Starting phenix.real_space_refine on Sun Jul 5 22:30:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f1k_28791/07_2026/8f1k_28791.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 1.112 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 19057 2.51 5 N 5437 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30854 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 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: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10450 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1270} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 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: 3250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 389} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 389} Chain breaks: 1 bond proxies already assigned to first conformer: 3293 Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16027 SG CYS J 70 105.451 99.331 129.651 1.00 45.57 S ATOM 16041 SG CYS J 72 104.116 98.628 133.017 1.00 59.51 S ATOM 16149 SG CYS J 85 107.521 97.218 132.171 1.00 61.17 S ATOM 16173 SG CYS J 88 104.464 95.692 130.621 1.00 52.63 S ATOM 21861 SG CYS J 814 114.290 70.250 68.683 1.00 43.60 S ATOM 22426 SG CYS J 888 111.272 71.086 70.882 1.00 37.73 S ATOM 22477 SG CYS J 895 112.816 73.704 68.530 1.00 39.94 S ATOM 22498 SG CYS J 898 110.808 70.911 67.121 1.00 46.81 S Time building chain proxies: 6.91, per 1000 atoms: 0.22 Number of scatterers: 30854 At special positions: 0 Unit cell: (151.62, 167.865, 179.778, 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 6144 8.00 N 5437 7.00 C 19057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.5 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 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 50 sheets defined 42.6% alpha, 15.9% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.648A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.706A 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: 4.439A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.525A 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 154 through 159 removed outlier: 3.555A pdb=" N ILE H 159 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.587A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'H' and resid 285 through 291 Processing helix chain 'H' and resid 296 through 309 removed outlier: 3.828A pdb=" N LEU H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.592A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.777A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.154A 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 removed outlier: 3.667A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 359 through 371 removed outlier: 3.526A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.928A 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: 3.686A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.738A 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: 3.569A 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: 4.036A pdb=" N VAL I 650 " --> pdb=" O ARG I 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.691A 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: 4.049A 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: 3.825A 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 896 through 907 Processing helix chain 'I' and resid 942 through 984 removed outlier: 3.837A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY I 983 " --> pdb=" O LEU I 979 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 984 " --> pdb=" O VAL I 980 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.536A pdb=" N LEU I 989 " --> pdb=" O GLU I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 1011 through 1037 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.571A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.453A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.508A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.549A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.828A 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 1243 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: 3.574A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.875A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 11 removed outlier: 3.799A pdb=" N GLN J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) 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: 3.770A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.626A 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: 3.509A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.733A pdb=" N THR J 208 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.513A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.799A 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: 3.612A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.519A pdb=" N ARG J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.088A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.156A 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: 3.502A 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: 3.816A 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: 3.744A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.632A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) 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 805 removed outlier: 3.882A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.524A 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: 3.509A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1074 removed outlier: 3.728A 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 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.802A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.411A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.517A 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: 3.572A 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: 4.474A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 25 removed outlier: 3.875A pdb=" N GLN M 21 " --> pdb=" O PRO M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 42 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.501A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.798A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.929A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 Processing helix chain 'M' and resid 212 through 222 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: 4.039A pdb=" N GLU M 248 " --> pdb=" O ASP M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 removed outlier: 3.510A pdb=" N GLN M 262 " --> pdb=" O ARG M 259 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 259 through 264' Processing helix chain 'M' and resid 300 through 306 removed outlier: 3.949A pdb=" N MET M 306 " --> pdb=" O HIS M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 351 removed outlier: 3.693A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG M 320 " --> pdb=" O SER M 316 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER M 321 " --> pdb=" O GLN M 317 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN M 322 " --> pdb=" O PHE M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 359 through 362 removed outlier: 3.731A pdb=" N MET M 362 " --> pdb=" O GLU M 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 359 through 362' Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.607A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.645A 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 18 removed outlier: 6.733A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.710A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.229A 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: 6.553A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.748A 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: 6.343A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.795A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 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: 6.541A 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: 6.767A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (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: 3.556A 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: 3.579A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.755A 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 249 through 250 removed outlier: 4.370A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.364A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.459A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.473A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.790A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.051A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.808A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD2, 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=AD3, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.771A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.835A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.624A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.831A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 253 through 254 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: 6.557A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.451A 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: 4.154A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 4.174A 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: 3.982A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE9, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 4.712A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1186 through 1188 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.406A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.713A 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 408 1270 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 9.88 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9382 1.33 - 1.45: 4355 1.45 - 1.57: 17371 1.57 - 1.69: 185 1.69 - 1.81: 206 Bond restraints: 31499 Sorted by residual: bond pdb=" C3' DG A 4 " pdb=" C2' DG A 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA A 16 " pdb=" C2' DA A 16 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA A 18 " pdb=" C2' DA A 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT B 46 " pdb=" C2' DT B 46 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DA B 53 " pdb=" C2' DA B 53 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.29e+00 ... (remaining 31494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 42440 1.98 - 3.96: 508 3.96 - 5.95: 15 5.95 - 7.93: 2 7.93 - 9.91: 1 Bond angle restraints: 42966 Sorted by residual: angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT A 20 " pdb=" C4 DT A 20 " pdb=" O4 DT A 20 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT D 57 " pdb=" C4 DT D 57 " pdb=" O4 DT D 57 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 42961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 17361 17.59 - 35.18: 1150 35.18 - 52.76: 499 52.76 - 70.35: 142 70.35 - 87.94: 25 Dihedral angle restraints: 19177 sinusoidal: 8552 harmonic: 10625 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 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 19174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3134 0.032 - 0.064: 1220 0.064 - 0.097: 332 0.097 - 0.129: 213 0.129 - 0.161: 27 Chirality restraints: 4926 Sorted by residual: chirality pdb=" CB VAL J1255 " pdb=" CA VAL J1255 " pdb=" CG1 VAL J1255 " pdb=" CG2 VAL J1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.48e-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 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE I 177 " pdb=" N ILE I 177 " pdb=" C ILE I 177 " pdb=" CB ILE I 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 4923 not shown) Planarity restraints: 5288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 292 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C ILE I 292 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE I 292 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA I 293 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO I 590 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO J 246 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " 0.021 5.00e-02 4.00e+02 ... (remaining 5285 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 542 2.68 - 3.24: 27709 3.24 - 3.79: 46198 3.79 - 4.35: 65914 4.35 - 4.90: 107639 Nonbonded interactions: 248002 Sorted by model distance: nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.143 2.170 nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 2.165 3.040 nonbonded pdb=" O PRO J 121 " pdb=" NH1 ARG J 123 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASP M 149 " pdb=" OG1 THR M 151 " model vdw 2.218 3.040 ... (remaining 247997 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 40.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31507 Z= 0.212 Angle : 0.505 9.909 42978 Z= 0.342 Chirality : 0.042 0.161 4926 Planarity : 0.004 0.041 5288 Dihedral : 15.011 87.940 12325 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.30 % Allowed : 6.58 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3664 helix: 1.52 (0.14), residues: 1391 sheet: 0.69 (0.25), residues: 463 loop : -0.59 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 342 TYR 0.013 0.001 TYR J 631 PHE 0.010 0.001 PHE I1164 TRP 0.008 0.001 TRP J 409 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.21 (31499) covalent geometry : angle 0.50341 / 0.34 (42966) hydrogen bonds : bond 0.14426 / 14.72 ( 1370) hydrogen bonds : angle 5.27639 / 5.47 ( 3744) metal coordination : bond 0.00328 / 0.42 ( 8) metal coordination : angle 2.60818 / 4.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 161 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8923 (p) outliers start: 41 outliers final: 11 residues processed: 231 average time/residue: 0.8872 time to fit residues: 235.4883 Evaluate side-chains 157 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS H 186 ASN I 519 ASN J 266 ASN J 424 ASN J 430 HIS J 651 HIS M 282 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052423 restraints weight = 91882.890| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.33 r_work: 0.2644 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31507 Z= 0.196 Angle : 0.565 8.392 42978 Z= 0.303 Chirality : 0.042 0.160 4926 Planarity : 0.004 0.077 5288 Dihedral : 15.587 68.165 5103 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.49 % Allowed : 9.81 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3664 helix: 1.71 (0.14), residues: 1430 sheet: 0.79 (0.25), residues: 464 loop : -0.54 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 371 TYR 0.034 0.001 TYR M 112 PHE 0.011 0.001 PHE J1034 TRP 0.031 0.001 TRP J1193 HIS 0.013 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (31499) covalent geometry : angle 0.56360 / 0.30 (42966) hydrogen bonds : bond 0.04798 / 5.01 ( 1370) hydrogen bonds : angle 4.38104 / 4.43 ( 3744) metal coordination : bond 0.00713 / 0.84 ( 8) metal coordination : angle 2.75864 / 5.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8615 (pp30) REVERT: G 186 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: H 294 ASN cc_start: 0.7757 (t0) cc_final: 0.7543 (t0) REVERT: I 357 ASN cc_start: 0.9244 (p0) cc_final: 0.8855 (m-40) REVERT: I 370 MET cc_start: 0.9213 (mmm) cc_final: 0.8998 (mmm) REVERT: I 1319 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8726 (ttp) REVERT: J 161 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (p) REVERT: J 1034 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7795 (t80) REVERT: J 1040 MET cc_start: 0.6595 (tmm) cc_final: 0.6353 (tpt) REVERT: J 1175 LEU cc_start: 0.8485 (tm) cc_final: 0.7895 (tt) REVERT: J 1188 GLU cc_start: 0.7450 (mp0) cc_final: 0.7123 (mp0) REVERT: J 1189 MET cc_start: 0.8734 (tpp) cc_final: 0.8484 (tpp) REVERT: K 70 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7579 (tm-30) REVERT: M 112 TYR cc_start: 0.7336 (t80) cc_final: 0.6968 (t80) outliers start: 47 outliers final: 12 residues processed: 186 average time/residue: 0.7831 time to fit residues: 170.9979 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 : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 430 HIS J1195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.051261 restraints weight = 91986.810| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.35 r_work: 0.2632 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31507 Z= 0.202 Angle : 0.547 8.531 42978 Z= 0.290 Chirality : 0.043 0.389 4926 Planarity : 0.004 0.073 5288 Dihedral : 15.905 67.783 5094 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.49 % Allowed : 10.19 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3664 helix: 1.81 (0.14), residues: 1427 sheet: 0.71 (0.25), residues: 464 loop : -0.51 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1194 TYR 0.018 0.001 TYR M 112 PHE 0.026 0.001 PHE I 230 TRP 0.081 0.002 TRP J1193 HIS 0.005 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (31499) covalent geometry : angle 0.54485 / 0.29 (42966) hydrogen bonds : bond 0.04651 / 4.84 ( 1370) hydrogen bonds : angle 4.16839 / 4.19 ( 3744) metal coordination : bond 0.00861 / 0.98 ( 8) metal coordination : angle 2.78452 / 5.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 186 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: H 294 ASN cc_start: 0.8000 (t0) cc_final: 0.7689 (t0) REVERT: I 124 MET cc_start: 0.9491 (mmt) cc_final: 0.9245 (mtp) REVERT: I 357 ASN cc_start: 0.9259 (p0) cc_final: 0.8878 (m-40) REVERT: I 370 MET cc_start: 0.9288 (mmm) cc_final: 0.8977 (mmm) REVERT: I 681 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8575 (mtt) REVERT: I 1119 MET cc_start: 0.8930 (tpt) cc_final: 0.8674 (tpt) REVERT: I 1319 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8788 (ttp) REVERT: J 161 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8102 (p) REVERT: J 260 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7859 (t80) REVERT: J 1034 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7773 (t80) REVERT: K 70 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7634 (tm-30) REVERT: M 112 TYR cc_start: 0.7371 (t80) cc_final: 0.7120 (t80) REVERT: M 240 ARG cc_start: 0.9118 (mpp80) cc_final: 0.8857 (mpp80) REVERT: M 452 MET cc_start: 0.8401 (mmm) cc_final: 0.8199 (mmm) outliers start: 47 outliers final: 16 residues processed: 181 average time/residue: 0.7558 time to fit residues: 159.9042 Evaluate side-chains 170 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 348 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 354 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 294 ASN I1070 HIS J 430 HIS J 762 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.080404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.051939 restraints weight = 109648.079| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.63 r_work: 0.2648 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31507 Z= 0.112 Angle : 0.501 9.079 42978 Z= 0.264 Chirality : 0.042 0.532 4926 Planarity : 0.004 0.064 5288 Dihedral : 15.846 66.239 5092 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.68 % Allowed : 10.57 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.14), residues: 3664 helix: 1.91 (0.14), residues: 1435 sheet: 0.81 (0.26), residues: 440 loop : -0.44 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 247 TYR 0.018 0.001 TYR M 112 PHE 0.009 0.001 PHE I 405 TRP 0.073 0.001 TRP J1193 HIS 0.003 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (31499) covalent geometry : angle 0.50005 / 0.26 (42966) hydrogen bonds : bond 0.03786 / 3.97 ( 1370) hydrogen bonds : angle 3.98103 / 4.02 ( 3744) metal coordination : bond 0.00399 / 0.48 ( 8) metal coordination : angle 2.30917 / 4.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 127 GLN cc_start: 0.9160 (mp10) cc_final: 0.8804 (pm20) REVERT: H 212 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7300 (t0) REVERT: H 268 ASN cc_start: 0.9158 (m110) cc_final: 0.8903 (m110) REVERT: H 294 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7639 (t0) REVERT: I 124 MET cc_start: 0.9488 (OUTLIER) cc_final: 0.9200 (mtp) REVERT: I 357 ASN cc_start: 0.9254 (p0) cc_final: 0.8860 (m-40) REVERT: I 681 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8594 (mtt) REVERT: I 1119 MET cc_start: 0.8903 (tpt) cc_final: 0.8686 (tpt) REVERT: I 1319 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8608 (tpp) REVERT: J 161 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8092 (p) REVERT: J 525 MET cc_start: 0.9005 (ptp) cc_final: 0.8688 (ptm) REVERT: J 821 MET cc_start: 0.9007 (mmm) cc_final: 0.8727 (tpt) REVERT: J 1034 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7781 (t80) REVERT: J 1040 MET cc_start: 0.5424 (tpt) cc_final: 0.5131 (tpt) REVERT: K 12 LYS cc_start: 0.8666 (tptm) cc_final: 0.8465 (tptm) REVERT: K 70 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7625 (tm-30) REVERT: M 112 TYR cc_start: 0.7387 (t80) cc_final: 0.6947 (t80) REVERT: M 240 ARG cc_start: 0.9130 (mpp80) cc_final: 0.8824 (mpp80) REVERT: M 452 MET cc_start: 0.8428 (mmm) cc_final: 0.8193 (mmm) outliers start: 53 outliers final: 17 residues processed: 188 average time/residue: 0.7353 time to fit residues: 162.2439 Evaluate side-chains 169 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 353 optimal weight: 0.9980 chunk 291 optimal weight: 30.0000 chunk 281 optimal weight: 20.0000 chunk 369 optimal weight: 20.0000 chunk 310 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 279 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 224 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 93 GLN I 554 HIS J 430 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052066 restraints weight = 110928.533| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.65 r_work: 0.2654 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31507 Z= 0.105 Angle : 0.498 11.217 42978 Z= 0.261 Chirality : 0.041 0.373 4926 Planarity : 0.004 0.063 5288 Dihedral : 15.810 66.039 5092 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.33 % Allowed : 10.79 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3664 helix: 2.00 (0.14), residues: 1434 sheet: 0.88 (0.26), residues: 441 loop : -0.40 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.014 0.001 TYR M 112 PHE 0.009 0.001 PHE J1319 TRP 0.066 0.001 TRP J1193 HIS 0.003 0.000 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (31499) covalent geometry : angle 0.49695 / 0.26 (42966) hydrogen bonds : bond 0.03604 / 3.78 ( 1370) hydrogen bonds : angle 3.89708 / 3.92 ( 3744) metal coordination : bond 0.00378 / 0.47 ( 8) metal coordination : angle 2.29846 / 4.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 127 GLN cc_start: 0.9123 (mp10) cc_final: 0.8729 (pm20) REVERT: G 186 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: H 212 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7306 (t0) REVERT: H 268 ASN cc_start: 0.9195 (m110) cc_final: 0.8921 (m110) REVERT: H 294 ASN cc_start: 0.8012 (t0) cc_final: 0.7668 (t0) REVERT: I 62 TYR cc_start: 0.8417 (m-80) cc_final: 0.8115 (m-80) REVERT: I 124 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9228 (mtp) REVERT: I 369 MET cc_start: 0.9348 (tmt) cc_final: 0.9117 (tmt) REVERT: I 370 MET cc_start: 0.9090 (tpp) cc_final: 0.8658 (mmp) REVERT: I 473 ARG cc_start: 0.8926 (tpp-160) cc_final: 0.8630 (tpm170) REVERT: I 681 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8583 (mtt) REVERT: I 1119 MET cc_start: 0.8814 (tpt) cc_final: 0.8604 (tpt) REVERT: I 1319 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8555 (tpp) REVERT: J 161 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8162 (p) REVERT: J 821 MET cc_start: 0.8910 (mmm) cc_final: 0.8655 (tpt) REVERT: J 1034 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7843 (t80) REVERT: J 1040 MET cc_start: 0.5774 (tpt) cc_final: 0.5478 (OUTLIER) REVERT: K 70 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7659 (tm-30) REVERT: M 112 TYR cc_start: 0.7502 (t80) cc_final: 0.6908 (t80) REVERT: M 452 MET cc_start: 0.8462 (mmm) cc_final: 0.8236 (mmm) outliers start: 42 outliers final: 15 residues processed: 178 average time/residue: 0.6911 time to fit residues: 144.4767 Evaluate side-chains 169 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 108 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 41 optimal weight: 0.0770 chunk 105 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 201 optimal weight: 0.3980 overall best weight: 1.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 430 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051239 restraints weight = 110926.223| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.65 r_work: 0.2632 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31507 Z= 0.158 Angle : 0.516 11.566 42978 Z= 0.269 Chirality : 0.042 0.392 4926 Planarity : 0.004 0.061 5288 Dihedral : 15.812 66.137 5091 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.33 % Allowed : 11.17 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3664 helix: 1.99 (0.14), residues: 1434 sheet: 0.81 (0.25), residues: 457 loop : -0.40 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 3 TYR 0.015 0.001 TYR M 401 PHE 0.010 0.001 PHE J 260 TRP 0.071 0.001 TRP J1193 HIS 0.003 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (31499) covalent geometry : angle 0.51393 / 0.27 (42966) hydrogen bonds : bond 0.03901 / 4.07 ( 1370) hydrogen bonds : angle 3.90096 / 3.94 ( 3744) metal coordination : bond 0.00686 / 0.80 ( 8) metal coordination : angle 2.50131 / 4.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 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: 42 poor density : 151 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 127 GLN cc_start: 0.9107 (mp10) cc_final: 0.8712 (pm20) REVERT: G 186 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8139 (m-40) REVERT: H 268 ASN cc_start: 0.9224 (m110) cc_final: 0.8954 (m110) REVERT: H 294 ASN cc_start: 0.8058 (t0) cc_final: 0.7652 (t0) REVERT: I 62 TYR cc_start: 0.8476 (m-80) cc_final: 0.8171 (m-80) REVERT: I 124 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9271 (mtp) REVERT: I 274 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9300 (mm) REVERT: I 357 ASN cc_start: 0.9217 (p0) cc_final: 0.8784 (m-40) REVERT: I 370 MET cc_start: 0.9211 (tpp) cc_final: 0.8898 (mmp) REVERT: I 473 ARG cc_start: 0.8891 (tpp-160) cc_final: 0.8579 (tpm170) REVERT: I 681 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8575 (mtt) REVERT: I 1119 MET cc_start: 0.8826 (tpt) cc_final: 0.8617 (tpt) REVERT: I 1319 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8656 (ttp) REVERT: J 161 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8229 (p) REVERT: J 962 ASN cc_start: 0.9176 (m-40) cc_final: 0.8571 (t0) REVERT: J 1034 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7854 (t80) REVERT: J 1040 MET cc_start: 0.5703 (tpt) cc_final: 0.5364 (OUTLIER) REVERT: K 3 ARG cc_start: 0.8270 (mmp80) cc_final: 0.7993 (mmp80) REVERT: K 70 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7681 (tm-30) REVERT: M 112 TYR cc_start: 0.7654 (t80) cc_final: 0.7102 (t80) REVERT: M 452 MET cc_start: 0.8481 (mmm) cc_final: 0.8256 (mmm) outliers start: 42 outliers final: 20 residues processed: 177 average time/residue: 0.7275 time to fit residues: 150.5766 Evaluate side-chains 173 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 365 MET Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 363 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 321 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 430 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.050245 restraints weight = 111187.025| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.66 r_work: 0.2603 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31507 Z= 0.207 Angle : 0.555 12.155 42978 Z= 0.287 Chirality : 0.043 0.353 4926 Planarity : 0.004 0.060 5288 Dihedral : 15.865 66.798 5090 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.30 % Allowed : 11.36 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3664 helix: 1.92 (0.14), residues: 1441 sheet: 0.71 (0.25), residues: 467 loop : -0.43 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 47 TYR 0.025 0.001 TYR J1186 PHE 0.015 0.001 PHE J 260 TRP 0.081 0.002 TRP J1193 HIS 0.003 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (31499) covalent geometry : angle 0.55376 / 0.29 (42966) hydrogen bonds : bond 0.04318 / 4.52 ( 1370) hydrogen bonds : angle 3.95218 / 3.99 ( 3744) metal coordination : bond 0.00890 / 1.02 ( 8) metal coordination : angle 2.62480 / 4.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 186 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8159 (m-40) REVERT: H 268 ASN cc_start: 0.9256 (m110) cc_final: 0.8977 (m110) REVERT: H 294 ASN cc_start: 0.8095 (t0) cc_final: 0.7675 (t0) REVERT: I 62 TYR cc_start: 0.8515 (m-80) cc_final: 0.8199 (m-80) REVERT: I 124 MET cc_start: 0.9543 (OUTLIER) cc_final: 0.9315 (mtp) REVERT: I 357 ASN cc_start: 0.9218 (p0) cc_final: 0.8772 (m-40) REVERT: I 473 ARG cc_start: 0.8944 (tpp-160) cc_final: 0.8637 (tpm170) REVERT: I 681 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (mtt) REVERT: I 1119 MET cc_start: 0.8884 (tpt) cc_final: 0.8667 (tpt) REVERT: I 1319 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8731 (ttp) REVERT: J 161 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8205 (p) REVERT: J 962 ASN cc_start: 0.9178 (m-40) cc_final: 0.8586 (t0) REVERT: J 1034 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7942 (t80) REVERT: J 1040 MET cc_start: 0.5833 (tpt) cc_final: 0.5466 (OUTLIER) REVERT: M 112 TYR cc_start: 0.7782 (t80) cc_final: 0.7411 (t80) REVERT: M 113 GLN cc_start: 0.8476 (mt0) cc_final: 0.8130 (pm20) REVERT: M 452 MET cc_start: 0.8510 (mmm) cc_final: 0.8303 (mmm) outliers start: 41 outliers final: 20 residues processed: 177 average time/residue: 0.7692 time to fit residues: 158.8948 Evaluate side-chains 170 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 365 MET Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 130 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 91 optimal weight: 0.0370 chunk 292 optimal weight: 50.0000 chunk 1 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 320 ASN J 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051201 restraints weight = 91290.929| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.32 r_work: 0.2642 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31507 Z= 0.137 Angle : 0.530 12.716 42978 Z= 0.274 Chirality : 0.042 0.376 4926 Planarity : 0.004 0.059 5288 Dihedral : 15.829 67.022 5090 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.04 % Allowed : 11.83 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3664 helix: 1.98 (0.14), residues: 1440 sheet: 0.78 (0.25), residues: 462 loop : -0.40 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 247 TYR 0.016 0.001 TYR J1186 PHE 0.013 0.001 PHE J1325 TRP 0.080 0.002 TRP J1193 HIS 0.003 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (31499) covalent geometry : angle 0.52882 / 0.27 (42966) hydrogen bonds : bond 0.03890 / 4.09 ( 1370) hydrogen bonds : angle 3.87140 / 3.92 ( 3744) metal coordination : bond 0.00578 / 0.68 ( 8) metal coordination : angle 2.32733 / 4.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 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: 33 poor density : 148 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 127 GLN cc_start: 0.9186 (mp10) cc_final: 0.8852 (pm20) REVERT: H 51 MET cc_start: 0.8946 (tpt) cc_final: 0.8666 (mmm) REVERT: H 212 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7385 (t0) REVERT: H 268 ASN cc_start: 0.9255 (m110) cc_final: 0.8973 (m110) REVERT: H 294 ASN cc_start: 0.8121 (t0) cc_final: 0.7707 (t0) REVERT: I 62 TYR cc_start: 0.8501 (m-80) cc_final: 0.8172 (m-80) REVERT: I 124 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.9310 (mtp) REVERT: I 357 ASN cc_start: 0.9201 (p0) cc_final: 0.8762 (m-40) REVERT: I 445 ILE cc_start: 0.9305 (pt) cc_final: 0.9001 (mp) REVERT: I 473 ARG cc_start: 0.8940 (tpp-160) cc_final: 0.8632 (tpm170) REVERT: I 681 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8576 (mtt) REVERT: I 1119 MET cc_start: 0.8827 (tpt) cc_final: 0.8615 (tpt) REVERT: J 161 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8184 (p) REVERT: J 821 MET cc_start: 0.8967 (mmm) cc_final: 0.8584 (tpt) REVERT: J 962 ASN cc_start: 0.9157 (m-40) cc_final: 0.8564 (t0) REVERT: J 1034 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8055 (t80) REVERT: J 1040 MET cc_start: 0.5892 (tpt) cc_final: 0.5523 (OUTLIER) REVERT: M 112 TYR cc_start: 0.7823 (t80) cc_final: 0.7367 (t80) REVERT: M 113 GLN cc_start: 0.8484 (mt0) cc_final: 0.8119 (pm20) REVERT: M 452 MET cc_start: 0.8454 (mmm) cc_final: 0.8164 (mmm) outliers start: 33 outliers final: 20 residues processed: 169 average time/residue: 0.7095 time to fit residues: 140.5717 Evaluate side-chains 171 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 365 MET Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 125 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 320 ASN J 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.051026 restraints weight = 106090.507| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.58 r_work: 0.2632 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31507 Z= 0.134 Angle : 0.523 12.979 42978 Z= 0.271 Chirality : 0.041 0.360 4926 Planarity : 0.004 0.058 5288 Dihedral : 15.798 67.016 5090 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.08 % Allowed : 11.80 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3664 helix: 2.06 (0.14), residues: 1428 sheet: 0.80 (0.25), residues: 463 loop : -0.39 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 247 TYR 0.017 0.001 TYR J1186 PHE 0.012 0.001 PHE J1325 TRP 0.084 0.002 TRP J1193 HIS 0.002 0.000 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (31499) covalent geometry : angle 0.52150 / 0.27 (42966) hydrogen bonds : bond 0.03753 / 3.94 ( 1370) hydrogen bonds : angle 3.81453 / 3.85 ( 3744) metal coordination : bond 0.00568 / 0.68 ( 8) metal coordination : angle 2.34155 / 4.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8232 (pp30) cc_final: 0.7955 (pm20) REVERT: G 127 GLN cc_start: 0.9178 (mp10) cc_final: 0.8849 (pm20) REVERT: H 51 MET cc_start: 0.8946 (tpt) cc_final: 0.8655 (mmm) REVERT: H 147 GLN cc_start: 0.9180 (mt0) cc_final: 0.8779 (mt0) REVERT: H 268 ASN cc_start: 0.9261 (m110) cc_final: 0.8980 (m110) REVERT: H 294 ASN cc_start: 0.8267 (t0) cc_final: 0.7854 (t0) REVERT: I 62 TYR cc_start: 0.8533 (m-80) cc_final: 0.8193 (m-80) REVERT: I 124 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.9313 (mtp) REVERT: I 445 ILE cc_start: 0.9306 (pt) cc_final: 0.9014 (mp) REVERT: I 473 ARG cc_start: 0.8968 (tpp-160) cc_final: 0.8628 (tpm170) REVERT: I 681 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8581 (mtt) REVERT: J 161 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8138 (p) REVERT: J 698 MET cc_start: 0.8916 (mmt) cc_final: 0.8675 (mmm) REVERT: J 962 ASN cc_start: 0.9156 (m-40) cc_final: 0.8572 (t0) REVERT: J 1034 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8082 (t80) REVERT: J 1040 MET cc_start: 0.6010 (tpt) cc_final: 0.5623 (OUTLIER) REVERT: M 112 TYR cc_start: 0.7771 (t80) cc_final: 0.7299 (t80) REVERT: M 113 GLN cc_start: 0.8600 (mt0) cc_final: 0.8129 (pm20) REVERT: M 452 MET cc_start: 0.8499 (mmm) cc_final: 0.8237 (mmm) outliers start: 34 outliers final: 20 residues processed: 173 average time/residue: 0.7112 time to fit residues: 144.1574 Evaluate side-chains 170 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 333 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 339 optimal weight: 0.9980 chunk 266 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 302 optimal weight: 9.9990 chunk 359 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 351 optimal weight: 0.6980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 294 ASN H 320 ASN I1013 GLN J 430 HIS J1195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051775 restraints weight = 92344.112| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.37 r_work: 0.2659 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31507 Z= 0.116 Angle : 0.528 13.071 42978 Z= 0.270 Chirality : 0.041 0.356 4926 Planarity : 0.004 0.058 5288 Dihedral : 15.746 67.038 5090 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.92 % Allowed : 12.05 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.14), residues: 3664 helix: 2.10 (0.14), residues: 1430 sheet: 0.81 (0.25), residues: 463 loop : -0.37 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 247 TYR 0.021 0.001 TYR J1186 PHE 0.011 0.001 PHE J1325 TRP 0.073 0.001 TRP J1193 HIS 0.003 0.000 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (31499) covalent geometry : angle 0.52692 / 0.27 (42966) hydrogen bonds : bond 0.03505 / 3.69 ( 1370) hydrogen bonds : angle 3.77028 / 3.82 ( 3744) metal coordination : bond 0.00460 / 0.56 ( 8) metal coordination : angle 2.23874 / 4.22 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8228 (pp30) cc_final: 0.8007 (pm20) REVERT: G 127 GLN cc_start: 0.9190 (mp10) cc_final: 0.8860 (pm20) REVERT: H 147 GLN cc_start: 0.9191 (mt0) cc_final: 0.8792 (mt0) REVERT: H 212 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7392 (t0) REVERT: H 268 ASN cc_start: 0.9263 (m110) cc_final: 0.8980 (m110) REVERT: H 294 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7841 (t0) REVERT: I 62 TYR cc_start: 0.8557 (m-80) cc_final: 0.8216 (m-80) REVERT: I 124 MET cc_start: 0.9522 (OUTLIER) cc_final: 0.9279 (mtp) REVERT: I 357 ASN cc_start: 0.9191 (p0) cc_final: 0.8803 (m-40) REVERT: I 445 ILE cc_start: 0.9310 (pt) cc_final: 0.9036 (mp) REVERT: I 473 ARG cc_start: 0.8973 (tpp-160) cc_final: 0.8652 (tpm170) REVERT: I 681 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8543 (mtt) REVERT: J 161 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8155 (p) REVERT: J 821 MET cc_start: 0.9064 (mmm) cc_final: 0.8621 (tpt) REVERT: J 962 ASN cc_start: 0.9151 (m-40) cc_final: 0.8606 (t0) REVERT: J 1034 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8073 (t80) REVERT: J 1040 MET cc_start: 0.5972 (tpt) cc_final: 0.5560 (tpt) REVERT: M 112 TYR cc_start: 0.7744 (t80) cc_final: 0.7196 (t80) REVERT: M 113 GLN cc_start: 0.8594 (mt0) cc_final: 0.8167 (pm20) REVERT: M 452 MET cc_start: 0.8460 (mmm) cc_final: 0.8237 (mmm) outliers start: 29 outliers final: 17 residues processed: 171 average time/residue: 0.7136 time to fit residues: 143.3844 Evaluate side-chains 169 residues out of total 3162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 892 GLU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 88 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 314 optimal weight: 0.8980 chunk 343 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 175 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 294 ASN H 320 ASN J 430 HIS ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.051938 restraints weight = 110079.643| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.71 r_work: 0.2638 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 31507 Z= 0.168 Angle : 0.659 59.196 42978 Z= 0.369 Chirality : 0.042 0.377 4926 Planarity : 0.004 0.058 5288 Dihedral : 15.746 67.021 5090 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.82 % Allowed : 12.18 % Favored : 87.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3664 helix: 2.09 (0.14), residues: 1430 sheet: 0.81 (0.25), residues: 463 loop : -0.37 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.021 0.001 TYR J1186 PHE 0.010 0.001 PHE J1325 TRP 0.065 0.001 TRP J1193 HIS 0.004 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (31499) covalent geometry : angle 0.65852 / 0.37 (42966) hydrogen bonds : bond 0.03575 / 3.76 ( 1370) hydrogen bonds : angle 3.77021 / 3.82 ( 3744) metal coordination : bond 0.00529 / 0.63 ( 8) metal coordination : angle 2.23669 / 4.21 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11169.73 seconds wall clock time: 190 minutes 34.26 seconds (11434.26 seconds total)