Starting phenix.real_space_refine on Mon Sep 14 11:42:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.cif" model { file = "/net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py6_13714/09_2026/7py6_13714.cif" } resolution = 4.1 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= 0.065 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 33 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 15996 SG CYS D 85 86.871 115.163 72.929 1.00135.73 S ATOM 16020 SG CYS D 88 91.015 115.944 71.586 1.00136.03 S ATOM 21708 SG CYS D 814 96.513 46.090 79.493 1.00 91.25 S ATOM 22273 SG CYS D 888 98.157 49.614 77.555 1.00 89.84 S ATOM 22345 SG CYS D 898 99.759 47.049 80.006 1.00 86.97 S Time building chain proxies: 6.33, per 1000 atoms: 0.21 Number of scatterers: 29959 At special positions: 0 Unit cell: (195.11, 153.69, 174.4, 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: 2.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " 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 814 " 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: 137 helices and 51 sheets defined 38.3% alpha, 13.4% beta 29 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.604A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.013A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) 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: 3.550A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.637A 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 50 removed outlier: 3.560A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 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 154 through 158 removed outlier: 3.623A pdb=" N THR B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.765A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.515A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.526A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.564A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.947A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.938A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.960A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.803A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.524A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 4.026A pdb=" N VAL C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.043A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.696A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.604A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.854A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 4.397A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' 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 688 removed outlier: 3.889A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 896 through 904 removed outlier: 3.501A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.930A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.687A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.517A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.968A 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 removed outlier: 3.824A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.617A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.027A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.789A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 4.245A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.508A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C1331 " --> pdb=" O LEU C1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.504A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.678A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.599A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 4.002A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.086A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.809A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.596A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.581A pdb=" N ARG D 293 " --> pdb=" O ASP D 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.646A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 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 405 through 416 removed outlier: 3.676A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (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 455 removed outlier: 3.674A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 450 through 455' Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.663A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.629A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.520A 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 640 through 644 removed outlier: 3.908A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.610A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.763A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.530A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 4.217A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.547A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.528A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 925 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: 4.021A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.529A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.829A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1259 removed outlier: 3.989A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.883A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 4.167A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.547A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.536A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.560A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.649A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 104 through 119 Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.623A pdb=" N VAL F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 39 removed outlier: 3.555A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 106 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 202 through 207 removed outlier: 4.538A pdb=" N GLU F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.516A pdb=" N ILE F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.991A pdb=" N ILE F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN F 286 " --> pdb=" O GLN F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 281 through 286' Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 313 through 318 removed outlier: 4.011A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 removed outlier: 3.522A pdb=" N ALA F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 346 through 358 removed outlier: 4.336A pdb=" N ALA F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA F 352 " --> pdb=" O HIS F 348 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS F 353 " --> pdb=" O GLN F 349 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA F 355 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 361 No H-bonds generated for 'chain 'F' and resid 359 through 361' Processing helix chain 'F' and resid 369 through 377 removed outlier: 4.052A pdb=" N LEU F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'F' and resid 399 through 402 Processing helix chain 'F' and resid 403 through 408 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.879A pdb=" N ALA F 420 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 421' Processing helix chain 'F' and resid 445 through 450 Processing helix chain 'F' and resid 455 through 459 removed outlier: 3.872A pdb=" N ASP F 458 " --> pdb=" O THR F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 491 removed outlier: 3.557A pdb=" N CYS F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 491 " --> pdb=" O ASN F 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.499A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.371A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.969A 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 removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.651A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.806A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.048A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.048A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.689A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.557A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.961A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.448A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.978A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.630A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.626A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 5.299A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.952A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.775A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.255A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.908A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.838A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.648A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 838 removed outlier: 6.981A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.573A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.573A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 111 removed outlier: 3.778A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.859A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.845A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.901A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.880A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.166A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1034 through 1035 removed outlier: 3.631A pdb=" N VAL D1081 " --> pdb=" O PHE D1034 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1046 through 1049 Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE8, first strand: chain 'D' and resid 1187 through 1190 Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.582A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 42 through 43 Processing sheet with id=AF2, first strand: chain 'G' and resid 47 through 48 removed outlier: 3.615A pdb=" N ARG G 62 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'F' and resid 141 through 142 removed outlier: 4.165A pdb=" N VAL F 141 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU F 159 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N VAL F 197 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL F 161 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER F 185 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 221 through 222 Processing sheet with id=AF6, first strand: chain 'F' and resid 226 through 228 1094 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 8.34 Time building geometry restraints manager: 3.61 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: 10017 1.34 - 1.46: 4417 1.46 - 1.58: 15745 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 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C1' DC T 25 " pdb=" N1 DC T 25 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.56e+00 bond pdb=" C3' DA N 28 " pdb=" C2' DA N 28 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.45e+00 bond pdb=" C3' DG T 27 " pdb=" O3' DG T 27 " ideal model delta sigma weight residual 1.435 1.471 -0.036 1.30e-02 5.92e+03 7.70e+00 bond pdb=" N CYS D 85 " pdb=" CA CYS D 85 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.13e+00 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 40643 1.99 - 3.98: 826 3.98 - 5.96: 90 5.96 - 7.95: 19 7.95 - 9.94: 8 Bond angle restraints: 41586 Sorted by residual: angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 111.91 107.11 4.80 8.90e-01 1.26e+00 2.91e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT N 11 " pdb=" C4 DT N 11 " pdb=" O4 DT N 11 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" O4 DT T 12 " pdb=" C4 DT T 12 " pdb=" C5 DT T 12 " ideal model delta sigma weight residual 124.90 121.97 2.93 7.00e-01 2.04e+00 1.76e+01 ... (remaining 41581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 17971 35.05 - 70.10: 506 70.10 - 105.14: 32 105.14 - 140.19: 3 140.19 - 175.24: 2 Dihedral angle restraints: 18514 sinusoidal: 7511 harmonic: 11003 Sorted by residual: 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 -36.03 72.37 1 3.10e+00 1.04e-01 6.96e+02 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 36.35 -35.35 71.69 1 3.10e+00 1.04e-01 6.85e+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 25.31 -60.45 1 4.00e+00 6.25e-02 3.04e+02 ... (remaining 18511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4051 0.062 - 0.123: 709 0.123 - 0.185: 43 0.185 - 0.247: 12 0.247 - 0.309: 5 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CB ILE D 147 " pdb=" CA ILE D 147 " pdb=" CG1 ILE D 147 " pdb=" CG2 ILE D 147 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' C R 5 " pdb=" C3' C R 5 " pdb=" O2' C R 5 " pdb=" C1' C R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.85e+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 -2.52 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4817 not shown) Planarity restraints: 5266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.061 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A 30 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 358 " 0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 359 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 359 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 359 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 233 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO D 234 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " -0.032 5.00e-02 4.00e+02 ... (remaining 5263 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 551 2.66 - 3.22: 28889 3.22 - 3.78: 46697 3.78 - 4.34: 59418 4.34 - 4.90: 93623 Nonbonded interactions: 229178 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.135 2.170 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR D1038 " pdb=" O ALA D1077 " model vdw 2.157 3.040 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.176 2.496 ... (remaining 229173 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: 2.000 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 37.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.004 0.342 30512 Z= 0.206 Angle : 0.674 9.938 41586 Z= 0.389 Chirality : 0.047 0.309 4820 Planarity : 0.005 0.094 5266 Dihedral : 15.682 175.241 11420 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.04 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3812 helix: 0.09 (0.15), residues: 1220 sheet: -0.56 (0.27), residues: 375 loop : -1.37 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 272 TYR 0.024 0.001 TYR G 68 PHE 0.020 0.001 PHE D1100 TRP 0.023 0.002 TRP D 236 HIS 0.016 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.19 (30507) covalent geometry : angle 0.67354 / 0.39 (41586) hydrogen bonds : bond 0.19025 / 20.82 ( 1161) hydrogen bonds : angle 7.03464 / 7.36 ( 3180) metal coordination : bond 0.18822 / 9.41 ( 5) *********************** 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 304 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6554 (m-80) cc_final: 0.5972 (m-10) REVERT: A 194 GLN cc_start: 0.8874 (pm20) cc_final: 0.8585 (pm20) REVERT: C 195 PHE cc_start: 0.7940 (m-80) cc_final: 0.6865 (m-80) REVERT: C 239 MET cc_start: 0.7870 (tpt) cc_final: 0.7515 (tpp) REVERT: C 684 ASN cc_start: 0.8223 (t0) cc_final: 0.7935 (t0) REVERT: C 951 MET cc_start: 0.9203 (tmm) cc_final: 0.8472 (tmm) REVERT: C 1131 MET cc_start: 0.8773 (ppp) cc_final: 0.7645 (ppp) REVERT: C 1243 MET cc_start: 0.8410 (tmm) cc_final: 0.8190 (tmm) REVERT: C 1315 MET cc_start: 0.8517 (ptm) cc_final: 0.8309 (ptt) REVERT: D 192 MET cc_start: 0.8436 (ttp) cc_final: 0.7893 (tmm) REVERT: D 581 MET cc_start: 0.8119 (mtp) cc_final: 0.7822 (mtt) REVERT: D 747 MET cc_start: 0.8155 (tpp) cc_final: 0.7672 (mmt) REVERT: D 1260 MET cc_start: 0.8324 (mtp) cc_final: 0.8116 (mtp) REVERT: E 10 VAL cc_start: 0.8985 (t) cc_final: 0.8755 (p) REVERT: E 60 ASN cc_start: 0.8459 (p0) cc_final: 0.7955 (p0) REVERT: G 9 TRP cc_start: 0.7715 (m100) cc_final: 0.7442 (m100) REVERT: G 35 MET cc_start: 0.9091 (mpp) cc_final: 0.8744 (mpp) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.1763 time to fit residues: 88.6689 Evaluate side-chains 211 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 46 GLN C 69 GLN C 604 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057859 restraints weight = 117028.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059578 restraints weight = 66055.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060723 restraints weight = 44228.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061523 restraints weight = 33594.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061976 restraints weight = 28036.694| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30512 Z= 0.158 Angle : 0.632 15.903 41586 Z= 0.329 Chirality : 0.049 0.952 4820 Planarity : 0.004 0.092 5266 Dihedral : 13.195 173.595 4876 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3812 helix: 0.42 (0.15), residues: 1247 sheet: -0.76 (0.25), residues: 430 loop : -1.35 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1231 TYR 0.019 0.001 TYR C1229 PHE 0.018 0.001 PHE D 141 TRP 0.012 0.001 TRP D 236 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (30507) covalent geometry : angle 0.63156 / 0.33 (41586) hydrogen bonds : bond 0.04825 / 5.49 ( 1161) hydrogen bonds : angle 5.37364 / 5.74 ( 3180) metal coordination : bond 0.00857 / 0.54 ( 5) *********************** 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 266 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8892 (m-10) cc_final: 0.8550 (m-10) REVERT: A 137 ASN cc_start: 0.8613 (p0) cc_final: 0.8359 (p0) REVERT: A 194 GLN cc_start: 0.8892 (pm20) cc_final: 0.8513 (pm20) REVERT: C 370 MET cc_start: 0.8756 (tmm) cc_final: 0.8550 (tpp) REVERT: C 684 ASN cc_start: 0.8490 (t0) cc_final: 0.8213 (t0) REVERT: C 704 MET cc_start: 0.8926 (mtp) cc_final: 0.8659 (mtp) REVERT: C 798 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7268 (mm-40) REVERT: C 951 MET cc_start: 0.9221 (tmm) cc_final: 0.8485 (tmm) REVERT: C 1131 MET cc_start: 0.8744 (ppp) cc_final: 0.7851 (ppp) REVERT: C 1243 MET cc_start: 0.8669 (tmm) cc_final: 0.8162 (tmm) REVERT: D 192 MET cc_start: 0.8345 (ttp) cc_final: 0.7958 (tmm) REVERT: D 466 MET cc_start: 0.9280 (pmm) cc_final: 0.8515 (pmm) REVERT: D 581 MET cc_start: 0.8192 (mtp) cc_final: 0.7957 (mtt) REVERT: D 1254 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7701 (tm-30) REVERT: E 10 VAL cc_start: 0.8978 (t) cc_final: 0.8718 (p) REVERT: G 41 GLU cc_start: 0.8676 (pp20) cc_final: 0.8105 (pp20) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.1795 time to fit residues: 81.2892 Evaluate side-chains 205 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 158 optimal weight: 0.0470 chunk 385 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.084462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.057276 restraints weight = 117747.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058868 restraints weight = 67772.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059976 restraints weight = 46237.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060708 restraints weight = 35495.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061106 restraints weight = 29771.306| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30512 Z= 0.182 Angle : 0.610 11.742 41586 Z= 0.322 Chirality : 0.045 0.463 4820 Planarity : 0.004 0.092 5266 Dihedral : 13.247 173.856 4876 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3812 helix: 0.50 (0.15), residues: 1246 sheet: -0.78 (0.24), residues: 443 loop : -1.38 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 114 TYR 0.017 0.001 TYR C1229 PHE 0.025 0.001 PHE G 64 TRP 0.012 0.001 TRP D 236 HIS 0.010 0.001 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (30507) covalent geometry : angle 0.60958 / 0.32 (41586) hydrogen bonds : bond 0.04586 / 5.23 ( 1161) hydrogen bonds : angle 5.14106 / 5.48 ( 3180) metal coordination : bond 0.00408 / 0.44 ( 5) *********************** 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 265 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8923 (m-10) cc_final: 0.8529 (m-10) REVERT: A 137 ASN cc_start: 0.8738 (p0) cc_final: 0.8464 (p0) REVERT: A 191 ARG cc_start: 0.8544 (ptm160) cc_final: 0.8212 (ptm160) REVERT: A 194 GLN cc_start: 0.8966 (pm20) cc_final: 0.8570 (pm20) REVERT: C 515 MET cc_start: 0.8936 (tmm) cc_final: 0.8485 (tmm) REVERT: C 684 ASN cc_start: 0.8665 (t0) cc_final: 0.8390 (t0) REVERT: C 798 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7309 (mm-40) REVERT: C 1131 MET cc_start: 0.8850 (ppp) cc_final: 0.8631 (tmm) REVERT: C 1243 MET cc_start: 0.8881 (tmm) cc_final: 0.8304 (tmm) REVERT: D 192 MET cc_start: 0.8481 (ttp) cc_final: 0.7999 (tmm) REVERT: D 466 MET cc_start: 0.9277 (pmm) cc_final: 0.8454 (pmm) REVERT: D 1260 MET cc_start: 0.8475 (mtp) cc_final: 0.8187 (mtp) REVERT: E 10 VAL cc_start: 0.9019 (t) cc_final: 0.8755 (p) REVERT: G 41 GLU cc_start: 0.8614 (pp20) cc_final: 0.8100 (pp20) REVERT: G 73 MET cc_start: 0.8520 (tpp) cc_final: 0.7507 (tpp) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1808 time to fit residues: 81.3489 Evaluate side-chains 202 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 357 optimal weight: 20.0000 chunk 254 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 372 optimal weight: 30.0000 chunk 115 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 114 optimal weight: 0.0970 chunk 356 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.085479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058342 restraints weight = 115970.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060040 restraints weight = 65292.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.061207 restraints weight = 43680.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061993 restraints weight = 33222.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062435 restraints weight = 27679.741| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30512 Z= 0.120 Angle : 0.580 10.177 41586 Z= 0.303 Chirality : 0.045 0.338 4820 Planarity : 0.004 0.086 5266 Dihedral : 13.216 174.120 4876 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3812 helix: 0.56 (0.15), residues: 1253 sheet: -0.62 (0.25), residues: 426 loop : -1.35 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 137 TYR 0.015 0.001 TYR D 512 PHE 0.030 0.001 PHE D1145 TRP 0.008 0.001 TRP D1193 HIS 0.005 0.001 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (30507) covalent geometry : angle 0.57950 / 0.30 (41586) hydrogen bonds : bond 0.04048 / 4.67 ( 1161) hydrogen bonds : angle 4.87182 / 5.15 ( 3180) metal coordination : bond 0.00312 / 0.28 ( 5) *********************** 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 272 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8891 (m-10) cc_final: 0.8515 (m-10) REVERT: A 93 GLN cc_start: 0.8206 (pp30) cc_final: 0.7951 (pp30) REVERT: A 137 ASN cc_start: 0.8682 (p0) cc_final: 0.8373 (p0) REVERT: A 191 ARG cc_start: 0.8473 (ptm160) cc_final: 0.8060 (ptm160) REVERT: A 194 GLN cc_start: 0.8919 (pm20) cc_final: 0.8454 (pm20) REVERT: B 95 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8009 (mtpt) REVERT: C 429 MET cc_start: 0.9107 (mmp) cc_final: 0.8850 (mmp) REVERT: C 515 MET cc_start: 0.8967 (tmm) cc_final: 0.8581 (tmm) REVERT: C 704 MET cc_start: 0.8898 (mtp) cc_final: 0.8473 (mtm) REVERT: C 1095 ASP cc_start: 0.8657 (m-30) cc_final: 0.8453 (m-30) REVERT: C 1119 MET cc_start: 0.9063 (tpp) cc_final: 0.8599 (tpp) REVERT: C 1243 MET cc_start: 0.8880 (tmm) cc_final: 0.8358 (tmm) REVERT: D 130 MET cc_start: 0.7590 (mpp) cc_final: 0.6989 (mpp) REVERT: D 192 MET cc_start: 0.8371 (ttp) cc_final: 0.7960 (tmm) REVERT: D 466 MET cc_start: 0.9070 (pmm) cc_final: 0.8777 (pmm) REVERT: D 610 ARG cc_start: 0.8587 (mmt-90) cc_final: 0.7738 (tpp80) REVERT: E 10 VAL cc_start: 0.8979 (t) cc_final: 0.8711 (p) REVERT: G 9 TRP cc_start: 0.7793 (m100) cc_final: 0.7124 (m100) REVERT: G 41 GLU cc_start: 0.8642 (pp20) cc_final: 0.7804 (pp20) REVERT: G 43 MET cc_start: 0.7580 (tmm) cc_final: 0.5566 (ptp) REVERT: G 73 MET cc_start: 0.8575 (tpp) cc_final: 0.7390 (tpp) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1691 time to fit residues: 78.1060 Evaluate side-chains 208 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 304 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 684 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 294 ASN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058083 restraints weight = 117346.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059740 restraints weight = 66973.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060866 restraints weight = 45187.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061535 restraints weight = 34675.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062045 restraints weight = 29289.850| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30512 Z= 0.137 Angle : 0.578 10.409 41586 Z= 0.304 Chirality : 0.045 0.337 4820 Planarity : 0.004 0.100 5266 Dihedral : 13.230 174.167 4876 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3812 helix: 0.60 (0.15), residues: 1258 sheet: -0.66 (0.25), residues: 436 loop : -1.34 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 371 TYR 0.015 0.001 TYR C1229 PHE 0.025 0.001 PHE D1100 TRP 0.009 0.001 TRP D 236 HIS 0.004 0.001 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (30507) covalent geometry : angle 0.57791 / 0.30 (41586) hydrogen bonds : bond 0.03931 / 4.55 ( 1161) hydrogen bonds : angle 4.77900 / 5.06 ( 3180) metal coordination : bond 0.00341 / 0.32 ( 5) *********************** 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 266 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8941 (m-10) cc_final: 0.8604 (m-10) REVERT: A 137 ASN cc_start: 0.8717 (p0) cc_final: 0.8429 (p0) REVERT: C 429 MET cc_start: 0.9175 (mmp) cc_final: 0.8926 (mmp) REVERT: C 515 MET cc_start: 0.9051 (tmm) cc_final: 0.8530 (tmm) REVERT: C 685 MET cc_start: 0.8409 (tmm) cc_final: 0.8010 (tmm) REVERT: C 1119 MET cc_start: 0.9198 (tpp) cc_final: 0.8416 (tpp) REVERT: C 1243 MET cc_start: 0.8894 (tmm) cc_final: 0.8390 (tmm) REVERT: D 192 MET cc_start: 0.8489 (ttp) cc_final: 0.7998 (tmm) REVERT: D 417 ARG cc_start: 0.8554 (ttt180) cc_final: 0.8229 (ttt180) REVERT: D 466 MET cc_start: 0.9079 (pmm) cc_final: 0.8746 (pmm) REVERT: D 581 MET cc_start: 0.8365 (mtp) cc_final: 0.8152 (mtt) REVERT: D 610 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.7841 (tpp80) REVERT: D 644 MET cc_start: 0.8743 (mpp) cc_final: 0.8521 (mpp) REVERT: D 697 MET cc_start: 0.8605 (tmm) cc_final: 0.8374 (tmm) REVERT: D 1260 MET cc_start: 0.8424 (mtp) cc_final: 0.8180 (mtp) REVERT: E 10 VAL cc_start: 0.9015 (t) cc_final: 0.8741 (p) REVERT: E 43 ASN cc_start: 0.8524 (t0) cc_final: 0.8218 (t0) REVERT: E 44 ASP cc_start: 0.8631 (t0) cc_final: 0.8420 (t0) REVERT: G 9 TRP cc_start: 0.7727 (m100) cc_final: 0.7304 (m100) REVERT: G 35 MET cc_start: 0.9166 (mpp) cc_final: 0.8910 (mpp) REVERT: G 41 GLU cc_start: 0.8649 (pp20) cc_final: 0.8082 (pp20) REVERT: G 73 MET cc_start: 0.8497 (tpp) cc_final: 0.7421 (tpp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1636 time to fit residues: 73.9150 Evaluate side-chains 207 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 365 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 130 optimal weight: 0.2980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058084 restraints weight = 116543.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059712 restraints weight = 66564.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060810 restraints weight = 45156.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.061591 restraints weight = 34679.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062019 restraints weight = 28954.410| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30512 Z= 0.132 Angle : 0.579 8.824 41586 Z= 0.302 Chirality : 0.044 0.339 4820 Planarity : 0.004 0.100 5266 Dihedral : 13.253 174.157 4876 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3812 helix: 0.64 (0.15), residues: 1260 sheet: -0.65 (0.25), residues: 446 loop : -1.30 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 352 TYR 0.012 0.001 TYR D 512 PHE 0.018 0.001 PHE G 39 TRP 0.010 0.001 TRP D1193 HIS 0.004 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (30507) covalent geometry : angle 0.57944 / 0.30 (41586) hydrogen bonds : bond 0.03814 / 4.42 ( 1161) hydrogen bonds : angle 4.68360 / 4.96 ( 3180) metal coordination : bond 0.00325 / 0.31 ( 5) *********************** 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 261 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8944 (m-10) cc_final: 0.8600 (m-10) REVERT: A 137 ASN cc_start: 0.8716 (p0) cc_final: 0.8423 (p0) REVERT: A 177 TYR cc_start: 0.7472 (m-10) cc_final: 0.7112 (m-80) REVERT: B 95 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8052 (mtpt) REVERT: C 429 MET cc_start: 0.9162 (mmp) cc_final: 0.8924 (mmp) REVERT: C 515 MET cc_start: 0.9085 (tmm) cc_final: 0.8586 (tmm) REVERT: C 685 MET cc_start: 0.8391 (tmm) cc_final: 0.8140 (tmm) REVERT: C 951 MET cc_start: 0.9256 (tmm) cc_final: 0.8516 (tmm) REVERT: C 1119 MET cc_start: 0.9177 (tpp) cc_final: 0.8372 (tpp) REVERT: C 1243 MET cc_start: 0.8917 (tmm) cc_final: 0.8349 (tmm) REVERT: D 130 MET cc_start: 0.7744 (mtt) cc_final: 0.7215 (mpp) REVERT: D 192 MET cc_start: 0.8455 (ttp) cc_final: 0.8007 (tmm) REVERT: D 298 MET cc_start: 0.8645 (ttm) cc_final: 0.8437 (ttp) REVERT: D 417 ARG cc_start: 0.8575 (ttt180) cc_final: 0.8127 (ttt180) REVERT: D 435 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7662 (mm110) REVERT: D 466 MET cc_start: 0.9126 (pmm) cc_final: 0.8651 (pmm) REVERT: D 610 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.7896 (tpp80) REVERT: D 644 MET cc_start: 0.8693 (mpp) cc_final: 0.8424 (mpp) REVERT: D 1189 MET cc_start: 0.7423 (tpt) cc_final: 0.7049 (tpt) REVERT: D 1260 MET cc_start: 0.8441 (mtp) cc_final: 0.8191 (mtp) REVERT: E 10 VAL cc_start: 0.8994 (t) cc_final: 0.8716 (p) REVERT: E 43 ASN cc_start: 0.8494 (t0) cc_final: 0.8066 (t0) REVERT: E 44 ASP cc_start: 0.8591 (t0) cc_final: 0.8373 (t0) REVERT: G 9 TRP cc_start: 0.7812 (m100) cc_final: 0.7329 (m100) REVERT: G 41 GLU cc_start: 0.8577 (pp20) cc_final: 0.7955 (pp20) REVERT: G 73 MET cc_start: 0.8467 (tpp) cc_final: 0.7495 (tpp) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.1729 time to fit residues: 77.0265 Evaluate side-chains 209 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 183 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 chunk 349 optimal weight: 50.0000 chunk 375 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 344 optimal weight: 40.0000 chunk 326 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 325 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 62 GLN ** 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 = 0.3579 r_free = 0.3579 target = 0.084313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.057208 restraints weight = 118021.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058815 restraints weight = 68030.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059914 restraints weight = 46319.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060688 restraints weight = 35497.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061107 restraints weight = 29708.546| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30512 Z= 0.170 Angle : 0.601 8.910 41586 Z= 0.316 Chirality : 0.045 0.337 4820 Planarity : 0.004 0.101 5266 Dihedral : 13.280 173.931 4876 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3812 helix: 0.62 (0.15), residues: 1266 sheet: -0.63 (0.25), residues: 434 loop : -1.30 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 202 TYR 0.014 0.001 TYR C 726 PHE 0.017 0.001 PHE C 337 TRP 0.011 0.001 TRP D 236 HIS 0.007 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (30507) covalent geometry : angle 0.60107 / 0.32 (41586) hydrogen bonds : bond 0.03920 / 4.52 ( 1161) hydrogen bonds : angle 4.73632 / 5.04 ( 3180) metal coordination : bond 0.00430 / 0.46 ( 5) *********************** 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 254 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8991 (m-10) cc_final: 0.8630 (m-10) REVERT: A 137 ASN cc_start: 0.8752 (p0) cc_final: 0.8461 (p0) REVERT: A 177 TYR cc_start: 0.7704 (m-10) cc_final: 0.7396 (m-80) REVERT: C 515 MET cc_start: 0.9157 (tmm) cc_final: 0.8630 (tmm) REVERT: C 1243 MET cc_start: 0.8964 (tmm) cc_final: 0.8398 (tmm) REVERT: D 192 MET cc_start: 0.8535 (ttp) cc_final: 0.8030 (tmm) REVERT: D 417 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8045 (ttt180) REVERT: D 435 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7641 (mm110) REVERT: D 581 MET cc_start: 0.8297 (mtp) cc_final: 0.8085 (mtt) REVERT: D 610 ARG cc_start: 0.8696 (mmt-90) cc_final: 0.7954 (tpp80) REVERT: D 644 MET cc_start: 0.8734 (mpp) cc_final: 0.8449 (mpp) REVERT: D 697 MET cc_start: 0.8651 (tmm) cc_final: 0.8408 (tmm) REVERT: D 747 MET cc_start: 0.8559 (tpp) cc_final: 0.8348 (mmm) REVERT: D 1189 MET cc_start: 0.7384 (tpt) cc_final: 0.6958 (tpt) REVERT: D 1260 MET cc_start: 0.8547 (mtp) cc_final: 0.8306 (mtp) REVERT: E 10 VAL cc_start: 0.8998 (t) cc_final: 0.8730 (p) REVERT: E 43 ASN cc_start: 0.8555 (t0) cc_final: 0.8343 (t0) REVERT: G 9 TRP cc_start: 0.7793 (m100) cc_final: 0.7012 (m100) REVERT: G 35 MET cc_start: 0.9267 (mpp) cc_final: 0.8731 (mpp) REVERT: G 41 GLU cc_start: 0.8412 (pp20) cc_final: 0.7723 (pp20) REVERT: G 43 MET cc_start: 0.7654 (tmm) cc_final: 0.5969 (ptp) REVERT: G 73 MET cc_start: 0.8395 (tpp) cc_final: 0.7363 (tpp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1737 time to fit residues: 76.2283 Evaluate side-chains 198 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 73 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 6 optimal weight: 0.0370 chunk 371 optimal weight: 5.9990 chunk 362 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 374 optimal weight: 30.0000 chunk 216 optimal weight: 0.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN C 387 ASN C 798 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.085946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058702 restraints weight = 117125.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060409 restraints weight = 65715.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061568 restraints weight = 43921.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062316 restraints weight = 33394.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062868 restraints weight = 27917.262| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 30512 Z= 0.112 Angle : 0.585 8.768 41586 Z= 0.304 Chirality : 0.045 0.342 4820 Planarity : 0.004 0.099 5266 Dihedral : 13.249 174.403 4876 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.04 % Allowed : 1.34 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3812 helix: 0.64 (0.15), residues: 1267 sheet: -0.50 (0.26), residues: 421 loop : -1.26 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG D1148 TYR 0.016 0.001 TYR D 512 PHE 0.022 0.001 PHE D1100 TRP 0.011 0.001 TRP D1193 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (30507) covalent geometry : angle 0.58469 / 0.30 (41586) hydrogen bonds : bond 0.03647 / 4.26 ( 1161) hydrogen bonds : angle 4.59063 / 4.87 ( 3180) metal coordination : bond 0.00319 / 0.19 ( 5) *********************** 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 276 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8892 (m-10) cc_final: 0.8585 (m-10) REVERT: A 137 ASN cc_start: 0.8636 (p0) cc_final: 0.8317 (p0) REVERT: A 177 TYR cc_start: 0.7524 (m-10) cc_final: 0.7147 (m-10) REVERT: B 95 LYS cc_start: 0.8266 (mtmt) cc_final: 0.8021 (mtpt) REVERT: C 515 MET cc_start: 0.9076 (tmm) cc_final: 0.8619 (tmm) REVERT: C 951 MET cc_start: 0.9231 (tmm) cc_final: 0.8463 (tmm) REVERT: C 1119 MET cc_start: 0.9097 (tpp) cc_final: 0.8491 (tpp) REVERT: C 1243 MET cc_start: 0.8865 (tmm) cc_final: 0.8351 (tmm) REVERT: D 130 MET cc_start: 0.7473 (mtt) cc_final: 0.7181 (mpp) REVERT: D 192 MET cc_start: 0.8433 (ttp) cc_final: 0.7974 (tmm) REVERT: D 295 GLU cc_start: 0.8679 (pm20) cc_final: 0.8403 (pm20) REVERT: D 466 MET cc_start: 0.9281 (pmm) cc_final: 0.8479 (pmm) REVERT: D 610 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.7928 (tpp80) REVERT: D 625 MET cc_start: 0.8397 (tmm) cc_final: 0.8150 (tmm) REVERT: D 697 MET cc_start: 0.8493 (tmm) cc_final: 0.8279 (tmm) REVERT: D 1189 MET cc_start: 0.7375 (tpt) cc_final: 0.7092 (tpt) REVERT: D 1260 MET cc_start: 0.8368 (mtp) cc_final: 0.8156 (mtp) REVERT: E 10 VAL cc_start: 0.8941 (t) cc_final: 0.8661 (p) REVERT: G 9 TRP cc_start: 0.7854 (m100) cc_final: 0.7092 (m100) REVERT: G 35 MET cc_start: 0.9220 (mpp) cc_final: 0.8766 (mpp) REVERT: G 41 GLU cc_start: 0.8370 (pp20) cc_final: 0.7800 (pp20) REVERT: G 43 MET cc_start: 0.7608 (tmm) cc_final: 0.5939 (ptm) REVERT: G 73 MET cc_start: 0.8370 (tpp) cc_final: 0.7055 (tpp) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1731 time to fit residues: 81.5991 Evaluate side-chains 205 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 112 optimal weight: 0.0870 chunk 161 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 295 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 287 optimal weight: 0.6980 chunk 252 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN C 387 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.086149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059036 restraints weight = 116295.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060781 restraints weight = 65498.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061930 restraints weight = 43756.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062691 restraints weight = 33306.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063127 restraints weight = 27818.314| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30512 Z= 0.109 Angle : 0.590 9.907 41586 Z= 0.306 Chirality : 0.044 0.338 4820 Planarity : 0.004 0.098 5266 Dihedral : 13.229 174.620 4876 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3812 helix: 0.67 (0.15), residues: 1269 sheet: -0.45 (0.26), residues: 406 loop : -1.25 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1148 TYR 0.014 0.001 TYR D 512 PHE 0.023 0.001 PHE G 39 TRP 0.015 0.001 TRP D 580 HIS 0.010 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (30507) covalent geometry : angle 0.58993 / 0.31 (41586) hydrogen bonds : bond 0.03583 / 4.19 ( 1161) hydrogen bonds : angle 4.55033 / 4.83 ( 3180) metal coordination : bond 0.00401 / 0.36 ( 5) *********************** 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 261 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8874 (m-10) cc_final: 0.8589 (m-10) REVERT: A 137 ASN cc_start: 0.8609 (p0) cc_final: 0.8286 (p0) REVERT: A 177 TYR cc_start: 0.7455 (m-10) cc_final: 0.7013 (m-80) REVERT: B 95 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7978 (mtpt) REVERT: C 515 MET cc_start: 0.9062 (tmm) cc_final: 0.8578 (tmm) REVERT: C 951 MET cc_start: 0.9242 (tmm) cc_final: 0.8477 (tmm) REVERT: C 1119 MET cc_start: 0.9090 (tpp) cc_final: 0.8419 (tpp) REVERT: C 1243 MET cc_start: 0.8847 (tmm) cc_final: 0.8378 (tmm) REVERT: D 130 MET cc_start: 0.7420 (mtt) cc_final: 0.7006 (mpp) REVERT: D 192 MET cc_start: 0.8424 (ttp) cc_final: 0.7996 (tmm) REVERT: D 295 GLU cc_start: 0.8642 (pm20) cc_final: 0.8282 (pm20) REVERT: D 466 MET cc_start: 0.9265 (pmm) cc_final: 0.8499 (pmm) REVERT: D 610 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.7919 (tpp80) REVERT: D 666 GLU cc_start: 0.8807 (mp0) cc_final: 0.8551 (mp0) REVERT: D 697 MET cc_start: 0.8486 (tmm) cc_final: 0.8270 (tmm) REVERT: D 1189 MET cc_start: 0.7396 (tpt) cc_final: 0.7102 (tpt) REVERT: D 1260 MET cc_start: 0.8399 (mtp) cc_final: 0.8182 (mtp) REVERT: E 10 VAL cc_start: 0.8964 (t) cc_final: 0.8717 (p) REVERT: G 9 TRP cc_start: 0.7823 (m100) cc_final: 0.7021 (m100) REVERT: G 35 MET cc_start: 0.9198 (mpp) cc_final: 0.8778 (mpp) REVERT: G 41 GLU cc_start: 0.8311 (pp20) cc_final: 0.7741 (pp20) REVERT: G 43 MET cc_start: 0.7533 (tmm) cc_final: 0.5830 (ptm) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1674 time to fit residues: 74.8788 Evaluate side-chains 210 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 108 optimal weight: 2.9990 chunk 334 optimal weight: 0.7980 chunk 257 optimal weight: 0.0870 chunk 140 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 318 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 62 GLN ** 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 = 0.3607 r_free = 0.3607 target = 0.085680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.058380 restraints weight = 116829.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060053 restraints weight = 66147.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061182 restraints weight = 44616.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061876 restraints weight = 34087.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.062477 restraints weight = 28681.380| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30512 Z= 0.124 Angle : 0.587 13.441 41586 Z= 0.304 Chirality : 0.044 0.336 4820 Planarity : 0.004 0.098 5266 Dihedral : 13.219 174.428 4876 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3812 helix: 0.70 (0.15), residues: 1268 sheet: -0.50 (0.25), residues: 422 loop : -1.23 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1148 TYR 0.013 0.001 TYR D 512 PHE 0.016 0.001 PHE D1100 TRP 0.011 0.001 TRP D1193 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30507) covalent geometry : angle 0.58703 / 0.30 (41586) hydrogen bonds : bond 0.03607 / 4.20 ( 1161) hydrogen bonds : angle 4.54069 / 4.83 ( 3180) metal coordination : bond 0.00450 / 0.49 ( 5) ********************** 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 249 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8995 (m-10) cc_final: 0.8685 (m-10) REVERT: A 137 ASN cc_start: 0.8745 (p0) cc_final: 0.8463 (p0) REVERT: A 177 TYR cc_start: 0.7635 (m-10) cc_final: 0.7141 (m-80) REVERT: B 95 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8018 (mtpt) REVERT: C 515 MET cc_start: 0.9143 (tmm) cc_final: 0.8569 (tmm) REVERT: C 1085 MET cc_start: 0.8947 (mmp) cc_final: 0.8701 (mmt) REVERT: C 1119 MET cc_start: 0.9164 (tpp) cc_final: 0.8354 (tpp) REVERT: C 1243 MET cc_start: 0.8967 (tmm) cc_final: 0.8511 (tmm) REVERT: D 129 ASP cc_start: 0.8094 (t0) cc_final: 0.7783 (t0) REVERT: D 130 MET cc_start: 0.7470 (mtt) cc_final: 0.6997 (mpp) REVERT: D 192 MET cc_start: 0.8576 (ttp) cc_final: 0.8040 (tmm) REVERT: D 466 MET cc_start: 0.9267 (pmm) cc_final: 0.8445 (pmm) REVERT: D 581 MET cc_start: 0.8634 (mmm) cc_final: 0.8415 (mtt) REVERT: D 610 ARG cc_start: 0.8783 (mmt-90) cc_final: 0.8225 (tpp80) REVERT: D 625 MET cc_start: 0.8470 (tmm) cc_final: 0.8269 (tmm) REVERT: D 666 GLU cc_start: 0.8864 (mp0) cc_final: 0.8584 (mp0) REVERT: D 697 MET cc_start: 0.8659 (tmm) cc_final: 0.8364 (tmm) REVERT: D 1260 MET cc_start: 0.8591 (mtp) cc_final: 0.8334 (mtp) REVERT: E 10 VAL cc_start: 0.9009 (t) cc_final: 0.8755 (p) REVERT: G 9 TRP cc_start: 0.7720 (m100) cc_final: 0.7175 (m100) REVERT: G 35 MET cc_start: 0.9277 (mpp) cc_final: 0.8854 (mpp) REVERT: G 41 GLU cc_start: 0.8287 (pp20) cc_final: 0.7727 (pp20) REVERT: G 43 MET cc_start: 0.7586 (tmm) cc_final: 0.5846 (ptp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1721 time to fit residues: 73.8870 Evaluate side-chains 199 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 92 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 380 optimal weight: 0.0370 chunk 176 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.084814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.057722 restraints weight = 118082.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.059353 restraints weight = 67805.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060436 restraints weight = 46001.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061183 restraints weight = 35387.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.061684 restraints weight = 29645.900| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30512 Z= 0.151 Angle : 0.602 12.637 41586 Z= 0.312 Chirality : 0.045 0.336 4820 Planarity : 0.004 0.098 5266 Dihedral : 13.242 174.138 4876 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3812 helix: 0.71 (0.15), residues: 1269 sheet: -0.54 (0.25), residues: 419 loop : -1.26 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1148 TYR 0.014 0.001 TYR D 512 PHE 0.015 0.001 PHE D1100 TRP 0.012 0.001 TRP D1193 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (30507) covalent geometry : angle 0.60250 / 0.31 (41586) hydrogen bonds : bond 0.03699 / 4.29 ( 1161) hydrogen bonds : angle 4.56876 / 4.88 ( 3180) metal coordination : bond 0.00492 / 0.52 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5334.56 seconds wall clock time: 93 minutes 14.71 seconds (5594.71 seconds total)