Starting phenix.real_space_refine on Mon Sep 14 11:29:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.map" model { file = "/net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py5_13713/09_2026/7py5_13713.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 18481 2.51 5 N 5372 2.21 5 O 5923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29959 Number of models: 1 Model: "" Number of chains: 11 Chain: "N" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'ASN:plan1': 19, 'GLU:plan': 56, 'ARG:plan': 33, 'PHE:plan': 14, 'TYR:plan': 6, 'GLN:plan1': 19, 'ASP:plan': 42, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 830 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 15888 SG CYS D 72 89.630 117.509 74.292 1.00 87.14 S ATOM 16020 SG CYS D 88 90.353 114.489 71.900 1.00 79.51 S ATOM 21708 SG CYS D 814 97.803 46.850 77.435 1.00 54.18 S ATOM 22273 SG CYS D 888 99.725 50.068 76.747 1.00 43.10 S ATOM 22324 SG CYS D 895 98.532 49.462 80.225 1.00 39.84 S ATOM 22345 SG CYS D 898 101.236 47.214 78.869 1.00 41.30 S Time building chain proxies: 5.82, per 1000 atoms: 0.19 Number of scatterers: 29959 At special positions: 0 Unit cell: (195.11, 154.78, 173.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 67 15.00 Mg 1 11.99 O 5923 8.00 N 5372 7.00 C 18481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 6 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 46 sheets defined 38.9% alpha, 13.9% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.901A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 162 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 49 removed outlier: 4.029A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.750A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.537A pdb=" N ALA B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.502A pdb=" N LYS C 8 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 39 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.791A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.745A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.728A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.510A pdb=" N ILE C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.680A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.526A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.573A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.137A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.549A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.176A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.799A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.603A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.620A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.925A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.592A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.963A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 4.134A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.623A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.647A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.504A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.567A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.509A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.577A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.730A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.754A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.640A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.706A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.505A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.876A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.562A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.930A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.738A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.602A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 4.186A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.750A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 802 removed outlier: 3.931A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 807 removed outlier: 4.322A pdb=" N ASP D 806 " --> pdb=" O VAL D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.814A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.696A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.930A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 4.169A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.558A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.663A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.203A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.657A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 3.630A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.592A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.939A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 91 removed outlier: 3.635A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 76 through 86 removed outlier: 4.080A pdb=" N VAL G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.538A pdb=" N VAL G 118 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 19 through 39 removed outlier: 3.567A pdb=" N ILE F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 106 through 130 Processing helix chain 'F' and resid 201 through 212 removed outlier: 4.494A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 212 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 256 through 266 removed outlier: 3.688A pdb=" N THR F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.868A pdb=" N ILE F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.798A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.566A pdb=" N ALA F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 364 removed outlier: 3.611A pdb=" N ASP F 364 " --> pdb=" O THR F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 375 Processing helix chain 'F' and resid 388 through 393 removed outlier: 3.556A pdb=" N LEU F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 Processing helix chain 'F' and resid 403 through 422 removed outlier: 3.694A pdb=" N ARG F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 425 No H-bonds generated for 'chain 'F' and resid 423 through 425' Processing helix chain 'F' and resid 442 through 452 removed outlier: 4.017A pdb=" N PHE F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 462 removed outlier: 3.867A pdb=" N LEU F 459 " --> pdb=" O THR F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 470 removed outlier: 3.734A pdb=" N ASP F 469 " --> pdb=" O ASP F 466 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 470 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 470' Processing helix chain 'F' and resid 474 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 6.426A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 7.375A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.528A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.893A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 4.916A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 201 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.484A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.694A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.594A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.283A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.742A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.619A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.646A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.636A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.571A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.267A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.005A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 4.097A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C1098 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.699A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AC6, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.041A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 890 removed outlier: 4.776A pdb=" N ASP C 912 " --> pdb=" O LYS C 890 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.561A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.561A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.503A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.541A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 104 through 112 removed outlier: 10.123A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.845A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.021A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD6, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AD7, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.875A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.679A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE2, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.582A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 4.080A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1187 through 1190 Processing sheet with id=AE5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AE6, first strand: chain 'G' and resid 39 through 42 removed outlier: 5.941A pdb=" N GLN G 72 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL G 42 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU G 70 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY G 91 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 45 through 49 removed outlier: 4.819A pdb=" N THR F 58 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 178 through 179 removed outlier: 3.906A pdb=" N VAL F 179 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY F 140 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 141 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP F 153 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL F 145 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN F 149 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 150 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE F 196 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 221 through 222 Processing sheet with id=AF1, first strand: chain 'F' and resid 227 through 229 removed outlier: 3.728A pdb=" N ALA F 227 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP F 272 " --> pdb=" O ALA F 234 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 8.16 Time building geometry restraints manager: 3.06 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: 10061 1.34 - 1.46: 4677 1.46 - 1.58: 15441 1.58 - 1.70: 130 1.70 - 1.82: 198 Bond restraints: 30507 Sorted by residual: bond pdb=" C3' DC N 35 " pdb=" C2' DC N 35 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C1' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.86e+00 bond pdb=" C3' DG T 24 " pdb=" C2' DG T 24 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.50e+00 bond pdb=" C3' DC T 9 " pdb=" C2' DC T 9 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.14e+00 bond pdb=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.52e+00 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 40961 2.33 - 4.67: 566 4.67 - 7.00: 50 7.00 - 9.33: 7 9.33 - 11.66: 2 Bond angle restraints: 41586 Sorted by residual: angle pdb=" O4' DG T 27 " pdb=" C4' DG T 27 " pdb=" C3' DG T 27 " ideal model delta sigma weight residual 106.00 102.56 3.44 6.00e-01 2.78e+00 3.29e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4' DT T 4 " pdb=" C4' DT T 4 " pdb=" C3' DT T 4 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N GLU E 76 " pdb=" CA GLU E 76 " pdb=" CB GLU E 76 " ideal model delta sigma weight residual 110.28 116.94 -6.66 1.55e+00 4.16e-01 1.84e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 41581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 17723 29.06 - 58.12: 705 58.12 - 87.18: 80 87.18 - 116.23: 3 116.23 - 145.29: 3 Dihedral angle restraints: 18514 sinusoidal: 7511 harmonic: 11003 Sorted by residual: dihedral pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.59 71.93 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' U R 4 " pdb=" C3' U R 4 " pdb=" C2' U R 4 " pdb=" C1' U R 4 " ideal model delta sinusoidal sigma weight residual 36.34 -35.18 71.52 1 3.10e+00 1.04e-01 6.82e+02 dihedral pdb=" O4' U R 4 " pdb=" C4' U R 4 " pdb=" C3' U R 4 " pdb=" C2' U R 4 " ideal model delta sinusoidal sigma weight residual -35.15 24.05 -59.20 1 4.00e+00 6.25e-02 2.93e+02 ... (remaining 18511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4137 0.063 - 0.127: 635 0.127 - 0.190: 28 0.190 - 0.253: 15 0.253 - 0.317: 5 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CB ILE B 140 " pdb=" CA ILE B 140 " pdb=" CG1 ILE B 140 " pdb=" CG2 ILE B 140 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C2' U R 4 " pdb=" C3' U R 4 " pdb=" O2' U R 4 " pdb=" C1' U R 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4817 not shown) Planarity restraints: 5266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.065 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 30 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 166 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 167 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO D 851 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.032 5.00e-02 4.00e+02 ... (remaining 5263 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 336 2.64 - 3.20: 26663 3.20 - 3.77: 45012 3.77 - 4.33: 57812 4.33 - 4.90: 94639 Nonbonded interactions: 224462 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.071 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.075 2.170 nonbonded pdb=" N2 DG N 37 " pdb=" O2 DC T 3 " model vdw 2.150 2.496 nonbonded pdb=" O LYS C 324 " pdb=" OG SER C 328 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR D 679 " pdb=" O ILE D 754 " model vdw 2.172 3.040 ... (remaining 224457 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' and (resid 7 through 158 or resid 170 through 234)) selection = (chain 'B' and resid 7 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 32.700 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 0.044 30513 Z= 0.187 Angle : 0.644 11.663 41592 Z= 0.381 Chirality : 0.046 0.317 4820 Planarity : 0.004 0.100 5266 Dihedral : 14.995 145.293 11420 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.13), residues: 3812 helix: 0.24 (0.14), residues: 1295 sheet: -0.88 (0.26), residues: 393 loop : -1.76 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 481 TYR 0.017 0.001 TYR C1229 PHE 0.013 0.001 PHE G 65 TRP 0.024 0.001 TRP D 236 HIS 0.009 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.19 (30507) covalent geometry : angle 0.64345 / 0.38 (41586) hydrogen bonds : bond 0.18515 / 20.93 ( 1212) hydrogen bonds : angle 6.83297 / 7.30 ( 3354) metal coordination : bond 0.00262 / 0.26 ( 6) metal coordination : angle 2.61790 / 5.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7596 (t70) cc_final: 0.7374 (t70) REVERT: A 137 ASN cc_start: 0.8061 (m-40) cc_final: 0.7487 (p0) REVERT: B 231 PHE cc_start: 0.7872 (m-10) cc_final: 0.7641 (m-10) REVERT: C 569 ILE cc_start: 0.9037 (tp) cc_final: 0.8802 (tt) REVERT: C 1023 HIS cc_start: 0.8171 (m-70) cc_final: 0.7719 (m-70) REVERT: C 1278 LEU cc_start: 0.9277 (tp) cc_final: 0.9067 (tp) REVERT: D 707 ILE cc_start: 0.8200 (mm) cc_final: 0.7967 (mt) REVERT: D 785 ASP cc_start: 0.8353 (t0) cc_final: 0.7996 (t70) REVERT: E 70 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8388 (mp10) REVERT: E 75 GLN cc_start: 0.8953 (pp30) cc_final: 0.8410 (pp30) REVERT: G 35 MET cc_start: 0.8418 (mpp) cc_final: 0.8194 (mpp) REVERT: G 90 MET cc_start: 0.7003 (mmm) cc_final: 0.6765 (mmm) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1654 time to fit residues: 96.6403 Evaluate side-chains 241 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 979 ASN G 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.146965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099453 restraints weight = 55323.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099195 restraints weight = 34975.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101528 restraints weight = 24641.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101450 restraints weight = 19270.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101719 restraints weight = 18016.765| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30513 Z= 0.146 Angle : 0.635 19.814 41592 Z= 0.326 Chirality : 0.050 1.036 4820 Planarity : 0.005 0.101 5266 Dihedral : 12.938 147.398 4876 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.81 % Allowed : 8.23 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 3812 helix: 0.64 (0.14), residues: 1326 sheet: -0.74 (0.26), residues: 408 loop : -1.68 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 101 TYR 0.024 0.001 TYR B 177 PHE 0.024 0.001 PHE C1025 TRP 0.032 0.001 TRP D 236 HIS 0.007 0.001 HIS G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (30507) covalent geometry : angle 0.63471 / 0.33 (41586) hydrogen bonds : bond 0.05227 / 6.28 ( 1212) hydrogen bonds : angle 5.11161 / 5.35 ( 3354) metal coordination : bond 0.00508 / 0.48 ( 6) metal coordination : angle 2.29890 / 4.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7855 (t70) cc_final: 0.7199 (t70) REVERT: A 137 ASN cc_start: 0.8623 (m-40) cc_final: 0.7746 (p0) REVERT: B 35 PHE cc_start: 0.8161 (m-80) cc_final: 0.7923 (m-80) REVERT: C 369 MET cc_start: 0.7671 (mmm) cc_final: 0.7435 (mmm) REVERT: C 636 CYS cc_start: 0.8137 (m) cc_final: 0.7518 (m) REVERT: C 768 MET cc_start: 0.7401 (mtm) cc_final: 0.6984 (mtm) REVERT: C 1023 HIS cc_start: 0.8559 (m-70) cc_final: 0.8065 (m-70) REVERT: C 1080 ASN cc_start: 0.8509 (t0) cc_final: 0.8221 (t0) REVERT: C 1278 LEU cc_start: 0.9219 (tp) cc_final: 0.8944 (tp) REVERT: C 1304 MET cc_start: 0.8709 (tpp) cc_final: 0.8345 (tpp) REVERT: D 821 MET cc_start: 0.8187 (tpt) cc_final: 0.7322 (mpp) REVERT: D 1254 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7733 (mm-30) REVERT: E 62 GLN cc_start: 0.8423 (tt0) cc_final: 0.7820 (tm-30) REVERT: G 35 MET cc_start: 0.8274 (mpp) cc_final: 0.6988 (ptp) outliers start: 23 outliers final: 16 residues processed: 270 average time/residue: 0.1668 time to fit residues: 76.7546 Evaluate side-chains 248 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 33 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 158 optimal weight: 2.9990 chunk 385 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 361 optimal weight: 10.0000 chunk 18 optimal weight: 0.0050 chunk 249 optimal weight: 0.4980 chunk 213 optimal weight: 6.9990 chunk 112 optimal weight: 0.0870 overall best weight: 0.9176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C1070 HIS ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.146554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100316 restraints weight = 56315.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099415 restraints weight = 36042.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102176 restraints weight = 26117.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102065 restraints weight = 19097.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102241 restraints weight = 18351.149| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30513 Z= 0.120 Angle : 0.570 13.180 41592 Z= 0.296 Chirality : 0.045 0.741 4820 Planarity : 0.004 0.094 5266 Dihedral : 12.863 147.636 4876 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.09 % Allowed : 10.70 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3812 helix: 0.85 (0.14), residues: 1335 sheet: -0.71 (0.25), residues: 415 loop : -1.61 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 211 TYR 0.028 0.001 TYR B 177 PHE 0.020 0.001 PHE C1025 TRP 0.016 0.001 TRP D 236 HIS 0.013 0.001 HIS G 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (30507) covalent geometry : angle 0.57015 / 0.30 (41586) hydrogen bonds : bond 0.04659 / 5.72 ( 1212) hydrogen bonds : angle 4.69772 / 4.87 ( 3354) metal coordination : bond 0.00445 / 0.45 ( 6) metal coordination : angle 1.71391 / 3.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8508 (m110) cc_final: 0.8235 (m-40) REVERT: A 135 ASP cc_start: 0.7852 (t70) cc_final: 0.7176 (t70) REVERT: A 137 ASN cc_start: 0.8697 (m-40) cc_final: 0.7725 (p0) REVERT: B 95 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8120 (mttt) REVERT: C 124 MET cc_start: 0.7391 (ttm) cc_final: 0.7188 (ttp) REVERT: C 158 ASP cc_start: 0.7739 (t70) cc_final: 0.7485 (t0) REVERT: C 636 CYS cc_start: 0.8155 (m) cc_final: 0.7578 (m) REVERT: C 760 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7976 (t0) REVERT: C 768 MET cc_start: 0.7315 (mtm) cc_final: 0.6897 (mtm) REVERT: C 1023 HIS cc_start: 0.8559 (m-70) cc_final: 0.8015 (m-70) REVERT: C 1080 ASN cc_start: 0.8603 (t0) cc_final: 0.8219 (t0) REVERT: C 1122 LYS cc_start: 0.6606 (tttt) cc_final: 0.6352 (tttt) REVERT: C 1278 LEU cc_start: 0.9150 (tp) cc_final: 0.8835 (tp) REVERT: C 1304 MET cc_start: 0.8638 (tpp) cc_final: 0.8122 (tpp) REVERT: D 821 MET cc_start: 0.8183 (tpt) cc_final: 0.7485 (mpp) REVERT: D 1156 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8273 (tp) REVERT: D 1254 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7762 (mt-10) REVERT: E 72 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7500 (tm-30) REVERT: E 75 GLN cc_start: 0.8803 (pp30) cc_final: 0.8562 (pp30) REVERT: G 35 MET cc_start: 0.8264 (mpp) cc_final: 0.7853 (mpp) outliers start: 31 outliers final: 19 residues processed: 274 average time/residue: 0.1618 time to fit residues: 76.0984 Evaluate side-chains 256 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 357 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 356 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 56 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 777 HIS ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.137394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094623 restraints weight = 54944.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093705 restraints weight = 40264.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.094868 restraints weight = 33575.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094960 restraints weight = 28217.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095115 restraints weight = 24439.078| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30513 Z= 0.201 Angle : 0.623 13.531 41592 Z= 0.322 Chirality : 0.045 0.426 4820 Planarity : 0.004 0.097 5266 Dihedral : 12.891 148.638 4876 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.94 % Allowed : 12.60 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 3812 helix: 0.82 (0.14), residues: 1350 sheet: -0.77 (0.25), residues: 423 loop : -1.65 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 974 TYR 0.029 0.002 TYR B 177 PHE 0.018 0.002 PHE C 390 TRP 0.018 0.001 TRP D 236 HIS 0.005 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (30507) covalent geometry : angle 0.62231 / 0.32 (41586) hydrogen bonds : bond 0.04716 / 5.80 ( 1212) hydrogen bonds : angle 4.63094 / 4.86 ( 3354) metal coordination : bond 0.01144 / 1.13 ( 6) metal coordination : angle 2.53939 / 5.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8413 (m110) cc_final: 0.8115 (m-40) REVERT: A 135 ASP cc_start: 0.7790 (t70) cc_final: 0.7280 (t70) REVERT: A 137 ASN cc_start: 0.8404 (m-40) cc_final: 0.7577 (p0) REVERT: B 35 PHE cc_start: 0.8178 (m-80) cc_final: 0.7942 (m-80) REVERT: C 124 MET cc_start: 0.7381 (ttm) cc_final: 0.7064 (ttp) REVERT: C 768 MET cc_start: 0.7568 (mtm) cc_final: 0.7217 (mtm) REVERT: C 1023 HIS cc_start: 0.8456 (m-70) cc_final: 0.7914 (m-70) REVERT: C 1080 ASN cc_start: 0.8551 (t0) cc_final: 0.8242 (t0) REVERT: D 697 MET cc_start: 0.8440 (tmm) cc_final: 0.8105 (tmm) REVERT: D 821 MET cc_start: 0.7968 (tpt) cc_final: 0.7678 (mpp) REVERT: D 1156 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8338 (tp) REVERT: E 75 GLN cc_start: 0.8732 (pp30) cc_final: 0.8505 (pp30) REVERT: G 35 MET cc_start: 0.8449 (mpp) cc_final: 0.7980 (mtm) outliers start: 55 outliers final: 29 residues processed: 280 average time/residue: 0.1639 time to fit residues: 78.7071 Evaluate side-chains 259 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 33 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 304 optimal weight: 0.2980 chunk 237 optimal weight: 3.9990 chunk 194 optimal weight: 0.0020 chunk 174 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 300 optimal weight: 0.0870 chunk 265 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 921 GLN ** D1366 HIS ** 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 = 0.4073 r_free = 0.4073 target = 0.148811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101938 restraints weight = 57629.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102443 restraints weight = 37467.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103398 restraints weight = 27585.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103977 restraints weight = 24869.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104112 restraints weight = 21179.485| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30513 Z= 0.108 Angle : 0.563 11.913 41592 Z= 0.291 Chirality : 0.044 0.415 4820 Planarity : 0.004 0.088 5266 Dihedral : 12.818 148.343 4876 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.58 % Allowed : 14.14 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3812 helix: 1.03 (0.14), residues: 1344 sheet: -0.63 (0.25), residues: 424 loop : -1.54 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 52 TYR 0.017 0.001 TYR A 177 PHE 0.016 0.001 PHE C1025 TRP 0.012 0.001 TRP D 236 HIS 0.010 0.001 HIS G 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (30507) covalent geometry : angle 0.56229 / 0.29 (41586) hydrogen bonds : bond 0.04261 / 5.33 ( 1212) hydrogen bonds : angle 4.37191 / 4.51 ( 3354) metal coordination : bond 0.00209 / 0.25 ( 6) metal coordination : angle 2.01501 / 4.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8489 (m110) cc_final: 0.8236 (m-40) REVERT: A 135 ASP cc_start: 0.7845 (t70) cc_final: 0.7145 (t70) REVERT: A 137 ASN cc_start: 0.8728 (m-40) cc_final: 0.7693 (p0) REVERT: C 158 ASP cc_start: 0.7799 (t70) cc_final: 0.7589 (t0) REVERT: C 219 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: C 369 MET cc_start: 0.7680 (mmm) cc_final: 0.7382 (mmm) REVERT: C 488 MET cc_start: 0.6803 (ttp) cc_final: 0.6568 (ttp) REVERT: C 569 ILE cc_start: 0.9061 (tp) cc_final: 0.8833 (tt) REVERT: C 636 CYS cc_start: 0.8187 (m) cc_final: 0.7657 (m) REVERT: C 760 ASN cc_start: 0.8285 (m-40) cc_final: 0.7905 (t0) REVERT: C 768 MET cc_start: 0.7338 (mtm) cc_final: 0.6918 (mtm) REVERT: C 1023 HIS cc_start: 0.8648 (m-70) cc_final: 0.8116 (m-70) REVERT: C 1080 ASN cc_start: 0.8476 (t0) cc_final: 0.8164 (t0) REVERT: C 1278 LEU cc_start: 0.9090 (tp) cc_final: 0.8778 (tp) REVERT: D 576 ARG cc_start: 0.8472 (mtt180) cc_final: 0.8251 (mtt180) REVERT: D 581 MET cc_start: 0.8660 (tpp) cc_final: 0.8242 (ttm) REVERT: D 821 MET cc_start: 0.8044 (tpt) cc_final: 0.7621 (mpp) REVERT: D 1156 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8286 (tp) REVERT: D 1254 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7900 (mm-30) REVERT: G 35 MET cc_start: 0.8278 (mpp) cc_final: 0.7770 (mtm) outliers start: 45 outliers final: 23 residues processed: 290 average time/residue: 0.1634 time to fit residues: 81.0202 Evaluate side-chains 261 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain G residue 33 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 365 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.144719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098089 restraints weight = 56234.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097213 restraints weight = 33409.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099301 restraints weight = 26077.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099949 restraints weight = 19593.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100172 restraints weight = 17394.611| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30513 Z= 0.126 Angle : 0.564 14.962 41592 Z= 0.291 Chirality : 0.043 0.377 4820 Planarity : 0.004 0.087 5266 Dihedral : 12.799 148.560 4876 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.79 % Allowed : 14.99 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3812 helix: 1.12 (0.14), residues: 1338 sheet: -0.62 (0.25), residues: 425 loop : -1.52 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.022 0.001 TYR C1229 PHE 0.015 0.001 PHE C1025 TRP 0.015 0.001 TRP D 236 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (30507) covalent geometry : angle 0.56391 / 0.29 (41586) hydrogen bonds : bond 0.04245 / 5.31 ( 1212) hydrogen bonds : angle 4.27831 / 4.45 ( 3354) metal coordination : bond 0.00555 / 0.56 ( 6) metal coordination : angle 1.84198 / 3.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8481 (m110) cc_final: 0.8226 (m-40) REVERT: A 135 ASP cc_start: 0.7866 (t70) cc_final: 0.7205 (t70) REVERT: A 137 ASN cc_start: 0.8687 (m-40) cc_final: 0.7649 (p0) REVERT: C 158 ASP cc_start: 0.7892 (t70) cc_final: 0.7676 (t0) REVERT: C 569 ILE cc_start: 0.9109 (tp) cc_final: 0.8899 (tt) REVERT: C 760 ASN cc_start: 0.8324 (m-40) cc_final: 0.7967 (t0) REVERT: C 768 MET cc_start: 0.7370 (mtm) cc_final: 0.6940 (mtm) REVERT: C 1023 HIS cc_start: 0.8654 (m-70) cc_final: 0.8113 (m-70) REVERT: C 1080 ASN cc_start: 0.8587 (t0) cc_final: 0.8233 (t0) REVERT: C 1119 MET cc_start: 0.8249 (tpp) cc_final: 0.7495 (tpp) REVERT: C 1278 LEU cc_start: 0.9139 (tp) cc_final: 0.8819 (tp) REVERT: D 581 MET cc_start: 0.8674 (tpp) cc_final: 0.8410 (ttm) REVERT: D 821 MET cc_start: 0.8027 (tpt) cc_final: 0.7712 (mpp) REVERT: D 953 LYS cc_start: 0.8115 (pttt) cc_final: 0.7706 (mmmm) REVERT: D 1156 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8239 (tp) REVERT: D 1254 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7916 (mm-30) REVERT: D 1293 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6570 (pt0) REVERT: E 62 GLN cc_start: 0.8358 (tt0) cc_final: 0.7939 (tm-30) REVERT: E 72 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7702 (tm-30) REVERT: G 35 MET cc_start: 0.8357 (mpp) cc_final: 0.7828 (mtm) outliers start: 51 outliers final: 35 residues processed: 282 average time/residue: 0.1582 time to fit residues: 77.2548 Evaluate side-chains 272 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 183 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 385 optimal weight: 50.0000 chunk 349 optimal weight: 10.0000 chunk 375 optimal weight: 40.0000 chunk 187 optimal weight: 0.9990 chunk 344 optimal weight: 40.0000 chunk 326 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 325 optimal weight: 0.0020 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.145395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099425 restraints weight = 55689.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098246 restraints weight = 36464.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099859 restraints weight = 25992.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102458 restraints weight = 20202.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102073 restraints weight = 16173.304| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30513 Z= 0.105 Angle : 0.554 13.944 41592 Z= 0.285 Chirality : 0.043 0.382 4820 Planarity : 0.004 0.083 5266 Dihedral : 12.761 148.580 4876 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.69 % Allowed : 15.45 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3812 helix: 1.13 (0.14), residues: 1352 sheet: -0.47 (0.25), residues: 416 loop : -1.52 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 974 TYR 0.016 0.001 TYR A 177 PHE 0.009 0.001 PHE C 186 TRP 0.013 0.001 TRP D 236 HIS 0.003 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (30507) covalent geometry : angle 0.55382 / 0.29 (41586) hydrogen bonds : bond 0.04077 / 5.13 ( 1212) hydrogen bonds : angle 4.17297 / 4.31 ( 3354) metal coordination : bond 0.00319 / 0.35 ( 6) metal coordination : angle 1.72237 / 3.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8491 (m110) cc_final: 0.8228 (m-40) REVERT: A 135 ASP cc_start: 0.7871 (t70) cc_final: 0.7244 (t70) REVERT: A 137 ASN cc_start: 0.8614 (m-40) cc_final: 0.7652 (p0) REVERT: B 96 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7109 (p0) REVERT: C 124 MET cc_start: 0.7645 (ttm) cc_final: 0.7227 (ttp) REVERT: C 158 ASP cc_start: 0.7912 (t70) cc_final: 0.7711 (t0) REVERT: C 369 MET cc_start: 0.7732 (mmm) cc_final: 0.7343 (mmm) REVERT: C 488 MET cc_start: 0.6850 (ttp) cc_final: 0.6639 (ttp) REVERT: C 569 ILE cc_start: 0.9098 (tp) cc_final: 0.8872 (tt) REVERT: C 636 CYS cc_start: 0.8161 (m) cc_final: 0.7676 (m) REVERT: C 760 ASN cc_start: 0.8263 (m-40) cc_final: 0.7927 (t0) REVERT: C 768 MET cc_start: 0.7335 (mtm) cc_final: 0.6843 (mtm) REVERT: C 1023 HIS cc_start: 0.8610 (m-70) cc_final: 0.8069 (m-70) REVERT: C 1080 ASN cc_start: 0.8695 (t0) cc_final: 0.8398 (t0) REVERT: C 1119 MET cc_start: 0.8280 (tpp) cc_final: 0.7523 (tpp) REVERT: C 1219 GLU cc_start: 0.8247 (tt0) cc_final: 0.8017 (tt0) REVERT: C 1278 LEU cc_start: 0.9134 (tp) cc_final: 0.8842 (tp) REVERT: D 114 ILE cc_start: 0.8887 (tp) cc_final: 0.8608 (tp) REVERT: D 304 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6829 (p0) REVERT: D 324 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6746 (pp) REVERT: D 821 MET cc_start: 0.7988 (tpt) cc_final: 0.7759 (mpp) REVERT: D 953 LYS cc_start: 0.8116 (pttt) cc_final: 0.7682 (mmmm) REVERT: D 1156 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 1254 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 1293 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6572 (pt0) REVERT: E 62 GLN cc_start: 0.8366 (tt0) cc_final: 0.8067 (tm-30) REVERT: E 72 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7679 (tm-30) REVERT: G 35 MET cc_start: 0.8406 (mpp) cc_final: 0.7891 (mtm) outliers start: 48 outliers final: 33 residues processed: 287 average time/residue: 0.1552 time to fit residues: 77.0364 Evaluate side-chains 281 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 73 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 6 optimal weight: 0.0670 chunk 371 optimal weight: 40.0000 chunk 362 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 374 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 419 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.147948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102863 restraints weight = 57694.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100549 restraints weight = 41025.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102411 restraints weight = 31737.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102910 restraints weight = 25021.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103058 restraints weight = 21708.383| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30513 Z= 0.143 Angle : 0.573 13.486 41592 Z= 0.295 Chirality : 0.043 0.385 4820 Planarity : 0.004 0.084 5266 Dihedral : 12.755 149.016 4876 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.79 % Allowed : 16.12 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3812 helix: 1.21 (0.15), residues: 1340 sheet: -0.52 (0.25), residues: 421 loop : -1.49 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 974 TYR 0.029 0.001 TYR G 10 PHE 0.010 0.001 PHE C 35 TRP 0.012 0.001 TRP D 236 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (30507) covalent geometry : angle 0.57292 / 0.29 (41586) hydrogen bonds : bond 0.04187 / 5.24 ( 1212) hydrogen bonds : angle 4.17481 / 4.35 ( 3354) metal coordination : bond 0.00690 / 0.68 ( 6) metal coordination : angle 1.90780 / 3.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8538 (m110) cc_final: 0.8279 (m-40) REVERT: A 135 ASP cc_start: 0.7886 (t70) cc_final: 0.7175 (t70) REVERT: A 137 ASN cc_start: 0.8710 (m-40) cc_final: 0.7646 (p0) REVERT: B 21 SER cc_start: 0.7588 (t) cc_final: 0.7221 (m) REVERT: B 96 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7233 (p0) REVERT: C 124 MET cc_start: 0.7758 (ttm) cc_final: 0.7315 (ttp) REVERT: C 158 ASP cc_start: 0.7935 (t70) cc_final: 0.7682 (t0) REVERT: C 369 MET cc_start: 0.7663 (mmm) cc_final: 0.7456 (mmm) REVERT: C 488 MET cc_start: 0.6945 (ttp) cc_final: 0.6693 (ttp) REVERT: C 685 MET cc_start: 0.7408 (mtp) cc_final: 0.7182 (mtt) REVERT: C 768 MET cc_start: 0.7353 (mtm) cc_final: 0.6826 (mtm) REVERT: C 1023 HIS cc_start: 0.8640 (m-70) cc_final: 0.8093 (m-70) REVERT: C 1080 ASN cc_start: 0.8703 (t0) cc_final: 0.8316 (t0) REVERT: C 1119 MET cc_start: 0.8402 (tpp) cc_final: 0.7643 (tpp) REVERT: C 1278 LEU cc_start: 0.9124 (tp) cc_final: 0.8800 (tp) REVERT: D 304 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6903 (p0) REVERT: D 324 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6921 (pp) REVERT: D 697 MET cc_start: 0.8088 (tmm) cc_final: 0.7741 (tmm) REVERT: D 821 MET cc_start: 0.7984 (tpt) cc_final: 0.7778 (mpp) REVERT: D 953 LYS cc_start: 0.8213 (pttt) cc_final: 0.7789 (mmmm) REVERT: D 1156 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8237 (tp) REVERT: D 1254 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 1293 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6581 (pt0) REVERT: E 62 GLN cc_start: 0.8377 (tt0) cc_final: 0.7930 (tm-30) REVERT: E 72 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7699 (tm-30) REVERT: G 35 MET cc_start: 0.8359 (mpp) cc_final: 0.7899 (mtm) outliers start: 51 outliers final: 36 residues processed: 279 average time/residue: 0.1580 time to fit residues: 75.9344 Evaluate side-chains 282 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 112 optimal weight: 0.0670 chunk 161 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 295 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 287 optimal weight: 0.0970 chunk 252 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN G 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.146374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099687 restraints weight = 56247.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099259 restraints weight = 33930.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101239 restraints weight = 24946.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101777 restraints weight = 19694.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102106 restraints weight = 17310.675| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30513 Z= 0.102 Angle : 0.556 13.636 41592 Z= 0.286 Chirality : 0.043 0.380 4820 Planarity : 0.004 0.081 5266 Dihedral : 12.699 148.672 4876 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.55 % Allowed : 16.68 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3812 helix: 1.19 (0.15), residues: 1361 sheet: -0.43 (0.25), residues: 422 loop : -1.48 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 933 TYR 0.017 0.001 TYR A 177 PHE 0.011 0.001 PHE C 514 TRP 0.017 0.001 TRP D 236 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (30507) covalent geometry : angle 0.55583 / 0.29 (41586) hydrogen bonds : bond 0.03977 / 5.01 ( 1212) hydrogen bonds : angle 4.06445 / 4.19 ( 3354) metal coordination : bond 0.00238 / 0.29 ( 6) metal coordination : angle 1.81792 / 3.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7873 (t70) cc_final: 0.7241 (t70) REVERT: A 137 ASN cc_start: 0.8670 (m-40) cc_final: 0.7677 (p0) REVERT: B 96 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7069 (p0) REVERT: C 124 MET cc_start: 0.7851 (ttm) cc_final: 0.7446 (ttp) REVERT: C 158 ASP cc_start: 0.7796 (t70) cc_final: 0.7568 (t0) REVERT: C 219 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: C 369 MET cc_start: 0.7622 (mmm) cc_final: 0.7396 (mmm) REVERT: C 488 MET cc_start: 0.7189 (ttp) cc_final: 0.6974 (ttp) REVERT: C 636 CYS cc_start: 0.8187 (m) cc_final: 0.7559 (m) REVERT: C 760 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7780 (t0) REVERT: C 768 MET cc_start: 0.7308 (mtm) cc_final: 0.6794 (mtm) REVERT: C 1023 HIS cc_start: 0.8622 (m-70) cc_final: 0.8072 (m-70) REVERT: C 1080 ASN cc_start: 0.8707 (t0) cc_final: 0.8366 (t0) REVERT: C 1119 MET cc_start: 0.8353 (tpp) cc_final: 0.7564 (tpp) REVERT: C 1219 GLU cc_start: 0.8104 (tt0) cc_final: 0.7893 (tt0) REVERT: C 1278 LEU cc_start: 0.9066 (tp) cc_final: 0.8784 (tp) REVERT: D 114 ILE cc_start: 0.8838 (tp) cc_final: 0.8527 (tp) REVERT: D 304 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6813 (p0) REVERT: D 324 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6781 (pp) REVERT: D 457 TYR cc_start: 0.8175 (m-10) cc_final: 0.7961 (m-80) REVERT: D 953 LYS cc_start: 0.8226 (pttt) cc_final: 0.7717 (mmmm) REVERT: D 1156 LEU cc_start: 0.8723 (mm) cc_final: 0.8201 (tp) REVERT: D 1254 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7981 (mm-30) REVERT: D 1293 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6671 (pt0) REVERT: E 62 GLN cc_start: 0.8257 (tt0) cc_final: 0.7858 (tm-30) REVERT: E 72 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7655 (tm-30) REVERT: G 35 MET cc_start: 0.8340 (mpp) cc_final: 0.7822 (mtm) outliers start: 44 outliers final: 29 residues processed: 287 average time/residue: 0.1618 time to fit residues: 79.5567 Evaluate side-chains 280 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 108 optimal weight: 0.8980 chunk 334 optimal weight: 9.9990 chunk 257 optimal weight: 0.2980 chunk 140 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 279 optimal weight: 0.9990 chunk 318 optimal weight: 0.0770 chunk 107 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 219 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105070 restraints weight = 57175.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104828 restraints weight = 37202.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106386 restraints weight = 28236.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106877 restraints weight = 23291.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107220 restraints weight = 20210.748| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30513 Z= 0.104 Angle : 0.570 14.139 41592 Z= 0.289 Chirality : 0.043 0.377 4820 Planarity : 0.004 0.080 5266 Dihedral : 12.680 148.727 4876 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.34 % Allowed : 17.10 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3812 helix: 1.22 (0.14), residues: 1360 sheet: -0.41 (0.25), residues: 424 loop : -1.46 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.016 0.001 TYR A 177 PHE 0.014 0.001 PHE C 514 TRP 0.052 0.002 TRP D 236 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (30507) covalent geometry : angle 0.56266 / 0.29 (41586) hydrogen bonds : bond 0.03926 / 4.96 ( 1212) hydrogen bonds : angle 4.03114 / 4.18 ( 3354) metal coordination : bond 0.01552 / 2.06 ( 6) metal coordination : angle 7.38280 / 11.43 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7851 (t70) cc_final: 0.7229 (t70) REVERT: A 137 ASN cc_start: 0.8631 (m-40) cc_final: 0.7665 (p0) REVERT: B 21 SER cc_start: 0.7623 (t) cc_final: 0.7300 (m) REVERT: B 96 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7058 (p0) REVERT: C 124 MET cc_start: 0.7881 (ttm) cc_final: 0.7478 (ttp) REVERT: C 158 ASP cc_start: 0.7786 (t70) cc_final: 0.7564 (t0) REVERT: C 219 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: C 369 MET cc_start: 0.7626 (mmm) cc_final: 0.7396 (mmm) REVERT: C 636 CYS cc_start: 0.8129 (m) cc_final: 0.7515 (m) REVERT: C 760 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7758 (t0) REVERT: C 768 MET cc_start: 0.7308 (mtm) cc_final: 0.7107 (mtm) REVERT: C 1023 HIS cc_start: 0.8580 (m-70) cc_final: 0.8040 (m-70) REVERT: C 1080 ASN cc_start: 0.8635 (t0) cc_final: 0.8250 (t0) REVERT: C 1119 MET cc_start: 0.8326 (tpp) cc_final: 0.7556 (tpp) REVERT: C 1278 LEU cc_start: 0.9054 (tp) cc_final: 0.8773 (tp) REVERT: D 114 ILE cc_start: 0.8870 (tp) cc_final: 0.8568 (tp) REVERT: D 304 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6798 (p0) REVERT: D 324 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6734 (pp) REVERT: D 457 TYR cc_start: 0.8192 (m-10) cc_final: 0.7983 (m-80) REVERT: D 953 LYS cc_start: 0.8125 (pttt) cc_final: 0.7666 (mmmm) REVERT: D 1156 LEU cc_start: 0.8720 (mm) cc_final: 0.8224 (tp) REVERT: D 1196 LEU cc_start: 0.8585 (tt) cc_final: 0.7941 (mt) REVERT: D 1293 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6711 (pt0) REVERT: E 62 GLN cc_start: 0.8201 (tt0) cc_final: 0.7822 (tm-30) REVERT: E 72 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7652 (tm-30) REVERT: G 35 MET cc_start: 0.8386 (mpp) cc_final: 0.7887 (mtm) outliers start: 38 outliers final: 30 residues processed: 283 average time/residue: 0.1541 time to fit residues: 75.4286 Evaluate side-chains 281 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 104 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 92 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 380 optimal weight: 0.0870 chunk 176 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 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 = 0.4079 r_free = 0.4079 target = 0.149578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103920 restraints weight = 57735.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.102996 restraints weight = 38513.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104128 restraints weight = 28640.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104637 restraints weight = 24674.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104818 restraints weight = 22090.290| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30513 Z= 0.113 Angle : 0.568 13.660 41592 Z= 0.289 Chirality : 0.043 0.363 4820 Planarity : 0.004 0.085 5266 Dihedral : 12.668 148.895 4876 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.58 % Allowed : 17.03 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3812 helix: 1.25 (0.15), residues: 1361 sheet: -0.39 (0.25), residues: 423 loop : -1.46 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 974 TYR 0.018 0.001 TYR C1229 PHE 0.014 0.001 PHE C 514 TRP 0.040 0.002 TRP D 236 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (30507) covalent geometry : angle 0.56416 / 0.29 (41586) hydrogen bonds : bond 0.03940 / 4.97 ( 1212) hydrogen bonds : angle 4.01474 / 4.18 ( 3354) metal coordination : bond 0.01066 / 1.41 ( 6) metal coordination : angle 5.78110 / 8.72 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4324.23 seconds wall clock time: 75 minutes 53.88 seconds (4553.88 seconds total)