Starting phenix.real_space_refine on Thu Jun 26 16:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1j_28785/06_2025/8f1j_28785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1j_28785/06_2025/8f1j_28785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f1j_28785/06_2025/8f1j_28785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1j_28785/06_2025/8f1j_28785.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1j_28785/06_2025/8f1j_28785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1j_28785/06_2025/8f1j_28785.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 1.131 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 94 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 19045 2.51 5 N 5432 2.21 5 O 6136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30829 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 695 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "C" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "G" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1738 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 215} Chain breaks: 1 Chain: "H" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2336 Classifications: {'peptide': 302} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 287} Chain breaks: 2 Chain: "I" Number of atoms: 10446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10446 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1270} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 10498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 10498 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3232 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 388} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 715 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 34, 694 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Conformer: "B" Number of residues, atoms: 34, 694 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} bond proxies already assigned to first conformer: 749 Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 283 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16020 SG CYS J 70 46.053 79.301 53.523 1.00 66.14 S ATOM 16034 SG CYS J 72 47.462 77.291 50.715 1.00 76.14 S ATOM 16142 SG CYS J 85 44.013 76.399 51.944 1.00 74.60 S ATOM 16166 SG CYS J 88 47.002 75.581 54.080 1.00 67.88 S ATOM 21854 SG CYS J 814 35.807 78.111 121.037 1.00 81.67 S ATOM 22419 SG CYS J 888 38.790 77.840 118.699 1.00 65.58 S ATOM 22470 SG CYS J 895 37.266 81.262 119.645 1.00 59.85 S ATOM 22491 SG CYS J 898 39.273 79.386 122.159 1.00 66.99 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA B 49 " occ=0.55 ... (40 atoms not shown) pdb=" C4 B DA B 49 " occ=0.45 Time building chain proxies: 18.46, per 1000 atoms: 0.60 Number of scatterers: 30829 At special positions: 0 Unit cell: (152.28, 168.48, 176.04, 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 119 16.00 P 94 15.00 Mg 1 11.99 O 6136 8.00 N 5432 7.00 C 19045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6848 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 50 sheets defined 42.3% alpha, 15.8% beta 44 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 12.17 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.564A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.754A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.523A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.516A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 250 through 255 removed outlier: 3.809A pdb=" N LEU H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG H 255 " --> pdb=" O PRO H 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 250 through 255' Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'H' and resid 263 through 273 Processing helix chain 'H' and resid 277 through 283 removed outlier: 3.504A pdb=" N LEU H 281 " --> pdb=" O TYR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 291 Processing helix chain 'H' and resid 296 through 309 Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.601A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.712A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.522A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.043A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 359 through 371 removed outlier: 4.084A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.996A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.610A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.721A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.654A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.636A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 646 through 650 removed outlier: 3.876A pdb=" N VAL I 650 " --> pdb=" O ARG I 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.716A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.059A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.685A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 980 removed outlier: 3.788A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 992 Processing helix chain 'I' and resid 1011 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.529A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.510A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.619A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.671A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.595A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.908A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.809A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.667A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.604A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 255 through 259 removed outlier: 4.088A pdb=" N ARG J 259 " --> pdb=" O ASP J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.930A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.605A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.109A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.504A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.777A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.735A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.511A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.114A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.505A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1074 removed outlier: 3.985A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.781A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.381A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.790A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.540A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.516A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.637A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 4.476A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 25 Processing helix chain 'M' and resid 29 through 42 Processing helix chain 'M' and resid 119 through 130 Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.715A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.773A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.745A pdb=" N GLU M 248 " --> pdb=" O ASP M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 removed outlier: 3.776A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 305 Processing helix chain 'M' and resid 312 through 351 removed outlier: 3.731A pdb=" N SER M 316 " --> pdb=" O ASN M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 358 removed outlier: 3.601A pdb=" N GLU M 356 " --> pdb=" O GLN M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.557A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA M 373 " --> pdb=" O ASP M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 447 Processing helix chain 'M' and resid 454 through 465 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 20 removed outlier: 6.598A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.664A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.552A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 6.407A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.861A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.542A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.692A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.616A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.725A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.715A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR I 262 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.993A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.604A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE I 310 " --> pdb=" O TYR I 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.582A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.438A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.755A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.061A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.838A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.705A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.794A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.846A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.660A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.923A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.727A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.552A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 7.178A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL J1017 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.914A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE9, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 4.494A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1187 through 1189 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.386A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AF4, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.710A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 406 through 407 1267 hydrogen bonds defined for protein. 3531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 20.16 Time building geometry restraints manager: 9.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9786 1.34 - 1.45: 4065 1.45 - 1.57: 17234 1.57 - 1.69: 186 1.69 - 1.81: 206 Bond restraints: 31477 Sorted by residual: bond pdb=" CB PRO I 855 " pdb=" CG PRO I 855 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.19e+00 bond pdb=" C3' DC A 24 " pdb=" O3' DC A 24 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CG PRO M 17 " pdb=" CD PRO M 17 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.79e-01 bond pdb=" CB PRO J 254 " pdb=" CG PRO J 254 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.57e-01 bond pdb=" C ASP I 959 " pdb=" O ASP I 959 " ideal model delta sigma weight residual 1.236 1.246 -0.009 1.15e-02 7.56e+03 6.66e-01 ... (remaining 31472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 42592 2.00 - 4.00: 330 4.00 - 6.00: 14 6.00 - 8.01: 2 8.01 - 10.01: 1 Bond angle restraints: 42939 Sorted by residual: angle pdb=" C ASP J 902 " pdb=" N LEU J 903 " pdb=" CA LEU J 903 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY J 613 " pdb=" CA GLY J 613 " pdb=" C GLY J 613 " ideal model delta sigma weight residual 110.60 115.19 -4.59 1.46e+00 4.69e-01 9.87e+00 angle pdb=" C ARG I 233 " pdb=" N ASP I 234 " pdb=" CA ASP I 234 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.69e+00 angle pdb=" C LEU I1291 " pdb=" N THR I1292 " pdb=" CA THR I1292 " ideal model delta sigma weight residual 122.56 118.98 3.58 1.50e+00 4.44e-01 5.70e+00 angle pdb=" C LYS I1294 " pdb=" N SER I1295 " pdb=" CA SER I1295 " ideal model delta sigma weight residual 122.17 118.64 3.53 1.54e+00 4.22e-01 5.24e+00 ... (remaining 42934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 18160 24.85 - 49.70: 799 49.70 - 74.54: 184 74.54 - 99.39: 17 99.39 - 124.24: 1 Dihedral angle restraints: 19161 sinusoidal: 8543 harmonic: 10618 Sorted by residual: dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN I 235 " pdb=" C ASN I 235 " pdb=" N LYS I 236 " pdb=" CA LYS I 236 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C4' DC A 24 " pdb=" C3' DC A 24 " pdb=" O3' DC A 24 " pdb=" P DT A 25 " ideal model delta sinusoidal sigma weight residual 220.00 95.76 124.24 1 3.50e+01 8.16e-04 1.22e+01 ... (remaining 19158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3214 0.029 - 0.058: 1138 0.058 - 0.088: 280 0.088 - 0.117: 241 0.117 - 0.146: 51 Chirality restraints: 4924 Sorted by residual: chirality pdb=" CA VAL I 700 " pdb=" N VAL I 700 " pdb=" C VAL I 700 " pdb=" CB VAL I 700 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE J 434 " pdb=" N ILE J 434 " pdb=" C ILE J 434 " pdb=" CB ILE J 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL H 192 " pdb=" N VAL H 192 " pdb=" C VAL H 192 " pdb=" CB VAL H 192 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 4921 not shown) Planarity restraints: 5283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO J 246 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 392 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO M 393 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO M 393 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO M 393 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO I 590 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " -0.019 5.00e-02 4.00e+02 ... (remaining 5280 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 313 2.66 - 3.22: 26802 3.22 - 3.78: 45970 3.78 - 4.34: 65401 4.34 - 4.90: 106555 Nonbonded interactions: 245041 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.096 2.170 nonbonded pdb=" O2 DC C 14 " pdb=" N2 DG D 59 " model vdw 2.121 2.496 nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.147 3.040 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.184 3.040 nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 2.223 3.040 ... (remaining 245036 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.200 Check model and map are aligned: 0.240 Set scattering table: 0.360 Process input model: 93.530 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 31485 Z= 0.097 Angle : 0.443 10.008 42951 Z= 0.247 Chirality : 0.039 0.146 4924 Planarity : 0.003 0.042 5283 Dihedral : 13.896 124.238 12313 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.98 % Allowed : 5.13 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3662 helix: 1.96 (0.15), residues: 1390 sheet: 0.61 (0.24), residues: 471 loop : -0.50 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 409 HIS 0.003 0.000 HIS I 447 PHE 0.008 0.001 PHE M 318 TYR 0.010 0.001 TYR J 679 ARG 0.004 0.000 ARG M 296 Details of bonding type rmsd hydrogen bonds : bond 0.14012 ( 1368) hydrogen bonds : angle 5.04124 ( 3733) metal coordination : bond 0.00239 ( 8) metal coordination : angle 2.33389 ( 12) covalent geometry : bond 0.00189 (31477) covalent geometry : angle 0.44100 (42939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 268 ASN cc_start: 0.9526 (m-40) cc_final: 0.9280 (m110) REVERT: J 161 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8165 (p) REVERT: J 466 MET cc_start: 0.8645 (mtt) cc_final: 0.8342 (mtt) REVERT: J 979 ASN cc_start: 0.9227 (m-40) cc_final: 0.8728 (m-40) REVERT: J 1189 MET cc_start: 0.8393 (tpp) cc_final: 0.8004 (tmm) REVERT: K 70 GLN cc_start: 0.8918 (tt0) cc_final: 0.8557 (tm-30) REVERT: M 281 HIS cc_start: 0.8557 (t-90) cc_final: 0.7735 (t-90) outliers start: 31 outliers final: 5 residues processed: 247 average time/residue: 1.8274 time to fit residues: 517.7838 Evaluate side-chains 160 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain M residue 13 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 7.9990 chunk 282 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 292 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 338 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN I1023 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053471 restraints weight = 91805.877| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.26 r_work: 0.2680 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31485 Z= 0.151 Angle : 0.511 10.145 42951 Z= 0.272 Chirality : 0.041 0.285 4924 Planarity : 0.004 0.052 5283 Dihedral : 15.294 124.377 5094 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.11 % Allowed : 8.46 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3662 helix: 2.04 (0.15), residues: 1410 sheet: 0.52 (0.25), residues: 466 loop : -0.50 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 126 HIS 0.010 0.001 HIS I1023 PHE 0.011 0.001 PHE M 318 TYR 0.018 0.001 TYR I 291 ARG 0.007 0.000 ARG M 240 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 1368) hydrogen bonds : angle 4.12096 ( 3733) metal coordination : bond 0.00598 ( 8) metal coordination : angle 2.32033 ( 12) covalent geometry : bond 0.00348 (31477) covalent geometry : angle 0.50998 (42939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 4.643 Fit side-chains revert: symmetry clash REVERT: H 66 HIS cc_start: 0.8565 (t70) cc_final: 0.8311 (t70) REVERT: H 268 ASN cc_start: 0.9554 (m-40) cc_final: 0.9328 (m110) REVERT: I 951 MET cc_start: 0.8606 (mmp) cc_final: 0.8341 (mtp) REVERT: J 102 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.9261 (mtp) REVERT: J 161 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.7941 (p) REVERT: J 413 ASP cc_start: 0.9015 (t0) cc_final: 0.8702 (t0) REVERT: J 466 MET cc_start: 0.9378 (mtt) cc_final: 0.9089 (mtt) REVERT: J 1189 MET cc_start: 0.8284 (tpp) cc_final: 0.7856 (tpt) REVERT: K 70 GLN cc_start: 0.8542 (tt0) cc_final: 0.8118 (tm-30) outliers start: 35 outliers final: 14 residues processed: 185 average time/residue: 1.5833 time to fit residues: 348.2650 Evaluate side-chains 166 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain M residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 34 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 335 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 352 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.082402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051668 restraints weight = 90251.273| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.27 r_work: 0.2648 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31485 Z= 0.181 Angle : 0.517 10.564 42951 Z= 0.272 Chirality : 0.042 0.286 4924 Planarity : 0.004 0.039 5283 Dihedral : 15.316 125.557 5092 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.17 % Allowed : 8.90 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3662 helix: 2.06 (0.14), residues: 1418 sheet: 0.59 (0.25), residues: 468 loop : -0.54 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 126 HIS 0.005 0.001 HIS J 777 PHE 0.021 0.001 PHE J1165 TYR 0.014 0.001 TYR I 291 ARG 0.005 0.000 ARG J 978 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1368) hydrogen bonds : angle 4.02014 ( 3733) metal coordination : bond 0.00688 ( 8) metal coordination : angle 2.50847 ( 12) covalent geometry : bond 0.00427 (31477) covalent geometry : angle 0.51523 (42939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 4.103 Fit side-chains revert: symmetry clash REVERT: G 86 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8871 (tttp) REVERT: G 93 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8757 (tm-30) REVERT: G 186 ASN cc_start: 0.8460 (m-40) cc_final: 0.8014 (m110) REVERT: H 147 GLN cc_start: 0.8431 (mt0) cc_final: 0.7965 (mt0) REVERT: H 268 ASN cc_start: 0.9523 (m-40) cc_final: 0.9288 (m110) REVERT: I 951 MET cc_start: 0.8653 (mmp) cc_final: 0.8392 (mtp) REVERT: J 161 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8213 (p) REVERT: J 466 MET cc_start: 0.9412 (mtt) cc_final: 0.9053 (mtt) REVERT: J 1189 MET cc_start: 0.8344 (tpp) cc_final: 0.8006 (tmm) REVERT: K 70 GLN cc_start: 0.8492 (tt0) cc_final: 0.8048 (tm-30) outliers start: 37 outliers final: 16 residues processed: 191 average time/residue: 1.6176 time to fit residues: 370.0196 Evaluate side-chains 166 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 254 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 329 optimal weight: 0.1980 chunk 266 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 297 optimal weight: 50.0000 chunk 63 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.082433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.052240 restraints weight = 84630.560| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.13 r_work: 0.2655 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31485 Z= 0.155 Angle : 0.494 10.230 42951 Z= 0.261 Chirality : 0.041 0.338 4924 Planarity : 0.003 0.050 5283 Dihedral : 15.300 125.758 5090 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.20 % Allowed : 9.82 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3662 helix: 2.06 (0.14), residues: 1428 sheet: 0.74 (0.25), residues: 451 loop : -0.48 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 126 HIS 0.005 0.001 HIS I1023 PHE 0.030 0.001 PHE I 230 TYR 0.015 0.001 TYR H 152 ARG 0.006 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 1368) hydrogen bonds : angle 3.93276 ( 3733) metal coordination : bond 0.00600 ( 8) metal coordination : angle 2.34610 ( 12) covalent geometry : bond 0.00364 (31477) covalent geometry : angle 0.49223 (42939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 3.596 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8716 (tm-30) REVERT: G 186 ASN cc_start: 0.8512 (m-40) cc_final: 0.8099 (m110) REVERT: H 268 ASN cc_start: 0.9525 (m-40) cc_final: 0.9290 (m110) REVERT: I 951 MET cc_start: 0.8639 (mmp) cc_final: 0.8383 (mtp) REVERT: J 161 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8232 (p) REVERT: J 413 ASP cc_start: 0.9056 (t0) cc_final: 0.8831 (t0) REVERT: J 1189 MET cc_start: 0.8450 (tpp) cc_final: 0.8080 (tmm) REVERT: K 70 GLN cc_start: 0.8462 (tt0) cc_final: 0.8018 (tm-30) REVERT: M 171 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8367 (t70) REVERT: M 292 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8884 (m-30) outliers start: 38 outliers final: 17 residues processed: 188 average time/residue: 1.3367 time to fit residues: 302.9032 Evaluate side-chains 170 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 115 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 306 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.051076 restraints weight = 94399.814| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.28 r_work: 0.2624 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31485 Z= 0.190 Angle : 0.515 12.143 42951 Z= 0.272 Chirality : 0.042 0.326 4924 Planarity : 0.003 0.042 5283 Dihedral : 15.333 125.534 5090 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.46 % Allowed : 9.98 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3662 helix: 2.07 (0.14), residues: 1426 sheet: 0.72 (0.25), residues: 451 loop : -0.49 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 126 HIS 0.005 0.001 HIS I1023 PHE 0.013 0.001 PHE I 230 TYR 0.015 0.001 TYR H 152 ARG 0.005 0.000 ARG J 275 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 1368) hydrogen bonds : angle 3.95245 ( 3733) metal coordination : bond 0.00763 ( 8) metal coordination : angle 2.32685 ( 12) covalent geometry : bond 0.00449 (31477) covalent geometry : angle 0.51395 (42939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 3.755 Fit side-chains revert: symmetry clash REVERT: G 86 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8874 (tttp) REVERT: G 93 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8790 (tm-30) REVERT: G 127 GLN cc_start: 0.8999 (mp10) cc_final: 0.8574 (pm20) REVERT: G 186 ASN cc_start: 0.8578 (m-40) cc_final: 0.8153 (m110) REVERT: H 147 GLN cc_start: 0.8439 (mt0) cc_final: 0.8016 (mt0) REVERT: H 268 ASN cc_start: 0.9516 (m-40) cc_final: 0.9280 (m110) REVERT: I 951 MET cc_start: 0.8663 (mmp) cc_final: 0.8411 (mtp) REVERT: J 161 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8265 (p) REVERT: J 821 MET cc_start: 0.8675 (tpp) cc_final: 0.8443 (mmm) REVERT: K 70 GLN cc_start: 0.8436 (tt0) cc_final: 0.8030 (tm-30) REVERT: M 171 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8415 (t70) REVERT: M 292 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8913 (m-30) outliers start: 46 outliers final: 20 residues processed: 192 average time/residue: 1.3358 time to fit residues: 311.2603 Evaluate side-chains 172 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 274 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 371 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS H 75 GLN J 430 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049520 restraints weight = 90435.025| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.22 r_work: 0.2580 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 31485 Z= 0.331 Angle : 0.615 10.891 42951 Z= 0.322 Chirality : 0.045 0.308 4924 Planarity : 0.004 0.052 5283 Dihedral : 15.448 125.800 5089 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.20 % Allowed : 10.64 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3662 helix: 1.87 (0.14), residues: 1427 sheet: 0.72 (0.25), residues: 450 loop : -0.58 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 126 HIS 0.006 0.001 HIS J 777 PHE 0.014 0.002 PHE I 230 TYR 0.018 0.001 TYR J 631 ARG 0.006 0.000 ARG J 275 Details of bonding type rmsd hydrogen bonds : bond 0.05701 ( 1368) hydrogen bonds : angle 4.22707 ( 3733) metal coordination : bond 0.01296 ( 8) metal coordination : angle 2.66596 ( 12) covalent geometry : bond 0.00787 (31477) covalent geometry : angle 0.61362 (42939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 86 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8897 (tttp) REVERT: G 93 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8764 (tm-30) REVERT: G 127 GLN cc_start: 0.9005 (mp10) cc_final: 0.8521 (pm20) REVERT: H 147 GLN cc_start: 0.8411 (mt0) cc_final: 0.7991 (mt0) REVERT: H 268 ASN cc_start: 0.9514 (m-40) cc_final: 0.9275 (m110) REVERT: I 277 LEU cc_start: 0.9746 (mm) cc_final: 0.9492 (tp) REVERT: I 951 MET cc_start: 0.8698 (mmp) cc_final: 0.8442 (mtp) REVERT: J 161 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8384 (p) REVERT: J 821 MET cc_start: 0.8809 (tpp) cc_final: 0.8564 (mmm) REVERT: J 1165 PHE cc_start: 0.8466 (m-80) cc_final: 0.7267 (t80) REVERT: K 70 GLN cc_start: 0.8406 (tt0) cc_final: 0.7991 (tm-30) REVERT: M 171 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8475 (t70) REVERT: M 292 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8960 (t0) outliers start: 38 outliers final: 21 residues processed: 184 average time/residue: 1.3111 time to fit residues: 290.1446 Evaluate side-chains 172 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 21 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 342 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 618 GLN J 424 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052074 restraints weight = 107737.083| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.51 r_work: 0.2638 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31485 Z= 0.108 Angle : 0.479 10.578 42951 Z= 0.254 Chirality : 0.040 0.293 4924 Planarity : 0.003 0.050 5283 Dihedral : 15.302 125.038 5089 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.86 % Allowed : 11.18 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3662 helix: 2.12 (0.14), residues: 1428 sheet: 0.85 (0.25), residues: 439 loop : -0.49 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.004 0.001 HIS I1023 PHE 0.010 0.001 PHE M 318 TYR 0.013 0.001 TYR H 152 ARG 0.004 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1368) hydrogen bonds : angle 3.84295 ( 3733) metal coordination : bond 0.00371 ( 8) metal coordination : angle 2.12845 ( 12) covalent geometry : bond 0.00245 (31477) covalent geometry : angle 0.47819 (42939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 3.308 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8770 (tm-30) REVERT: G 127 GLN cc_start: 0.9057 (mp10) cc_final: 0.8548 (pm20) REVERT: G 186 ASN cc_start: 0.8599 (m-40) cc_final: 0.8167 (m110) REVERT: H 147 GLN cc_start: 0.8366 (mt0) cc_final: 0.7926 (mt0) REVERT: H 268 ASN cc_start: 0.9532 (m-40) cc_final: 0.9292 (m110) REVERT: I 277 LEU cc_start: 0.9737 (mm) cc_final: 0.9495 (tp) REVERT: I 951 MET cc_start: 0.8668 (mmp) cc_final: 0.8426 (mtp) REVERT: I 1023 HIS cc_start: 0.8987 (t70) cc_final: 0.8766 (t-90) REVERT: J 161 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8278 (p) REVERT: J 821 MET cc_start: 0.8782 (tpp) cc_final: 0.8505 (mmm) REVERT: J 1165 PHE cc_start: 0.8325 (m-80) cc_final: 0.7256 (t80) REVERT: K 70 GLN cc_start: 0.8389 (tt0) cc_final: 0.8082 (tm-30) outliers start: 27 outliers final: 15 residues processed: 175 average time/residue: 1.6236 time to fit residues: 340.4055 Evaluate side-chains 165 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 336 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 354 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051775 restraints weight = 83615.813| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.12 r_work: 0.2651 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31485 Z= 0.138 Angle : 0.497 13.479 42951 Z= 0.260 Chirality : 0.041 0.280 4924 Planarity : 0.003 0.057 5283 Dihedral : 15.297 124.344 5089 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.92 % Allowed : 11.40 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3662 helix: 2.17 (0.14), residues: 1427 sheet: 0.68 (0.25), residues: 449 loop : -0.43 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.004 0.001 HIS I1023 PHE 0.011 0.001 PHE I 230 TYR 0.015 0.001 TYR H 152 ARG 0.004 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 1368) hydrogen bonds : angle 3.83122 ( 3733) metal coordination : bond 0.00577 ( 8) metal coordination : angle 2.16617 ( 12) covalent geometry : bond 0.00323 (31477) covalent geometry : angle 0.49584 (42939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8748 (tm-30) REVERT: G 127 GLN cc_start: 0.9050 (mp10) cc_final: 0.8531 (pm20) REVERT: G 186 ASN cc_start: 0.8600 (m-40) cc_final: 0.8162 (m110) REVERT: H 147 GLN cc_start: 0.8374 (mt0) cc_final: 0.7945 (mt0) REVERT: H 268 ASN cc_start: 0.9539 (m-40) cc_final: 0.9297 (m110) REVERT: I 277 LEU cc_start: 0.9724 (mm) cc_final: 0.9500 (tp) REVERT: I 349 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9046 (mp0) REVERT: I 951 MET cc_start: 0.8653 (mmp) cc_final: 0.8437 (mtp) REVERT: I 1023 HIS cc_start: 0.8988 (t70) cc_final: 0.8768 (t-90) REVERT: J 161 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8283 (p) REVERT: J 1165 PHE cc_start: 0.8384 (m-80) cc_final: 0.7314 (t80) REVERT: K 70 GLN cc_start: 0.8449 (tt0) cc_final: 0.8080 (tm-30) outliers start: 29 outliers final: 19 residues processed: 176 average time/residue: 1.5406 time to fit residues: 325.3890 Evaluate side-chains 173 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 195 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.081992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.051410 restraints weight = 89033.283| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.23 r_work: 0.2641 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31485 Z= 0.151 Angle : 0.504 14.969 42951 Z= 0.263 Chirality : 0.041 0.256 4924 Planarity : 0.003 0.064 5283 Dihedral : 15.287 124.201 5089 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.92 % Allowed : 11.66 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3662 helix: 2.17 (0.14), residues: 1427 sheet: 0.65 (0.25), residues: 441 loop : -0.44 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.004 0.001 HIS I1023 PHE 0.010 0.001 PHE J1037 TYR 0.020 0.001 TYR M 112 ARG 0.008 0.000 ARG I 478 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1368) hydrogen bonds : angle 3.84122 ( 3733) metal coordination : bond 0.00635 ( 8) metal coordination : angle 2.15868 ( 12) covalent geometry : bond 0.00355 (31477) covalent geometry : angle 0.50324 (42939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 3.487 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8724 (tm-30) REVERT: G 186 ASN cc_start: 0.8609 (m-40) cc_final: 0.8177 (m110) REVERT: H 147 GLN cc_start: 0.8391 (mt0) cc_final: 0.7956 (mt0) REVERT: H 268 ASN cc_start: 0.9538 (m-40) cc_final: 0.9297 (m110) REVERT: I 277 LEU cc_start: 0.9712 (mm) cc_final: 0.9508 (tp) REVERT: I 349 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.9054 (mp0) REVERT: I 492 MET cc_start: 0.8925 (tpt) cc_final: 0.8643 (tpt) REVERT: I 951 MET cc_start: 0.8656 (mmp) cc_final: 0.8439 (mtp) REVERT: I 1023 HIS cc_start: 0.8969 (t70) cc_final: 0.8744 (t-90) REVERT: J 161 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8304 (p) REVERT: J 1165 PHE cc_start: 0.8446 (m-80) cc_final: 0.7360 (t80) REVERT: J 1275 LEU cc_start: 0.8950 (mt) cc_final: 0.8721 (mm) REVERT: K 70 GLN cc_start: 0.8437 (tt0) cc_final: 0.8082 (tm-30) REVERT: M 292 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8913 (t0) outliers start: 29 outliers final: 17 residues processed: 179 average time/residue: 1.4546 time to fit residues: 312.2820 Evaluate side-chains 170 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 261 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051121 restraints weight = 83645.669| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.11 r_work: 0.2635 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31485 Z= 0.186 Angle : 0.533 14.611 42951 Z= 0.277 Chirality : 0.041 0.244 4924 Planarity : 0.004 0.072 5283 Dihedral : 15.326 124.097 5089 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.76 % Allowed : 11.78 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3662 helix: 2.14 (0.14), residues: 1427 sheet: 0.65 (0.25), residues: 448 loop : -0.46 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.004 0.001 HIS J 777 PHE 0.010 0.001 PHE J1319 TYR 0.028 0.001 TYR M 112 ARG 0.006 0.000 ARG J 259 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 1368) hydrogen bonds : angle 3.90828 ( 3733) metal coordination : bond 0.00758 ( 8) metal coordination : angle 2.17543 ( 12) covalent geometry : bond 0.00441 (31477) covalent geometry : angle 0.53156 (42939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8722 (tm-30) REVERT: G 186 ASN cc_start: 0.8610 (m-40) cc_final: 0.8184 (m110) REVERT: H 147 GLN cc_start: 0.8412 (mt0) cc_final: 0.7973 (mt0) REVERT: H 268 ASN cc_start: 0.9540 (m-40) cc_final: 0.9298 (m110) REVERT: I 349 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9058 (mp0) REVERT: I 492 MET cc_start: 0.8935 (tpt) cc_final: 0.8545 (tpt) REVERT: I 951 MET cc_start: 0.8669 (mmp) cc_final: 0.8447 (mtp) REVERT: I 1023 HIS cc_start: 0.8986 (t70) cc_final: 0.8763 (t-90) REVERT: J 161 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8345 (p) REVERT: J 1165 PHE cc_start: 0.8490 (m-80) cc_final: 0.7378 (t80) REVERT: K 70 GLN cc_start: 0.8441 (tt0) cc_final: 0.8087 (tm-30) REVERT: M 292 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8914 (t0) outliers start: 24 outliers final: 20 residues processed: 173 average time/residue: 1.4361 time to fit residues: 297.4951 Evaluate side-chains 173 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 281 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 297 optimal weight: 40.0000 chunk 242 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 363 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052543 restraints weight = 87804.762| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.18 r_work: 0.2670 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31485 Z= 0.105 Angle : 0.495 15.751 42951 Z= 0.257 Chirality : 0.040 0.166 4924 Planarity : 0.003 0.077 5283 Dihedral : 15.276 123.733 5089 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 11.94 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3662 helix: 2.23 (0.14), residues: 1425 sheet: 0.70 (0.25), residues: 449 loop : -0.39 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.004 0.000 HIS I1023 PHE 0.010 0.001 PHE M 318 TYR 0.030 0.001 TYR M 112 ARG 0.006 0.000 ARG J 259 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1368) hydrogen bonds : angle 3.75295 ( 3733) metal coordination : bond 0.00391 ( 8) metal coordination : angle 1.95779 ( 12) covalent geometry : bond 0.00237 (31477) covalent geometry : angle 0.49370 (42939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28094.10 seconds wall clock time: 479 minutes 41.78 seconds (28781.78 seconds total)