A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.542A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.389A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.352A pdb=" N SER C 168 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 175 through 182 removed outlier: 4.013A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 removed outlier: 6.906A pdb=" N ILE C 503 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 522 " --> pdb=" O ILE C 503 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR C 505 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP C 520 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR C 507 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN C 518 " --> pdb=" O TYR C 507 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 509 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.577A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.868A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL C 644 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 650 " --> pdb=" O GLU C 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC4, first strand: chain 'C' and resid 998 through 999 removed outlier: 5.874A pdb=" N ILE C 726 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 888 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 740 through 751 removed outlier: 6.370A pdb=" N SER C 740 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS C 867 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS C 742 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C 865 " --> pdb=" O HIS C 742 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU C 744 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR C 863 " --> pdb=" O GLU C 744 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS C 746 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 861 " --> pdb=" O HIS C 746 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 748 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 859 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 750 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC7, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.994A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AC9, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 7.905A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 3.829A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1124 through 1129 removed outlier: 3.954A pdb=" N GLU D 9 " --> pdb=" O LEU C1129 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.254A pdb=" N SER D 24 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS D 94 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLU D 96 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 10.202A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 4.161A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD7, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 903 Processing sheet with id=AE1, first strand: chain 'D' and resid 928 through 929 removed outlier: 3.872A pdb=" N ILE D 937 " --> pdb=" O ALA D 928 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE3, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 5.519A pdb=" N VAL D1077 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE D1067 " --> pdb=" O VAL D1077 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP D1079 " --> pdb=" O ILE D1065 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D1065 " --> pdb=" O ASP D1079 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D1081 " --> pdb=" O PHE D1063 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 4.394A pdb=" N ARG D1165 " --> pdb=" O VAL D1207 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE6, first strand: chain 'H' and resid 90 through 91 removed outlier: 6.197A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N PHE H 72 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN H 128 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG H 74 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG H 126 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP H 76 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP H 138 " --> pdb=" O HIS H 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 254 through 257 removed outlier: 7.004A pdb=" N VAL H 525 " --> pdb=" O THR H 551 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL H 553 " --> pdb=" O VAL H 525 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL H 527 " --> pdb=" O VAL H 553 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY H 199 " --> pdb=" O GLY H 554 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL H 194 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS H 583 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL H 196 " --> pdb=" O LYS H 583 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU H 585 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU H 198 " --> pdb=" O LEU H 585 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 304 through 305 Processing sheet with id=AE9, first strand: chain 'H' and resid 587 through 588 Processing sheet with id=AF1, first strand: chain 'H' and resid 624 through 627 removed outlier: 6.674A pdb=" N TRP H 624 " --> pdb=" O VAL H 708 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR H 710 " --> pdb=" O TRP H 624 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG H 626 " --> pdb=" O TYR H 710 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP H 674 " --> pdb=" O ARG H 705 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLY H 707 " --> pdb=" O ASP H 674 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL H 676 " --> pdb=" O GLY H 707 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU H 709 " --> pdb=" O VAL H 676 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 678 " --> pdb=" O LEU H 709 " (cutoff:3.500A) 1333 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.86 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10191 1.34 - 1.46: 4677 1.46 - 1.58: 14858 1.58 - 1.69: 0 1.69 - 1.81: 181 Bond restraints: 29907 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" C THR H 273 " pdb=" N PRO H 274 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.34e+00 bond pdb=" CB PRO C 451 " pdb=" CG PRO C 451 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.28e+00 bond pdb=" CA VAL H 621 " pdb=" CB VAL H 621 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.05e-02 9.07e+03 1.54e+00 ... (remaining 29902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 39842 1.53 - 3.06: 531 3.06 - 4.59: 152 4.59 - 6.12: 3 6.12 - 7.65: 4 Bond angle restraints: 40532 Sorted by residual: angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 119.98 -6.08 1.80e+00 3.09e-01 1.14e+01 angle pdb=" CB ARG C 412 " pdb=" CG ARG C 412 " pdb=" CD ARG C 412 " ideal model delta sigma weight residual 111.30 118.95 -7.65 2.30e+00 1.89e-01 1.11e+01 angle pdb=" C SER D 338 " pdb=" N ASP D 339 " pdb=" CA ASP D 339 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" CA PRO H 612 " pdb=" N PRO H 612 " pdb=" CD PRO H 612 " ideal model delta sigma weight residual 112.00 107.81 4.19 1.40e+00 5.10e-01 8.94e+00 angle pdb=" CB ARG D 350 " pdb=" CG ARG D 350 " pdb=" CD ARG D 350 " ideal model delta sigma weight residual 111.30 117.94 -6.64 2.30e+00 1.89e-01 8.32e+00 ... (remaining 40527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16765 17.95 - 35.90: 1235 35.90 - 53.85: 212 53.85 - 71.79: 47 71.79 - 89.74: 39 Dihedral angle restraints: 18298 sinusoidal: 7424 harmonic: 10874 Sorted by residual: dihedral pdb=" CA TYR D1078 " pdb=" C TYR D1078 " pdb=" N ASP D1079 " pdb=" CA ASP D1079 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP F 156 " pdb=" C ASP F 156 " pdb=" N ALA F 157 " pdb=" CA ALA F 157 " ideal model delta harmonic sigma weight residual 180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N SER A 45 " pdb=" CA SER A 45 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 18295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3058 0.031 - 0.062: 986 0.062 - 0.093: 295 0.093 - 0.124: 231 0.124 - 0.155: 33 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ILE C 196 " pdb=" N ILE C 196 " pdb=" C ILE C 196 " pdb=" CB ILE C 196 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA VAL H 663 " pdb=" N VAL H 663 " pdb=" C VAL H 663 " pdb=" CB VAL H 663 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 4600 not shown) Planarity restraints: 5362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 611 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO H 612 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO H 612 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO H 612 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 450 " -0.053 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO C 451 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 451 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 451 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 53 " -0.022 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR E 53 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 53 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 53 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 53 " -0.005 2.00e-02 2.50e+03 ... (remaining 5359 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 198 2.57 - 3.15: 24776 3.15 - 3.74: 44551 3.74 - 4.32: 63378 4.32 - 4.90: 106116 Nonbonded interactions: 239019 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2003 " model vdw 1.991 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2003 " model vdw 2.116 2.170 nonbonded pdb=" OD1 ASP B 90 " pdb=" NE ARG B 142 " model vdw 2.155 3.120 nonbonded pdb=" O GLU E 39 " pdb=" OG SER E 42 " model vdw 2.160 3.040 nonbonded pdb=" O ILE D 320 " pdb=" NH1 ARG D 325 " model vdw 2.218 3.120 ... (remaining 239014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.050 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 72.850 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.110 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:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.003 0.159 29915 Z= 0.112 Angle : 0.504 8.756 40544 Z= 0.267 Chirality : 0.041 0.155 4603 Planarity : 0.004 0.108 5362 Dihedral : 13.604 89.743 11294 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3768 helix: 1.25 (0.14), residues: 1451 sheet: 0.46 (0.24), residues: 459 loop : -0.02 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 370 HIS 0.013 0.001 HIS B 61 PHE 0.021 0.001 PHE C 364 TYR 0.038 0.001 TYR E 53 ARG 0.008 0.000 ARG C 686 Details of bonding type rmsd hydrogen bonds : bond 0.14349 ( 1331) hydrogen bonds : angle 5.98654 ( 3750) metal coordination : bond 0.08169 ( 8) metal coordination : angle 4.20200 ( 12) covalent geometry : bond 0.00214 (29907) covalent geometry : angle 0.49874 (40532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 3.255 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: D 373 MET cc_start: 0.6926 (mtp) cc_final: 0.6686 (mtp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5132 time to fit residues: 255.8408 Evaluate side-chains 185 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 0.0770 chunk 151 optimal weight: 5.9990 chunk 293 optimal weight: 0.0010 chunk 113 optimal weight: 0.3980 chunk 178 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 overall best weight: 1.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 534 GLN D 375 GLN D 941 HIS H 152 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.075772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057728 restraints weight = 97036.425| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.96 r_work: 0.2990 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29915 Z= 0.138 Angle : 0.576 9.437 40544 Z= 0.300 Chirality : 0.043 0.160 4603 Planarity : 0.004 0.064 5362 Dihedral : 4.273 20.389 4161 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.61 % Allowed : 5.46 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3768 helix: 1.41 (0.14), residues: 1491 sheet: 0.25 (0.23), residues: 482 loop : -0.02 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 221 HIS 0.006 0.001 HIS D 94 PHE 0.014 0.002 PHE C 364 TYR 0.035 0.001 TYR E 53 ARG 0.010 0.000 ARG D1192 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 1331) hydrogen bonds : angle 4.82347 ( 3750) metal coordination : bond 0.01047 ( 8) metal coordination : angle 5.41896 ( 12) covalent geometry : bond 0.00310 (29907) covalent geometry : angle 0.56900 (40532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 704 MET cc_start: 0.8737 (mmt) cc_final: 0.8454 (mmt) REVERT: D 143 MET cc_start: 0.4722 (tpt) cc_final: 0.4056 (ptm) REVERT: D 155 MET cc_start: 0.5740 (mmp) cc_final: 0.5049 (tpp) REVERT: D 373 MET cc_start: 0.6944 (mtp) cc_final: 0.6524 (mtp) REVERT: F 173 ILE cc_start: 0.8969 (pt) cc_final: 0.8668 (pt) REVERT: F 237 ASN cc_start: 0.7435 (t0) cc_final: 0.7186 (t0) REVERT: F 297 MET cc_start: 0.6993 (mtp) cc_final: 0.6773 (ppp) REVERT: H 457 GLU cc_start: 0.8579 (tt0) cc_final: 0.8133 (tp30) outliers start: 19 outliers final: 11 residues processed: 213 average time/residue: 0.4611 time to fit residues: 155.9565 Evaluate side-chains 185 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 321 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 357 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 348 optimal weight: 6.9990 chunk 328 optimal weight: 1.9990 chunk 368 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN C 223 GLN D 600 GLN D 941 HIS ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.074576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056565 restraints weight = 97837.267| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.95 r_work: 0.2962 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29915 Z= 0.144 Angle : 0.529 7.947 40544 Z= 0.276 Chirality : 0.042 0.160 4603 Planarity : 0.004 0.061 5362 Dihedral : 4.155 19.381 4161 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.09 % Allowed : 6.93 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3768 helix: 1.54 (0.14), residues: 1489 sheet: 0.33 (0.23), residues: 495 loop : -0.06 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 221 HIS 0.006 0.001 HIS D 94 PHE 0.015 0.001 PHE C 364 TYR 0.032 0.001 TYR E 53 ARG 0.010 0.000 ARG H 617 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1331) hydrogen bonds : angle 4.61871 ( 3750) metal coordination : bond 0.00712 ( 8) metal coordination : angle 4.50437 ( 12) covalent geometry : bond 0.00328 (29907) covalent geometry : angle 0.52313 (40532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 3.191 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: C 250 MET cc_start: 0.8701 (mmm) cc_final: 0.8311 (mtt) REVERT: D 108 LYS cc_start: 0.8634 (tptm) cc_final: 0.8140 (ttmm) REVERT: D 155 MET cc_start: 0.5692 (mmp) cc_final: 0.5141 (tpp) REVERT: D 373 MET cc_start: 0.7084 (mtp) cc_final: 0.6622 (mtp) REVERT: F 173 ILE cc_start: 0.8948 (pt) cc_final: 0.8597 (pt) REVERT: H 457 GLU cc_start: 0.8608 (tt0) cc_final: 0.8285 (tp30) outliers start: 34 outliers final: 16 residues processed: 211 average time/residue: 0.4388 time to fit residues: 146.1061 Evaluate side-chains 186 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 422 CYS Chi-restraints excluded: chain H residue 639 GLU Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 3.9990 chunk 374 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 241 optimal weight: 0.0370 chunk 327 optimal weight: 0.4980 chunk 42 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 544 HIS D 600 GLN D 941 HIS H 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.075342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057399 restraints weight = 98517.009| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.94 r_work: 0.2981 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29915 Z= 0.104 Angle : 0.492 7.612 40544 Z= 0.256 Chirality : 0.041 0.163 4603 Planarity : 0.004 0.049 5362 Dihedral : 3.958 19.374 4161 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.28 % Allowed : 7.96 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3768 helix: 1.64 (0.14), residues: 1498 sheet: 0.35 (0.23), residues: 494 loop : -0.05 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 221 HIS 0.005 0.001 HIS D 94 PHE 0.017 0.001 PHE F 281 TYR 0.025 0.001 TYR E 53 ARG 0.013 0.000 ARG D1192 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1331) hydrogen bonds : angle 4.37806 ( 3750) metal coordination : bond 0.00518 ( 8) metal coordination : angle 3.82688 ( 12) covalent geometry : bond 0.00229 (29907) covalent geometry : angle 0.48733 (40532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6910 (tpt) cc_final: 0.6173 (ptt) REVERT: C 250 MET cc_start: 0.8688 (mmm) cc_final: 0.8358 (mtt) REVERT: C 551 MET cc_start: 0.8196 (tpp) cc_final: 0.7828 (tpt) REVERT: C 766 ASN cc_start: 0.8899 (p0) cc_final: 0.8655 (p0) REVERT: C 992 MET cc_start: 0.8523 (mtp) cc_final: 0.8235 (mtt) REVERT: D 108 LYS cc_start: 0.8604 (tptm) cc_final: 0.8202 (ttmm) REVERT: D 143 MET cc_start: 0.4389 (tpt) cc_final: 0.3489 (ttt) REVERT: D 155 MET cc_start: 0.5893 (mmp) cc_final: 0.5309 (tpp) REVERT: D 373 MET cc_start: 0.7202 (mtp) cc_final: 0.6781 (mtp) REVERT: D 462 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8560 (m-30) REVERT: F 173 ILE cc_start: 0.8947 (pt) cc_final: 0.8602 (pt) REVERT: F 237 ASN cc_start: 0.7588 (t0) cc_final: 0.7333 (t0) REVERT: H 444 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8698 (m-30) REVERT: H 457 GLU cc_start: 0.8583 (tt0) cc_final: 0.8225 (tp30) REVERT: H 699 LEU cc_start: 0.8650 (mt) cc_final: 0.8107 (pp) outliers start: 40 outliers final: 15 residues processed: 217 average time/residue: 0.4230 time to fit residues: 146.3219 Evaluate side-chains 182 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 HIS ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS C1033 HIS D 600 GLN D 941 HIS ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.072014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054264 restraints weight = 98358.809| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.87 r_work: 0.2895 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 29915 Z= 0.248 Angle : 0.593 7.866 40544 Z= 0.308 Chirality : 0.045 0.159 4603 Planarity : 0.005 0.050 5362 Dihedral : 4.328 19.466 4161 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.53 % Allowed : 9.39 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3768 helix: 1.38 (0.14), residues: 1501 sheet: 0.32 (0.23), residues: 488 loop : -0.14 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 221 HIS 0.007 0.001 HIS D 748 PHE 0.017 0.002 PHE C 897 TYR 0.031 0.002 TYR E 53 ARG 0.012 0.001 ARG D1192 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 1331) hydrogen bonds : angle 4.61145 ( 3750) metal coordination : bond 0.00972 ( 8) metal coordination : angle 4.12953 ( 12) covalent geometry : bond 0.00584 (29907) covalent geometry : angle 0.58838 (40532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 3.151 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8140 (mtm) REVERT: C 250 MET cc_start: 0.8692 (mmm) cc_final: 0.8435 (mtt) REVERT: C 289 ASN cc_start: 0.8188 (m-40) cc_final: 0.7953 (t0) REVERT: C 516 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8870 (p) REVERT: D 155 MET cc_start: 0.6047 (mmp) cc_final: 0.5397 (tpt) REVERT: D 205 MET cc_start: 0.3442 (tpt) cc_final: 0.3119 (tpt) REVERT: D 327 MET cc_start: 0.6130 (tmm) cc_final: 0.5869 (tmm) REVERT: D 373 MET cc_start: 0.7199 (mtp) cc_final: 0.6722 (mtp) REVERT: D 952 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8924 (mm) REVERT: F 173 ILE cc_start: 0.9002 (pt) cc_final: 0.8643 (pt) REVERT: F 237 ASN cc_start: 0.7827 (t0) cc_final: 0.7399 (t0) REVERT: H 444 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8690 (m-30) REVERT: H 457 GLU cc_start: 0.8630 (tt0) cc_final: 0.8200 (tm-30) outliers start: 48 outliers final: 27 residues processed: 209 average time/residue: 0.4073 time to fit residues: 137.1487 Evaluate side-chains 191 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 628 VAL Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 179 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 601 ASN C 926 HIS E 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056251 restraints weight = 98129.786| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.92 r_work: 0.2951 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29915 Z= 0.104 Angle : 0.489 9.851 40544 Z= 0.253 Chirality : 0.041 0.159 4603 Planarity : 0.004 0.051 5362 Dihedral : 4.004 20.816 4161 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.21 % Allowed : 10.29 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3768 helix: 1.67 (0.14), residues: 1493 sheet: 0.32 (0.23), residues: 490 loop : -0.07 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 221 HIS 0.004 0.001 HIS D 94 PHE 0.016 0.001 PHE D1227 TYR 0.018 0.001 TYR E 53 ARG 0.006 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1331) hydrogen bonds : angle 4.31190 ( 3750) metal coordination : bond 0.00444 ( 8) metal coordination : angle 3.30801 ( 12) covalent geometry : bond 0.00224 (29907) covalent geometry : angle 0.48576 (40532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 3.356 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6855 (tpt) cc_final: 0.5952 (ptt) REVERT: C 250 MET cc_start: 0.8670 (mmm) cc_final: 0.8409 (mtt) REVERT: C 876 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8795 (mp) REVERT: C 992 MET cc_start: 0.8603 (mtp) cc_final: 0.8242 (mtt) REVERT: D 108 LYS cc_start: 0.8662 (tptm) cc_final: 0.8170 (ttmm) REVERT: D 143 MET cc_start: 0.4490 (tpt) cc_final: 0.3728 (ttt) REVERT: D 155 MET cc_start: 0.6057 (mmp) cc_final: 0.5407 (tpt) REVERT: D 414 ARG cc_start: 0.7809 (tmm160) cc_final: 0.7240 (tmm-80) REVERT: D 462 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8525 (m-30) REVERT: F 173 ILE cc_start: 0.8958 (pt) cc_final: 0.8607 (pt) REVERT: F 199 GLN cc_start: 0.6334 (tp-100) cc_final: 0.5834 (pt0) REVERT: F 237 ASN cc_start: 0.7718 (t0) cc_final: 0.7421 (t0) REVERT: H 444 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: H 457 GLU cc_start: 0.8619 (tt0) cc_final: 0.8233 (tm-30) outliers start: 38 outliers final: 23 residues processed: 210 average time/residue: 0.4235 time to fit residues: 143.5751 Evaluate side-chains 189 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 444 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 268 optimal weight: 0.6980 chunk 369 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 926 HIS ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054688 restraints weight = 98663.964| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.88 r_work: 0.2909 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29915 Z= 0.192 Angle : 0.535 8.042 40544 Z= 0.277 Chirality : 0.043 0.150 4603 Planarity : 0.004 0.049 5362 Dihedral : 4.105 20.774 4161 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.47 % Allowed : 10.73 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3768 helix: 1.56 (0.14), residues: 1505 sheet: 0.39 (0.23), residues: 493 loop : -0.12 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1221 HIS 0.005 0.001 HIS D 748 PHE 0.023 0.002 PHE D 252 TYR 0.023 0.002 TYR E 53 ARG 0.009 0.000 ARG D1192 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 1331) hydrogen bonds : angle 4.41617 ( 3750) metal coordination : bond 0.00724 ( 8) metal coordination : angle 3.65575 ( 12) covalent geometry : bond 0.00453 (29907) covalent geometry : angle 0.53183 (40532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 3.175 Fit side-chains revert: symmetry clash REVERT: C 250 MET cc_start: 0.8665 (mmm) cc_final: 0.8415 (mtt) REVERT: C 289 ASN cc_start: 0.8188 (m-40) cc_final: 0.7942 (t0) REVERT: C 876 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8836 (mp) REVERT: D 143 MET cc_start: 0.4410 (tpt) cc_final: 0.3648 (ttt) REVERT: D 155 MET cc_start: 0.6207 (mmp) cc_final: 0.5492 (tpt) REVERT: D 205 MET cc_start: 0.3604 (tpt) cc_final: 0.3311 (tpt) REVERT: D 414 ARG cc_start: 0.7936 (tmm160) cc_final: 0.7391 (tmm-80) REVERT: D 462 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8521 (m-30) REVERT: F 173 ILE cc_start: 0.9000 (pt) cc_final: 0.8649 (pt) REVERT: F 199 GLN cc_start: 0.6516 (tp-100) cc_final: 0.5914 (pt0) REVERT: F 237 ASN cc_start: 0.7713 (t0) cc_final: 0.7264 (t0) REVERT: H 444 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8700 (m-30) REVERT: H 457 GLU cc_start: 0.8647 (tt0) cc_final: 0.8244 (tm-30) outliers start: 46 outliers final: 32 residues processed: 207 average time/residue: 0.4215 time to fit residues: 145.3331 Evaluate side-chains 199 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 628 VAL Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 295 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 344 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 235 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 926 HIS ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.072234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054462 restraints weight = 98610.126| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.93 r_work: 0.2911 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29915 Z= 0.165 Angle : 0.524 10.923 40544 Z= 0.271 Chirality : 0.042 0.219 4603 Planarity : 0.004 0.049 5362 Dihedral : 4.082 20.918 4161 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.44 % Allowed : 11.28 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3768 helix: 1.57 (0.14), residues: 1505 sheet: 0.42 (0.23), residues: 487 loop : -0.13 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1221 HIS 0.004 0.001 HIS D 748 PHE 0.023 0.001 PHE D 252 TYR 0.021 0.001 TYR E 53 ARG 0.010 0.000 ARG F 247 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1331) hydrogen bonds : angle 4.38023 ( 3750) metal coordination : bond 0.00648 ( 8) metal coordination : angle 3.57901 ( 12) covalent geometry : bond 0.00387 (29907) covalent geometry : angle 0.52032 (40532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 250 MET cc_start: 0.8668 (mmm) cc_final: 0.8421 (mtt) REVERT: C 876 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8835 (mp) REVERT: C 992 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8406 (mtp) REVERT: D 143 MET cc_start: 0.4282 (tpt) cc_final: 0.3584 (ttp) REVERT: D 205 MET cc_start: 0.3560 (tpt) cc_final: 0.3253 (tpt) REVERT: D 462 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8528 (m-30) REVERT: F 173 ILE cc_start: 0.9006 (pt) cc_final: 0.8652 (pt) REVERT: F 199 GLN cc_start: 0.6439 (tp-100) cc_final: 0.5808 (pt0) REVERT: F 237 ASN cc_start: 0.7768 (t0) cc_final: 0.7324 (t0) REVERT: H 444 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8706 (m-30) REVERT: H 457 GLU cc_start: 0.8636 (tt0) cc_final: 0.8247 (tm-30) outliers start: 45 outliers final: 37 residues processed: 204 average time/residue: 0.4024 time to fit residues: 135.2933 Evaluate side-chains 199 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 628 VAL Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 103 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 314 optimal weight: 0.9980 chunk 266 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 290 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 334 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 926 HIS ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 GLN H 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.073611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055861 restraints weight = 97490.259| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.94 r_work: 0.2951 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29915 Z= 0.097 Angle : 0.486 10.659 40544 Z= 0.250 Chirality : 0.041 0.186 4603 Planarity : 0.004 0.047 5362 Dihedral : 3.866 20.574 4161 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.21 % Allowed : 11.63 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3768 helix: 1.77 (0.14), residues: 1494 sheet: 0.45 (0.23), residues: 500 loop : -0.07 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 221 HIS 0.004 0.001 HIS D 94 PHE 0.024 0.001 PHE D 252 TYR 0.017 0.001 TYR E 53 ARG 0.008 0.000 ARG F 247 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 1331) hydrogen bonds : angle 4.21706 ( 3750) metal coordination : bond 0.00407 ( 8) metal coordination : angle 3.18781 ( 12) covalent geometry : bond 0.00215 (29907) covalent geometry : angle 0.48260 (40532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 3.250 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6873 (tpt) cc_final: 0.5890 (ptt) REVERT: C 250 MET cc_start: 0.8650 (mmm) cc_final: 0.8414 (mtt) REVERT: C 876 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8838 (mp) REVERT: C 992 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: D 143 MET cc_start: 0.4394 (tpt) cc_final: 0.3818 (ttp) REVERT: D 155 MET cc_start: 0.6298 (mmp) cc_final: 0.5599 (tpt) REVERT: D 205 MET cc_start: 0.3548 (tpt) cc_final: 0.3239 (tpt) REVERT: D 462 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8509 (m-30) REVERT: F 173 ILE cc_start: 0.8962 (pt) cc_final: 0.8626 (pt) REVERT: F 237 ASN cc_start: 0.7809 (t0) cc_final: 0.7544 (t0) REVERT: H 444 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8621 (m-30) REVERT: H 457 GLU cc_start: 0.8605 (tt0) cc_final: 0.8237 (tm-30) outliers start: 38 outliers final: 31 residues processed: 199 average time/residue: 0.4153 time to fit residues: 133.9809 Evaluate side-chains 193 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 628 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 39 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 291 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 chunk 270 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 926 HIS ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.071310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053297 restraints weight = 99192.840| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.95 r_work: 0.2883 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29915 Z= 0.242 Angle : 0.581 10.034 40544 Z= 0.300 Chirality : 0.044 0.184 4603 Planarity : 0.005 0.050 5362 Dihedral : 4.186 19.861 4161 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.21 % Allowed : 11.69 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3768 helix: 1.56 (0.14), residues: 1502 sheet: 0.42 (0.23), residues: 486 loop : -0.15 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 223 HIS 0.006 0.001 HIS C 470 PHE 0.021 0.002 PHE D 252 TYR 0.023 0.002 TYR E 53 ARG 0.008 0.000 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 1331) hydrogen bonds : angle 4.48986 ( 3750) metal coordination : bond 0.00956 ( 8) metal coordination : angle 3.76584 ( 12) covalent geometry : bond 0.00568 (29907) covalent geometry : angle 0.57773 (40532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 3.444 Fit side-chains revert: symmetry clash REVERT: C 250 MET cc_start: 0.8653 (mmm) cc_final: 0.8392 (mtt) REVERT: C 704 MET cc_start: 0.8894 (mmt) cc_final: 0.8198 (mmt) REVERT: C 876 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8861 (mp) REVERT: C 992 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8194 (mtt) REVERT: C 1099 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8350 (pttm) REVERT: D 143 MET cc_start: 0.4285 (tpt) cc_final: 0.3738 (ttt) REVERT: D 205 MET cc_start: 0.3474 (tpt) cc_final: 0.3160 (tpt) REVERT: D 462 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8489 (m-30) REVERT: F 173 ILE cc_start: 0.9025 (pt) cc_final: 0.8688 (pt) REVERT: F 237 ASN cc_start: 0.7926 (t0) cc_final: 0.7370 (t0) REVERT: H 444 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: H 457 GLU cc_start: 0.8643 (tt0) cc_final: 0.8254 (tm-30) outliers start: 38 outliers final: 31 residues processed: 196 average time/residue: 0.4052 time to fit residues: 130.1269 Evaluate side-chains 196 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 628 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 151 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 312 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 926 HIS ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053748 restraints weight = 98494.894| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.92 r_work: 0.2895 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29915 Z= 0.195 Angle : 0.547 9.785 40544 Z= 0.283 Chirality : 0.043 0.188 4603 Planarity : 0.004 0.049 5362 Dihedral : 4.177 19.909 4161 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.28 % Allowed : 11.82 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3768 helix: 1.58 (0.14), residues: 1500 sheet: 0.40 (0.24), residues: 481 loop : -0.16 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 221 HIS 0.005 0.001 HIS D 748 PHE 0.021 0.001 PHE D 252 TYR 0.021 0.001 TYR E 53 ARG 0.008 0.000 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1331) hydrogen bonds : angle 4.45390 ( 3750) metal coordination : bond 0.00796 ( 8) metal coordination : angle 3.61601 ( 12) covalent geometry : bond 0.00458 (29907) covalent geometry : angle 0.54316 (40532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13314.76 seconds wall clock time: 231 minutes 14.87 seconds (13874.87 seconds total)