Starting phenix.real_space_refine on Mon Sep 14 16:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pst_20463/09_2026/6pst_20463_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pst_20463/09_2026/6pst_20463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pst_20463/09_2026/6pst_20463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pst_20463/09_2026/6pst_20463.map" model { file = "/net/cci-nas-00/data/ceres_data/6pst_20463/09_2026/6pst_20463_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pst_20463/09_2026/6pst_20463_trim.cif" } resolution = 3.0 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= 0.000 sd= 0.006 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 3 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 19429 2.51 5 N 5552 2.21 5 O 6229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31452 Number of models: 1 Model: "" Number of chains: 13 Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 566 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1026 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "P" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1045 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 221} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 10512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10512 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 9109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9109 Classifications: {'peptide': 1164} Link IDs: {'CIS': 2, 'PTRANS': 47, 'TRANS': 1114} Chain breaks: 1 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4495 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 276 SG CYS N 37 71.467 155.895 80.709 1.00 65.23 S ATOM 296 SG CYS N 40 74.086 157.690 82.200 1.00 68.45 S ATOM 433 SG CYS N 58 75.810 154.743 80.028 1.00 55.45 S ATOM 455 SG CYS N 61 74.037 154.341 83.014 1.00 58.83 S ATOM 17608 SG CYS J 70 50.517 63.438 118.070 1.00 43.81 S ATOM 17622 SG CYS J 72 52.811 62.337 120.392 1.00 48.86 S ATOM 17730 SG CYS J 85 48.536 62.461 121.062 1.00 51.62 S ATOM 17754 SG CYS J 88 50.816 65.668 120.683 1.00 50.83 S ATOM 23442 SG CYS J 814 20.920 114.756 84.751 1.00 42.80 S ATOM 24007 SG CYS J 888 24.691 113.213 85.642 1.00 32.62 S ATOM 24058 SG CYS J 895 23.079 111.627 82.766 1.00 29.59 S ATOM 24079 SG CYS J 898 23.659 114.993 82.736 1.00 27.55 S Time building chain proxies: 6.48, per 1000 atoms: 0.21 Number of scatterers: 31452 At special positions: 0 Unit cell: (149.5, 183.3, 193.7, 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 3 29.99 S 137 16.00 P 101 15.00 Mg 1 11.99 O 6229 8.00 N 5552 7.00 C 19429 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 18 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6938 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 44 sheets defined 44.8% alpha, 14.5% beta 44 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'N' and resid 5 through 26 Processing helix chain 'N' and resid 45 through 52 Processing helix chain 'N' and resid 58 through 72 Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 277 through 282 Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.924A pdb=" N ARG M 310 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 4.037A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 4.171A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.584A pdb=" N GLN G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.006A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.585A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'H' and resid 229 through 231 No H-bonds generated for 'chain 'H' and resid 229 through 231' Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.758A 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 270 through 280 Processing helix chain 'I' and resid 290 through 294 removed outlier: 3.800A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.877A 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 removed outlier: 3.730A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.758A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 4.281A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.861A 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 898 through 907 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.988A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.713A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.550A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.230A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1149 Processing helix chain 'I' and resid 1160 through 1164 Processing helix chain 'I' and resid 1165 through 1176 removed outlier: 3.629A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.686A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 4.088A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 114 through 119 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 170 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.502A pdb=" N MET J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.710A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.967A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (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 285 removed outlier: 4.056A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 removed outlier: 3.871A pdb=" N GLN J 340 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 406 through 417 removed outlier: 4.082A 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 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.573A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.737A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.530A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.531A 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 741 Processing helix chain 'J' and resid 768 through 790 removed outlier: 3.659A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 794 through 804 removed outlier: 3.797A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.722A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 928 removed outlier: 3.511A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.610A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 3.524A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.199A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.800A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.720A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1375 removed outlier: 4.335A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.741A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 24 through 31 Processing helix chain 'L' and resid 38 through 51 Processing helix chain 'L' and resid 61 through 68 removed outlier: 3.778A pdb=" N MET L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 88 removed outlier: 3.791A pdb=" N SER L 86 " --> pdb=" O GLN L 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 107 Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.680A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 233 removed outlier: 3.539A pdb=" N ALA L 217 " --> pdb=" O ASP L 213 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 258 removed outlier: 3.671A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 293 removed outlier: 3.614A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 310 removed outlier: 3.613A pdb=" N PHE L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 350 removed outlier: 3.532A pdb=" N VAL L 337 " --> pdb=" O VAL L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 392 removed outlier: 3.612A pdb=" N VAL L 358 " --> pdb=" O THR L 354 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.588A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 4.037A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 492 through 500 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.681A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 removed outlier: 3.846A pdb=" N GLN L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 604 through 611 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.190A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.612A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.612A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.326A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.448A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.448A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 60 removed outlier: 6.699A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA H 138 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'H' and resid 110 through 111 removed outlier: 7.038A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.654A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.782A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.661A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.568A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 284 through 286 removed outlier: 5.185A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.855A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.542A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.642A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.172A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.426A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1066 through 1068 removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE I1096 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1066 through 1068 Processing sheet with id=AC9, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.549A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD2, first strand: chain 'I' and resid 888 through 889 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.060A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA J 446 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1268 through 1270 Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.602A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.826A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 704 through 706 Processing sheet with id=AE2, first strand: chain 'J' and resid 745 through 748 removed outlier: 5.460A pdb=" N MET J 747 " --> pdb=" O THR J 757 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR J 757 " --> pdb=" O MET J 747 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.511A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.554A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.960A pdb=" N LEU L 22 " --> pdb=" O MET L 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 1380 hydrogen bonds defined for protein. 3954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9210 1.33 - 1.45: 6013 1.45 - 1.58: 16446 1.58 - 1.70: 217 1.70 - 1.82: 247 Bond restraints: 32133 Sorted by residual: bond pdb=" C19 1N7 J1505 " pdb=" C3 1N7 J1505 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 N 102 " pdb=" C3 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 N 102 " pdb=" C4 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.722 -0.190 2.00e-02 2.50e+03 8.99e+01 ... (remaining 32128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 42596 2.39 - 4.77: 1120 4.77 - 7.16: 113 7.16 - 9.54: 16 9.54 - 11.93: 5 Bond angle restraints: 43850 Sorted by residual: angle pdb=" C THR L 569 " pdb=" N ASP L 570 " pdb=" CA ASP L 570 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C GLU H 7 " pdb=" N PHE H 8 " pdb=" CA PHE H 8 " ideal model delta sigma weight residual 121.90 114.21 7.69 1.26e+00 6.30e-01 3.73e+01 angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 131.66 -9.96 1.80e+00 3.09e-01 3.06e+01 angle pdb=" O4' DT P 34 " pdb=" C4' DT P 34 " pdb=" C3' DT P 34 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.45e+01 angle pdb=" O4' DC O 30 " pdb=" C1' DC O 30 " pdb=" N1 DC O 30 " ideal model delta sigma weight residual 108.00 111.44 -3.44 7.00e-01 2.04e+00 2.41e+01 ... (remaining 43845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 18628 35.39 - 70.78: 1115 70.78 - 106.17: 23 106.17 - 141.56: 1 141.56 - 176.95: 8 Dihedral angle restraints: 19775 sinusoidal: 9026 harmonic: 10749 Sorted by residual: dihedral pdb=" CA ILE J 707 " pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta harmonic sigma weight residual 0.00 -41.00 41.00 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA ASP I 254 " pdb=" C ASP I 254 " pdb=" N ILE I 255 " pdb=" CA ILE I 255 " ideal model delta harmonic sigma weight residual 180.00 146.09 33.91 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA GLU J1343 " pdb=" C GLU J1343 " pdb=" N LEU J1344 " pdb=" CA LEU J1344 " ideal model delta harmonic sigma weight residual -180.00 -147.07 -32.93 0 5.00e+00 4.00e-02 4.34e+01 ... (remaining 19772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4149 0.066 - 0.133: 810 0.133 - 0.199: 60 0.199 - 0.265: 10 0.265 - 0.332: 2 Chirality restraints: 5031 Sorted by residual: chirality pdb=" C19 1N7 J1505 " pdb=" C18 1N7 J1505 " pdb=" C2 1N7 J1505 " pdb=" C3 1N7 J1505 " both_signs ideal model delta sigma weight residual False -2.53 -2.87 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C19 1N7 N 102 " pdb=" C18 1N7 N 102 " pdb=" C2 1N7 N 102 " pdb=" C3 1N7 N 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE L 505 " pdb=" CA ILE L 505 " pdb=" CG1 ILE L 505 " pdb=" CG2 ILE L 505 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 5028 not shown) Planarity restraints: 5353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 79 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU H 79 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU H 79 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU H 80 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I1223 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO I1224 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO I1224 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO I1224 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 898 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C GLU I 898 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU I 898 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 899 " -0.016 2.00e-02 2.50e+03 ... (remaining 5350 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 183 2.40 - 3.03: 20293 3.03 - 3.65: 47585 3.65 - 4.28: 75254 4.28 - 4.90: 122848 Nonbonded interactions: 266163 Sorted by model distance: nonbonded pdb=" CD2 LEU I 237 " pdb=" O PRO I 288 " model vdw 1.777 3.460 nonbonded pdb=" CD1 LEU I 237 " pdb=" CD1 ILE I 292 " model vdw 1.820 3.880 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.010 2.170 nonbonded pdb=" O ARG L 436 " pdb=" OG1 THR L 440 " model vdw 2.029 3.040 nonbonded pdb=" O ILE J 918 " pdb=" OG SER J 922 " model vdw 2.043 3.040 ... (remaining 266158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 158 or resid 171 through 233)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 228 or (resid 229 through 230 an \ d (name N or name CA or name C or name O or name CB )) or resid 231 through 233) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.012 0.531 32145 Z= 0.554 Angle : 1.006 35.977 43868 Z= 0.575 Chirality : 0.051 0.332 5031 Planarity : 0.005 0.076 5353 Dihedral : 19.327 176.954 12837 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 36.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.03 % Favored : 91.67 % Rotamer: Outliers : 13.13 % Allowed : 13.38 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.17 % 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: -3.42 (0.12), residues: 3698 helix: -1.75 (0.11), residues: 1565 sheet: -2.27 (0.23), residues: 394 loop : -2.73 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I1246 TYR 0.024 0.003 TYR I1087 PHE 0.027 0.003 PHE I 586 TRP 0.014 0.003 TRP I 807 HIS 0.010 0.002 HIS I 551 Details of bonding type rmsd/Z covalent geometry : bond 0.01112 / 0.54 (32133) covalent geometry : angle 0.93502 / 0.57 (43850) hydrogen bonds : bond 0.14110 / 13.60 ( 1465) hydrogen bonds : angle 7.00071 / 8.57 ( 4170) metal coordination : bond 0.16262 / 8.12 ( 12) metal coordination : angle 18.32510 / 11.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 417 poor density : 562 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 LYS cc_start: 0.8550 (tttt) cc_final: 0.8287 (tttp) REVERT: N 72 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6697 (t80) REVERT: M 294 ASN cc_start: 0.5760 (m-40) cc_final: 0.5223 (p0) REVERT: G 7 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6137 (mm-30) REVERT: G 76 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: G 93 GLN cc_start: 0.8312 (tp40) cc_final: 0.8033 (tp-100) REVERT: G 125 LYS cc_start: 0.7992 (tttt) cc_final: 0.7771 (tppp) REVERT: G 231 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6809 (t80) REVERT: H 12 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6529 (ptp-170) REVERT: I 60 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6691 (pt0) REVERT: I 65 ASN cc_start: 0.6339 (OUTLIER) cc_final: 0.5732 (p0) REVERT: I 203 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7807 (ttmt) REVERT: I 314 ASN cc_start: 0.8291 (t0) cc_final: 0.7954 (t0) REVERT: I 483 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.3940 (m-30) REVERT: I 484 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7774 (pp) REVERT: I 623 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7886 (mt) REVERT: I 631 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: I 764 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7938 (p) REVERT: I 796 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8835 (mp) REVERT: I 1296 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7644 (t70) REVERT: J 126 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8706 (pp) REVERT: J 169 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6958 (tt) REVERT: J 180 MET cc_start: 0.8190 (ptm) cc_final: 0.7909 (ptm) REVERT: J 195 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: J 227 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7985 (t80) REVERT: J 256 ASP cc_start: 0.6683 (m-30) cc_final: 0.6098 (p0) REVERT: J 304 ASP cc_start: 0.7330 (t70) cc_final: 0.7095 (t0) REVERT: J 545 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.7963 (p-80) REVERT: J 594 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8203 (pp30) REVERT: J 664 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (tp) REVERT: J 709 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6794 (mtp180) REVERT: J 1222 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7684 (mtm110) REVERT: J 1355 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7847 (ptm-80) REVERT: L 56 MET cc_start: 0.7343 (mtm) cc_final: 0.6942 (mtp) REVERT: L 93 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6264 (mmm160) REVERT: L 127 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7664 (pp) REVERT: L 221 PHE cc_start: 0.3711 (m-80) cc_final: 0.3430 (m-80) REVERT: L 277 MET cc_start: 0.5903 (tpt) cc_final: 0.5572 (tpt) REVERT: L 300 LYS cc_start: 0.5028 (ttpt) cc_final: 0.4608 (tptp) outliers start: 417 outliers final: 229 residues processed: 914 average time/residue: 0.7012 time to fit residues: 756.2489 Evaluate side-chains 645 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 390 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 350 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 734 ILE Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 833 ILE Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 848 GLU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain I residue 1325 VAL Chi-restraints excluded: chain I residue 1336 ASN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 440 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 506 SER Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain L residue 611 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 65 GLN N 68 GLN M 268 ASN M 320 ASN H 84 ASN H 93 GLN H 227 GLN I 258 ASN I 314 ASN I 343 HIS I 526 HIS I 554 HIS I 620 ASN I 628 HIS I 761 GLN I 811 ASN I 922 ASN I 965 GLN I1116 HIS I1237 HIS J 157 GLN J 364 HIS J 365 GLN J 450 HIS J 488 ASN J 665 GLN J 680 ASN J1227 HIS J1244 GLN J1268 ASN J1279 GLN J1350 ASN L 30 HIS L 246 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.161307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120313 restraints weight = 43222.140| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.89 r_work: 0.3230 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32145 Z= 0.170 Angle : 0.775 13.647 43868 Z= 0.400 Chirality : 0.048 0.320 5031 Planarity : 0.006 0.071 5353 Dihedral : 19.547 179.399 5948 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.10 % Rotamer: Outliers : 10.30 % Allowed : 19.87 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.02 (0.13), residues: 3698 helix: -0.32 (0.12), residues: 1580 sheet: -1.80 (0.25), residues: 370 loop : -2.21 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J1372 TYR 0.023 0.002 TYR N 35 PHE 0.016 0.002 PHE L 306 TRP 0.015 0.002 TRP I 807 HIS 0.007 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (32133) covalent geometry : angle 0.76865 / 0.40 (43850) hydrogen bonds : bond 0.04929 / 4.74 ( 1465) hydrogen bonds : angle 5.41998 / 6.68 ( 4170) metal coordination : bond 0.00898 / 0.48 ( 12) metal coordination : angle 5.13020 / 2.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 327 poor density : 462 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 72 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7012 (t80) REVERT: G 13 LEU cc_start: 0.8321 (pt) cc_final: 0.8089 (pp) REVERT: G 93 GLN cc_start: 0.8594 (tp40) cc_final: 0.8282 (tp-100) REVERT: G 129 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8545 (t) REVERT: G 147 GLN cc_start: 0.8734 (pt0) cc_final: 0.8481 (pt0) REVERT: G 231 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6817 (t80) REVERT: H 12 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7472 (ptp-170) REVERT: H 96 ASP cc_start: 0.6795 (t70) cc_final: 0.6412 (p0) REVERT: H 118 ASP cc_start: 0.5802 (m-30) cc_final: 0.5212 (t0) REVERT: H 120 ASP cc_start: 0.6013 (m-30) cc_final: 0.5564 (m-30) REVERT: H 135 ASP cc_start: 0.7224 (m-30) cc_final: 0.6612 (t0) REVERT: H 174 ASP cc_start: 0.8234 (m-30) cc_final: 0.7968 (m-30) REVERT: H 199 ASP cc_start: 0.8606 (t70) cc_final: 0.8120 (m-30) REVERT: I 7 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: I 36 GLN cc_start: 0.8214 (tp40) cc_final: 0.7899 (tt0) REVERT: I 60 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: I 67 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: I 161 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8524 (ptpt) REVERT: I 163 LYS cc_start: 0.8126 (mtpm) cc_final: 0.7606 (mmtt) REVERT: I 223 LEU cc_start: 0.8535 (mt) cc_final: 0.8296 (mp) REVERT: I 289 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7827 (m) REVERT: I 478 ARG cc_start: 0.7809 (tpt90) cc_final: 0.7432 (tpm170) REVERT: I 510 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: I 513 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8772 (mt0) REVERT: I 953 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8628 (mt) REVERT: I 955 GLN cc_start: 0.8932 (tp40) cc_final: 0.8661 (tp-100) REVERT: I 957 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7814 (tptt) REVERT: I 1133 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8351 (ptmt) REVERT: I 1160 ASP cc_start: 0.8190 (p0) cc_final: 0.7897 (p0) REVERT: I 1296 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8052 (t0) REVERT: J 97 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8409 (m) REVERT: J 126 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8712 (pt) REVERT: J 143 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8849 (t) REVERT: J 169 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6685 (tp) REVERT: J 170 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5377 (mp0) REVERT: J 195 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: J 227 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.7759 (t80) REVERT: J 256 ASP cc_start: 0.7016 (m-30) cc_final: 0.6253 (p0) REVERT: J 365 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8874 (pt0) REVERT: J 399 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7792 (mptt) REVERT: J 545 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.7757 (p-80) REVERT: J 594 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8163 (pp30) REVERT: J 648 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6920 (tm-30) REVERT: J 709 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7018 (mtp180) REVERT: J 821 MET cc_start: 0.7681 (tpt) cc_final: 0.7395 (tpt) REVERT: J 1146 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7351 (tp30) REVERT: J 1189 MET cc_start: 0.6423 (mmm) cc_final: 0.6193 (mmm) REVERT: J 1284 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7591 (tpp80) REVERT: J 1292 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5477 (mp) REVERT: J 1355 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7540 (ptm-80) REVERT: K 72 GLN cc_start: 0.6706 (tp40) cc_final: 0.5894 (tm-30) REVERT: L 8 GLN cc_start: 0.7532 (mp10) cc_final: 0.6933 (tp-100) REVERT: L 78 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: L 273 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.5294 (ttt) REVERT: L 300 LYS cc_start: 0.5363 (ttpt) cc_final: 0.4743 (tptp) REVERT: L 310 GLU cc_start: 0.2454 (tt0) cc_final: 0.2181 (pp20) REVERT: L 386 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8631 (tp) REVERT: L 471 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (tp) REVERT: L 511 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7296 (tp) REVERT: L 581 ASP cc_start: 0.6741 (t70) cc_final: 0.6477 (t0) outliers start: 327 outliers final: 139 residues processed: 723 average time/residue: 0.6469 time to fit residues: 558.4646 Evaluate side-chains 555 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 382 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 263 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 277 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 91 optimal weight: 40.0000 chunk 53 optimal weight: 10.0000 chunk 321 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 257 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 28 ASN N 65 GLN G 127 GLN H 41 ASN ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 922 ASN J 157 GLN J 320 ASN J 875 ASN J1295 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN L 446 GLN L 600 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.160887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120297 restraints weight = 43039.022| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.92 r_work: 0.3218 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32145 Z= 0.174 Angle : 0.714 12.953 43868 Z= 0.369 Chirality : 0.046 0.335 5031 Planarity : 0.005 0.056 5353 Dihedral : 18.819 177.585 5703 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 8.44 % Allowed : 22.61 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.08 % 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: -1.45 (0.13), residues: 3698 helix: 0.22 (0.13), residues: 1592 sheet: -1.55 (0.25), residues: 369 loop : -1.96 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J1345 TYR 0.017 0.002 TYR G 177 PHE 0.015 0.002 PHE L 306 TRP 0.013 0.002 TRP I 807 HIS 0.006 0.001 HIS J 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (32133) covalent geometry : angle 0.70893 / 0.37 (43850) hydrogen bonds : bond 0.04559 / 4.42 ( 1465) hydrogen bonds : angle 5.08630 / 6.27 ( 4170) metal coordination : bond 0.00553 / 0.34 ( 12) metal coordination : angle 4.11896 / 2.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 415 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 72 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7446 (t80) REVERT: G 13 LEU cc_start: 0.8290 (pt) cc_final: 0.8069 (pp) REVERT: G 93 GLN cc_start: 0.8385 (tp40) cc_final: 0.8144 (tp-100) REVERT: G 129 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8624 (t) REVERT: G 147 GLN cc_start: 0.8722 (pt0) cc_final: 0.8459 (pt0) REVERT: G 231 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6890 (t80) REVERT: H 12 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7423 (ptp-170) REVERT: H 96 ASP cc_start: 0.6740 (t70) cc_final: 0.6358 (p0) REVERT: H 118 ASP cc_start: 0.5525 (m-30) cc_final: 0.5196 (t0) REVERT: H 120 ASP cc_start: 0.6369 (m-30) cc_final: 0.6056 (m-30) REVERT: H 199 ASP cc_start: 0.8407 (t70) cc_final: 0.7820 (m-30) REVERT: I 7 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: I 36 GLN cc_start: 0.8276 (tp40) cc_final: 0.7901 (tt0) REVERT: I 44 GLU cc_start: 0.7706 (pm20) cc_final: 0.7210 (tt0) REVERT: I 67 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: I 223 LEU cc_start: 0.8562 (mt) cc_final: 0.8290 (mp) REVERT: I 478 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7425 (tpm170) REVERT: I 779 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7559 (ttm-80) REVERT: I 953 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8616 (mt) REVERT: I 955 GLN cc_start: 0.8994 (tp40) cc_final: 0.8679 (tp-100) REVERT: I 1024 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7014 (tp30) REVERT: I 1133 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8331 (ptmt) REVERT: I 1160 ASP cc_start: 0.8001 (p0) cc_final: 0.7536 (p0) REVERT: I 1296 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8006 (t70) REVERT: J 97 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8377 (m) REVERT: J 126 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8708 (pp) REVERT: J 195 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: J 227 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.7658 (t80) REVERT: J 256 ASP cc_start: 0.7146 (m-30) cc_final: 0.6384 (p0) REVERT: J 322 ARG cc_start: 0.8020 (ptm160) cc_final: 0.7760 (ptm160) REVERT: J 399 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7806 (mptt) REVERT: J 594 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8041 (pp30) REVERT: J 648 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6687 (tm-30) REVERT: J 821 MET cc_start: 0.7702 (tpt) cc_final: 0.7407 (tpt) REVERT: J 1146 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7384 (tp30) REVERT: J 1189 MET cc_start: 0.6298 (mmm) cc_final: 0.5870 (mmm) REVERT: J 1208 ASP cc_start: 0.7997 (t0) cc_final: 0.7437 (t70) REVERT: J 1253 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8444 (mm) REVERT: J 1292 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5584 (mp) REVERT: J 1372 ARG cc_start: 0.6136 (mpp80) cc_final: 0.5905 (ptp-170) REVERT: L 117 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7946 (tp) REVERT: L 276 MET cc_start: 0.6015 (ppp) cc_final: 0.5582 (mtp) REVERT: L 341 LEU cc_start: 0.1772 (OUTLIER) cc_final: 0.1279 (tm) REVERT: L 386 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8685 (tp) REVERT: L 471 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8478 (tp) REVERT: L 511 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7206 (tp) REVERT: L 533 ASP cc_start: 0.7315 (m-30) cc_final: 0.7056 (m-30) REVERT: L 538 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7948 (tm-30) REVERT: L 554 ARG cc_start: 0.7376 (mtp85) cc_final: 0.6765 (ttt180) REVERT: L 581 ASP cc_start: 0.6741 (t70) cc_final: 0.6539 (t0) outliers start: 268 outliers final: 148 residues processed: 627 average time/residue: 0.6370 time to fit residues: 478.5700 Evaluate side-chains 550 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 378 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 568 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 20 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 347 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 331 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 GLN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN I 510 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 811 ASN I 922 ASN J 320 ASN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN J1295 ASN J1366 HIS L 129 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116851 restraints weight = 42781.032| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.90 r_work: 0.3164 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 32145 Z= 0.308 Angle : 0.784 15.104 43868 Z= 0.405 Chirality : 0.050 0.363 5031 Planarity : 0.006 0.080 5353 Dihedral : 18.709 176.628 5658 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.81 % Favored : 93.08 % Rotamer: Outliers : 8.97 % Allowed : 22.76 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.46 (0.13), residues: 3698 helix: 0.17 (0.13), residues: 1600 sheet: -1.39 (0.26), residues: 368 loop : -1.99 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 431 TYR 0.022 0.002 TYR G 177 PHE 0.026 0.002 PHE J 461 TRP 0.014 0.002 TRP I 807 HIS 0.009 0.002 HIS G 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.31 (32133) covalent geometry : angle 0.78027 / 0.40 (43850) hydrogen bonds : bond 0.05033 / 4.83 ( 1465) hydrogen bonds : angle 5.11849 / 6.31 ( 4170) metal coordination : bond 0.01020 / 0.65 ( 12) metal coordination : angle 3.97752 / 2.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 394 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.9147 (t) cc_final: 0.8775 (p) REVERT: G 93 GLN cc_start: 0.8559 (tp40) cc_final: 0.8350 (tp40) REVERT: G 129 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8720 (t) REVERT: G 150 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7560 (ptp90) REVERT: G 215 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: G 231 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.6901 (t80) REVERT: H 96 ASP cc_start: 0.6705 (t70) cc_final: 0.6445 (p0) REVERT: H 118 ASP cc_start: 0.5646 (m-30) cc_final: 0.5349 (t0) REVERT: H 191 ARG cc_start: 0.8155 (ptt-90) cc_final: 0.7949 (ptt-90) REVERT: I 7 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: I 36 GLN cc_start: 0.8463 (tp40) cc_final: 0.8055 (tt0) REVERT: I 44 GLU cc_start: 0.7659 (pm20) cc_final: 0.7129 (tt0) REVERT: I 223 LEU cc_start: 0.8560 (mt) cc_final: 0.8285 (mp) REVERT: I 319 LEU cc_start: 0.7920 (mp) cc_final: 0.7633 (mp) REVERT: I 478 ARG cc_start: 0.7733 (tpt90) cc_final: 0.7360 (tpm170) REVERT: I 515 MET cc_start: 0.8988 (ttp) cc_final: 0.8597 (ttt) REVERT: I 602 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: I 631 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: I 639 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7967 (mppt) REVERT: I 922 ASN cc_start: 0.7429 (t0) cc_final: 0.7225 (t160) REVERT: I 942 ASP cc_start: 0.7720 (p0) cc_final: 0.7504 (p0) REVERT: I 953 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (mt) REVERT: I 955 GLN cc_start: 0.9093 (tp40) cc_final: 0.8769 (tp-100) REVERT: I 1085 MET cc_start: 0.9171 (mmm) cc_final: 0.8965 (mmm) REVERT: I 1133 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8411 (ptmt) REVERT: I 1160 ASP cc_start: 0.8052 (p0) cc_final: 0.7709 (p0) REVERT: I 1296 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8146 (t70) REVERT: J 97 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8504 (m) REVERT: J 195 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: J 227 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.7630 (t80) REVERT: J 256 ASP cc_start: 0.7199 (m-30) cc_final: 0.6161 (p0) REVERT: J 399 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7858 (mptt) REVERT: J 413 ASP cc_start: 0.8617 (m-30) cc_final: 0.8406 (m-30) REVERT: J 594 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: J 648 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7046 (tm-30) REVERT: J 821 MET cc_start: 0.7731 (tpt) cc_final: 0.7474 (tpt) REVERT: J 1146 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7408 (tp30) REVERT: J 1208 ASP cc_start: 0.7959 (t0) cc_final: 0.7419 (t70) REVERT: J 1253 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8423 (mm) REVERT: J 1266 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7915 (mm) REVERT: J 1292 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5587 (mp) REVERT: J 1305 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: J 1355 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7751 (ptm-80) REVERT: J 1372 ARG cc_start: 0.6229 (mpp80) cc_final: 0.5960 (ptp-170) REVERT: L 117 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7948 (tp) REVERT: L 273 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5704 (ttt) REVERT: L 276 MET cc_start: 0.5890 (ppp) cc_final: 0.5435 (mtp) REVERT: L 288 MET cc_start: 0.3121 (OUTLIER) cc_final: 0.2670 (mpp) REVERT: L 341 LEU cc_start: 0.1752 (OUTLIER) cc_final: 0.1251 (tm) REVERT: L 386 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8807 (tp) REVERT: L 471 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8452 (tp) REVERT: L 511 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7354 (tp) REVERT: L 532 LEU cc_start: 0.8503 (tt) cc_final: 0.8266 (tt) REVERT: L 538 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7942 (tm-30) REVERT: L 554 ARG cc_start: 0.7431 (mtp85) cc_final: 0.6785 (ttt180) REVERT: L 581 ASP cc_start: 0.6810 (t70) cc_final: 0.6586 (t0) outliers start: 285 outliers final: 178 residues processed: 612 average time/residue: 0.6540 time to fit residues: 482.3727 Evaluate side-chains 568 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 362 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 13 optimal weight: 30.0000 chunk 251 optimal weight: 0.0980 chunk 311 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 340 optimal weight: 30.0000 chunk 301 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 68 GLN ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I1017 GLN J 157 GLN J 320 ASN J 365 GLN J 720 ASN J1295 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.161847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121150 restraints weight = 43178.132| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.89 r_work: 0.3229 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32145 Z= 0.137 Angle : 0.676 13.705 43868 Z= 0.350 Chirality : 0.045 0.351 5031 Planarity : 0.005 0.101 5353 Dihedral : 18.462 179.525 5654 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.60 % Favored : 94.24 % Rotamer: Outliers : 7.43 % Allowed : 23.99 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.68 % Twisted General : 0.08 % 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: -0.93 (0.14), residues: 3698 helix: 0.64 (0.13), residues: 1584 sheet: -1.15 (0.26), residues: 360 loop : -1.70 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 272 TYR 0.014 0.001 TYR N 64 PHE 0.019 0.001 PHE L 221 TRP 0.015 0.001 TRP I 807 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (32133) covalent geometry : angle 0.67208 / 0.35 (43850) hydrogen bonds : bond 0.04093 / 3.95 ( 1465) hydrogen bonds : angle 4.80957 / 5.89 ( 4170) metal coordination : bond 0.00361 / 0.22 ( 12) metal coordination : angle 3.52830 / 2.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 421 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 318 LEU cc_start: 0.2841 (OUTLIER) cc_final: 0.2623 (tt) REVERT: G 93 GLN cc_start: 0.8361 (tp40) cc_final: 0.8128 (tp-100) REVERT: G 129 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8578 (t) REVERT: G 147 GLN cc_start: 0.8701 (pt0) cc_final: 0.8424 (pt0) REVERT: G 150 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7407 (ptp90) REVERT: G 231 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7246 (t80) REVERT: H 12 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6745 (ptt90) REVERT: H 69 SER cc_start: 0.5395 (OUTLIER) cc_final: 0.4757 (p) REVERT: H 78 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.7897 (pp) REVERT: H 226 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8142 (mt-10) REVERT: I 7 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: I 36 GLN cc_start: 0.8369 (tp40) cc_final: 0.8140 (tt0) REVERT: I 44 GLU cc_start: 0.7661 (pm20) cc_final: 0.7093 (tt0) REVERT: I 77 GLU cc_start: 0.8540 (pt0) cc_final: 0.8068 (pm20) REVERT: I 88 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8295 (mtt90) REVERT: I 223 LEU cc_start: 0.8501 (mt) cc_final: 0.8253 (mp) REVERT: I 289 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8148 (m) REVERT: I 319 LEU cc_start: 0.7908 (mp) cc_final: 0.7621 (mp) REVERT: I 337 PHE cc_start: 0.7843 (t80) cc_final: 0.7512 (t80) REVERT: I 478 ARG cc_start: 0.7639 (tpt90) cc_final: 0.7306 (tpm170) REVERT: I 618 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: I 634 VAL cc_start: 0.8609 (m) cc_final: 0.8256 (p) REVERT: I 639 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7860 (mppt) REVERT: I 654 ASP cc_start: 0.8036 (m-30) cc_final: 0.7804 (m-30) REVERT: I 779 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7611 (ttm-80) REVERT: I 953 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8593 (mt) REVERT: I 955 GLN cc_start: 0.8968 (tp40) cc_final: 0.8677 (tp-100) REVERT: I 1131 MET cc_start: 0.8238 (mtp) cc_final: 0.7978 (mtm) REVERT: I 1133 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (ptmt) REVERT: I 1140 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8310 (mmmt) REVERT: I 1160 ASP cc_start: 0.7994 (p0) cc_final: 0.7492 (p0) REVERT: I 1296 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8062 (t70) REVERT: J 83 VAL cc_start: 0.8307 (p) cc_final: 0.7946 (m) REVERT: J 97 VAL cc_start: 0.8864 (p) cc_final: 0.8353 (m) REVERT: J 126 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8815 (pt) REVERT: J 170 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: J 195 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: J 205 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5220 (pt) REVERT: J 227 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.7517 (t80) REVERT: J 256 ASP cc_start: 0.7288 (m-30) cc_final: 0.6442 (p0) REVERT: J 322 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7584 (ptm160) REVERT: J 365 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.9032 (pt0) REVERT: J 399 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7837 (mptt) REVERT: J 594 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8058 (pp30) REVERT: J 648 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6780 (tm-30) REVERT: J 821 MET cc_start: 0.7748 (tpt) cc_final: 0.7493 (tpt) REVERT: J 1146 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7375 (tp30) REVERT: J 1149 ARG cc_start: 0.7533 (tpp-160) cc_final: 0.6955 (mmm160) REVERT: J 1189 MET cc_start: 0.6408 (mmm) cc_final: 0.6161 (mmm) REVERT: J 1208 ASP cc_start: 0.7891 (t0) cc_final: 0.7440 (t70) REVERT: J 1253 ILE cc_start: 0.8736 (mm) cc_final: 0.8494 (mm) REVERT: J 1292 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5760 (mp) REVERT: J 1305 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: J 1372 ARG cc_start: 0.6267 (mpp80) cc_final: 0.5972 (ptp-170) REVERT: K 16 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8082 (ttm170) REVERT: L 117 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7943 (tp) REVERT: L 273 MET cc_start: 0.5816 (ttt) cc_final: 0.5477 (ttt) REVERT: L 276 MET cc_start: 0.5740 (ppp) cc_final: 0.5360 (mtt) REVERT: L 341 LEU cc_start: 0.1627 (OUTLIER) cc_final: 0.1154 (tm) REVERT: L 386 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8558 (tp) REVERT: L 511 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7224 (tp) REVERT: L 538 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8006 (tm-30) REVERT: L 554 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6718 (ttt180) outliers start: 236 outliers final: 124 residues processed: 600 average time/residue: 0.6485 time to fit residues: 467.1766 Evaluate side-chains 522 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 369 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 265 optimal weight: 0.8980 chunk 361 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 922 ASN J 157 GLN J1218 HIS J1295 ASN L 227 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119574 restraints weight = 42812.407| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.87 r_work: 0.3208 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32145 Z= 0.174 Angle : 0.688 13.350 43868 Z= 0.355 Chirality : 0.046 0.352 5031 Planarity : 0.005 0.098 5353 Dihedral : 18.295 177.313 5624 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 7.34 % Allowed : 24.94 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.81 (0.14), residues: 3698 helix: 0.72 (0.13), residues: 1590 sheet: -1.07 (0.26), residues: 361 loop : -1.62 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 272 TYR 0.016 0.001 TYR H 177 PHE 0.022 0.002 PHE I 230 TRP 0.013 0.001 TRP I 807 HIS 0.007 0.001 HIS J 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (32133) covalent geometry : angle 0.68463 / 0.35 (43850) hydrogen bonds : bond 0.04175 / 4.02 ( 1465) hydrogen bonds : angle 4.74781 / 5.81 ( 4170) metal coordination : bond 0.00560 / 0.35 ( 12) metal coordination : angle 3.22298 / 1.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 390 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 21 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7813 (t0) REVERT: M 318 LEU cc_start: 0.2852 (OUTLIER) cc_final: 0.2644 (tt) REVERT: G 93 GLN cc_start: 0.8366 (tp40) cc_final: 0.8141 (tp-100) REVERT: G 125 LYS cc_start: 0.8382 (tttt) cc_final: 0.7848 (tppp) REVERT: G 129 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8605 (t) REVERT: G 147 GLN cc_start: 0.8738 (pt0) cc_final: 0.8508 (pt0) REVERT: G 150 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7610 (ptp90) REVERT: G 231 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7291 (t80) REVERT: H 12 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6787 (ptt90) REVERT: H 69 SER cc_start: 0.5152 (OUTLIER) cc_final: 0.4610 (p) REVERT: H 77 ASP cc_start: 0.8411 (t70) cc_final: 0.8133 (t0) REVERT: H 78 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7785 (pp) REVERT: H 191 ARG cc_start: 0.8037 (ptt-90) cc_final: 0.7701 (ptt-90) REVERT: H 199 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: I 7 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: I 36 GLN cc_start: 0.8399 (tp40) cc_final: 0.8102 (tt0) REVERT: I 44 GLU cc_start: 0.7692 (pm20) cc_final: 0.7135 (tt0) REVERT: I 77 GLU cc_start: 0.8575 (pt0) cc_final: 0.8095 (pm20) REVERT: I 223 LEU cc_start: 0.8543 (mt) cc_final: 0.8271 (mp) REVERT: I 289 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8157 (m) REVERT: I 319 LEU cc_start: 0.7899 (mp) cc_final: 0.7619 (mp) REVERT: I 337 PHE cc_start: 0.7994 (t80) cc_final: 0.7652 (t80) REVERT: I 478 ARG cc_start: 0.7635 (tpt90) cc_final: 0.7318 (tpm170) REVERT: I 602 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: I 618 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: I 779 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7679 (ttm-80) REVERT: I 953 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8590 (mt) REVERT: I 955 GLN cc_start: 0.8994 (tp40) cc_final: 0.8707 (tp-100) REVERT: I 1085 MET cc_start: 0.9061 (mmm) cc_final: 0.8805 (mmm) REVERT: I 1131 MET cc_start: 0.8315 (mtp) cc_final: 0.8018 (mtm) REVERT: I 1133 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8434 (ptmt) REVERT: I 1140 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8330 (mmmt) REVERT: I 1160 ASP cc_start: 0.8020 (p0) cc_final: 0.7516 (p0) REVERT: I 1292 THR cc_start: 0.9441 (m) cc_final: 0.9199 (p) REVERT: I 1296 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8075 (t70) REVERT: J 83 VAL cc_start: 0.8334 (p) cc_final: 0.7977 (m) REVERT: J 94 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: J 97 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8362 (m) REVERT: J 170 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6763 (mm-30) REVERT: J 194 LEU cc_start: 0.8061 (mm) cc_final: 0.7742 (mt) REVERT: J 195 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: J 227 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.7502 (t80) REVERT: J 256 ASP cc_start: 0.7283 (m-30) cc_final: 0.6420 (p0) REVERT: J 289 ASP cc_start: 0.8170 (m-30) cc_final: 0.7943 (m-30) REVERT: J 304 ASP cc_start: 0.8414 (m-30) cc_final: 0.8213 (m-30) REVERT: J 399 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7863 (mptt) REVERT: J 594 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8075 (pp30) REVERT: J 648 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6822 (tm-30) REVERT: J 788 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8896 (tp) REVERT: J 821 MET cc_start: 0.7744 (tpt) cc_final: 0.7516 (tpt) REVERT: J 1146 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7392 (tp30) REVERT: J 1149 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7011 (mmm160) REVERT: J 1208 ASP cc_start: 0.7888 (t0) cc_final: 0.7438 (t70) REVERT: J 1253 ILE cc_start: 0.8765 (mm) cc_final: 0.8457 (mm) REVERT: J 1292 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6139 (mp) REVERT: J 1305 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: J 1372 ARG cc_start: 0.6336 (mpp80) cc_final: 0.6096 (ptp-170) REVERT: L 117 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7945 (tp) REVERT: L 288 MET cc_start: 0.1917 (mmm) cc_final: 0.1184 (mmt) REVERT: L 310 GLU cc_start: 0.2620 (tt0) cc_final: 0.2291 (tt0) REVERT: L 341 LEU cc_start: 0.1503 (OUTLIER) cc_final: 0.1060 (tm) REVERT: L 357 GLN cc_start: 0.7110 (mt0) cc_final: 0.6290 (pp30) REVERT: L 359 LYS cc_start: 0.5592 (OUTLIER) cc_final: 0.5264 (ttmp) REVERT: L 386 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8638 (tp) REVERT: L 511 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7279 (tp) REVERT: L 538 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8032 (tm-30) REVERT: L 554 ARG cc_start: 0.7346 (mtp85) cc_final: 0.6750 (ttt180) outliers start: 233 outliers final: 138 residues processed: 576 average time/residue: 0.6608 time to fit residues: 456.5294 Evaluate side-chains 536 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 366 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 315 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 317 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 932 GLN ** I1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J 320 ASN J1295 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119425 restraints weight = 42956.851| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.89 r_work: 0.3203 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32145 Z= 0.179 Angle : 0.689 13.259 43868 Z= 0.356 Chirality : 0.046 0.359 5031 Planarity : 0.005 0.096 5353 Dihedral : 18.186 177.338 5617 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.83 % Rotamer: Outliers : 7.27 % Allowed : 25.63 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3698 helix: 0.77 (0.13), residues: 1597 sheet: -1.10 (0.26), residues: 370 loop : -1.59 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 272 TYR 0.016 0.002 TYR J 144 PHE 0.019 0.002 PHE L 259 TRP 0.013 0.001 TRP I 807 HIS 0.005 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (32133) covalent geometry : angle 0.68660 / 0.36 (43850) hydrogen bonds : bond 0.04147 / 3.99 ( 1465) hydrogen bonds : angle 4.72729 / 5.77 ( 4170) metal coordination : bond 0.00576 / 0.36 ( 12) metal coordination : angle 3.04408 / 1.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 389 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 21 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7859 (t0) REVERT: N 60 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: G 33 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8339 (tpp-160) REVERT: G 93 GLN cc_start: 0.8330 (tp40) cc_final: 0.8116 (tp-100) REVERT: G 125 LYS cc_start: 0.8407 (tttt) cc_final: 0.7875 (tppp) REVERT: G 129 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8624 (t) REVERT: G 147 GLN cc_start: 0.8763 (pt0) cc_final: 0.8522 (pt0) REVERT: G 150 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7612 (ptp90) REVERT: G 231 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7314 (t80) REVERT: H 12 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6759 (ptt90) REVERT: H 48 LEU cc_start: 0.8490 (tt) cc_final: 0.8206 (tp) REVERT: H 69 SER cc_start: 0.5172 (OUTLIER) cc_final: 0.4431 (p) REVERT: H 78 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.7954 (pp) REVERT: H 96 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6319 (p0) REVERT: H 191 ARG cc_start: 0.7900 (ptt-90) cc_final: 0.7625 (ptt-90) REVERT: H 199 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8057 (t70) REVERT: H 226 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8159 (mt-10) REVERT: I 7 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: I 36 GLN cc_start: 0.8477 (tp40) cc_final: 0.8201 (tt0) REVERT: I 44 GLU cc_start: 0.7693 (pm20) cc_final: 0.7148 (tt0) REVERT: I 77 GLU cc_start: 0.8598 (pt0) cc_final: 0.8096 (pm20) REVERT: I 223 LEU cc_start: 0.8538 (mt) cc_final: 0.8276 (mp) REVERT: I 289 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8163 (m) REVERT: I 319 LEU cc_start: 0.7966 (mp) cc_final: 0.7727 (mp) REVERT: I 337 PHE cc_start: 0.7938 (t80) cc_final: 0.7572 (t80) REVERT: I 478 ARG cc_start: 0.7659 (tpt90) cc_final: 0.7339 (tpm170) REVERT: I 602 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: I 631 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: I 634 VAL cc_start: 0.8537 (m) cc_final: 0.8184 (p) REVERT: I 779 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7710 (ttm-80) REVERT: I 953 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8589 (mt) REVERT: I 955 GLN cc_start: 0.8994 (tp40) cc_final: 0.8740 (tp-100) REVERT: I 963 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7060 (pp20) REVERT: I 1131 MET cc_start: 0.8344 (mtp) cc_final: 0.8117 (mtm) REVERT: I 1133 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (ptmt) REVERT: I 1140 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8341 (mmmt) REVERT: I 1160 ASP cc_start: 0.8043 (p0) cc_final: 0.7506 (p0) REVERT: I 1292 THR cc_start: 0.9437 (m) cc_final: 0.9082 (p) REVERT: I 1296 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8090 (t70) REVERT: J 83 VAL cc_start: 0.8355 (p) cc_final: 0.7977 (m) REVERT: J 94 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: J 97 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8355 (m) REVERT: J 170 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: J 194 LEU cc_start: 0.8122 (mm) cc_final: 0.7830 (mt) REVERT: J 195 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: J 219 LYS cc_start: 0.7619 (pmtt) cc_final: 0.7222 (tptm) REVERT: J 256 ASP cc_start: 0.6981 (m-30) cc_final: 0.6202 (p0) REVERT: J 399 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7878 (mptt) REVERT: J 594 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: J 648 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6883 (tm-30) REVERT: J 788 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8919 (tp) REVERT: J 821 MET cc_start: 0.7751 (tpt) cc_final: 0.7532 (tpt) REVERT: J 1146 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7326 (tp30) REVERT: J 1149 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7029 (mmm160) REVERT: J 1189 MET cc_start: 0.6093 (mmp) cc_final: 0.5746 (mmm) REVERT: J 1205 GLU cc_start: 0.6140 (tp30) cc_final: 0.5736 (mt-10) REVERT: J 1208 ASP cc_start: 0.7911 (t0) cc_final: 0.7557 (t70) REVERT: J 1253 ILE cc_start: 0.8771 (mm) cc_final: 0.8440 (mm) REVERT: J 1292 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6145 (mp) REVERT: J 1305 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: J 1372 ARG cc_start: 0.6334 (mpp80) cc_final: 0.6098 (ptp-170) REVERT: J 1373 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6261 (ttp-110) REVERT: L 117 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7942 (tp) REVERT: L 288 MET cc_start: 0.1942 (mmm) cc_final: 0.1332 (mmt) REVERT: L 310 GLU cc_start: 0.2591 (tt0) cc_final: 0.2354 (tt0) REVERT: L 341 LEU cc_start: 0.1563 (OUTLIER) cc_final: 0.1120 (tm) REVERT: L 357 GLN cc_start: 0.7143 (mt0) cc_final: 0.6282 (pp30) REVERT: L 359 LYS cc_start: 0.5331 (OUTLIER) cc_final: 0.5045 (ttmp) REVERT: L 386 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8671 (tp) REVERT: L 511 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7283 (tp) REVERT: L 538 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8033 (tm-30) REVERT: L 546 ASP cc_start: 0.8151 (p0) cc_final: 0.7617 (t0) REVERT: L 554 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6672 (ttt180) outliers start: 231 outliers final: 143 residues processed: 575 average time/residue: 0.6617 time to fit residues: 457.8602 Evaluate side-chains 543 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 366 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 323 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 292 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 296 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 932 GLN ** I1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J1295 ASN L 54 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.160496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119437 restraints weight = 43051.220| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.94 r_work: 0.3205 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 32145 Z= 0.182 Angle : 0.689 12.983 43868 Z= 0.355 Chirality : 0.046 0.361 5031 Planarity : 0.005 0.079 5353 Dihedral : 18.096 177.503 5611 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.19 % Favored : 93.70 % Rotamer: Outliers : 7.24 % Allowed : 26.10 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.70 (0.14), residues: 3698 helix: 0.81 (0.13), residues: 1596 sheet: -1.08 (0.26), residues: 370 loop : -1.56 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 272 TYR 0.017 0.002 TYR G 177 PHE 0.021 0.001 PHE L 259 TRP 0.013 0.001 TRP I 807 HIS 0.005 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (32133) covalent geometry : angle 0.68664 / 0.35 (43850) hydrogen bonds : bond 0.04146 / 3.99 ( 1465) hydrogen bonds : angle 4.71789 / 5.74 ( 4170) metal coordination : bond 0.00598 / 0.38 ( 12) metal coordination : angle 2.99807 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 378 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 18 THR cc_start: 0.9122 (t) cc_final: 0.8777 (p) REVERT: N 21 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7860 (t0) REVERT: G 93 GLN cc_start: 0.8327 (tp40) cc_final: 0.8108 (tp-100) REVERT: G 125 LYS cc_start: 0.8390 (tttt) cc_final: 0.7850 (tppp) REVERT: G 129 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8684 (t) REVERT: G 147 GLN cc_start: 0.8766 (pt0) cc_final: 0.8515 (pt0) REVERT: G 150 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7601 (ptp90) REVERT: G 231 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7342 (t80) REVERT: H 12 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6809 (ptt90) REVERT: H 48 LEU cc_start: 0.8437 (tt) cc_final: 0.8133 (tp) REVERT: H 75 GLN cc_start: 0.8252 (pp30) cc_final: 0.7808 (tm-30) REVERT: H 78 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8075 (pp) REVERT: H 191 ARG cc_start: 0.7931 (ptt-90) cc_final: 0.7666 (ptt-90) REVERT: H 199 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (t70) REVERT: H 226 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8197 (mt-10) REVERT: I 36 GLN cc_start: 0.8524 (tp40) cc_final: 0.8256 (tt0) REVERT: I 44 GLU cc_start: 0.7695 (pm20) cc_final: 0.7169 (tt0) REVERT: I 77 GLU cc_start: 0.8554 (pt0) cc_final: 0.8091 (pm20) REVERT: I 223 LEU cc_start: 0.8513 (mt) cc_final: 0.8256 (mp) REVERT: I 289 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8151 (m) REVERT: I 319 LEU cc_start: 0.7958 (mp) cc_final: 0.7733 (mp) REVERT: I 337 PHE cc_start: 0.7950 (t80) cc_final: 0.7591 (t80) REVERT: I 602 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: I 618 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: I 631 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: I 634 VAL cc_start: 0.8552 (m) cc_final: 0.8202 (p) REVERT: I 779 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7665 (ttm-80) REVERT: I 790 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8351 (t0) REVERT: I 953 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8585 (mt) REVERT: I 955 GLN cc_start: 0.9003 (tp40) cc_final: 0.8703 (tp-100) REVERT: I 963 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7050 (pp20) REVERT: I 1133 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8405 (ptmt) REVERT: I 1160 ASP cc_start: 0.8032 (p0) cc_final: 0.7485 (p0) REVERT: I 1292 THR cc_start: 0.9445 (m) cc_final: 0.9183 (p) REVERT: I 1296 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8036 (t70) REVERT: J 83 VAL cc_start: 0.8357 (p) cc_final: 0.7979 (m) REVERT: J 97 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8352 (m) REVERT: J 126 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8799 (pt) REVERT: J 170 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: J 194 LEU cc_start: 0.8096 (mm) cc_final: 0.7799 (mt) REVERT: J 195 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: J 256 ASP cc_start: 0.6980 (m-30) cc_final: 0.6193 (p0) REVERT: J 594 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8040 (pp30) REVERT: J 648 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6925 (tm-30) REVERT: J 821 MET cc_start: 0.7744 (tpt) cc_final: 0.7535 (tpt) REVERT: J 1146 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7307 (tp30) REVERT: J 1149 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7055 (mmm160) REVERT: J 1189 MET cc_start: 0.6033 (mmp) cc_final: 0.5641 (mmm) REVERT: J 1208 ASP cc_start: 0.7895 (t0) cc_final: 0.7542 (t70) REVERT: J 1292 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5997 (mp) REVERT: J 1305 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: J 1372 ARG cc_start: 0.6350 (mpp80) cc_final: 0.6117 (ptp-170) REVERT: L 117 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7952 (tp) REVERT: L 288 MET cc_start: 0.1940 (mmm) cc_final: 0.1304 (mmt) REVERT: L 341 LEU cc_start: 0.1549 (OUTLIER) cc_final: 0.1106 (tm) REVERT: L 357 GLN cc_start: 0.7127 (mt0) cc_final: 0.6276 (pp30) REVERT: L 386 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8674 (tp) REVERT: L 511 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7277 (tp) REVERT: L 526 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8203 (p) REVERT: L 538 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8091 (tm-30) REVERT: L 546 ASP cc_start: 0.8143 (p0) cc_final: 0.7655 (t0) outliers start: 230 outliers final: 155 residues processed: 565 average time/residue: 0.6112 time to fit residues: 417.1975 Evaluate side-chains 542 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 358 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 790 ASP Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1336 ASN Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 356 optimal weight: 0.9990 chunk 251 optimal weight: 0.4980 chunk 342 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 371 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 21 ASN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN ** I1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J 341 ASN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.162684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121833 restraints weight = 42976.637| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.94 r_work: 0.3241 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32145 Z= 0.132 Angle : 0.669 12.797 43868 Z= 0.345 Chirality : 0.044 0.368 5031 Planarity : 0.005 0.101 5353 Dihedral : 17.933 178.184 5601 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 5.89 % Allowed : 27.52 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.52 (0.14), residues: 3698 helix: 0.95 (0.13), residues: 1601 sheet: -1.00 (0.27), residues: 362 loop : -1.45 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 272 TYR 0.019 0.001 TYR J 144 PHE 0.025 0.001 PHE L 259 TRP 0.013 0.001 TRP I 807 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (32133) covalent geometry : angle 0.66641 / 0.35 (43850) hydrogen bonds : bond 0.03835 / 3.68 ( 1465) hydrogen bonds : angle 4.61992 / 5.60 ( 4170) metal coordination : bond 0.00366 / 0.22 ( 12) metal coordination : angle 2.84407 / 1.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 388 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 21 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7990 (t0) REVERT: G 33 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8222 (tpp-160) REVERT: G 57 THR cc_start: 0.9017 (m) cc_final: 0.8776 (p) REVERT: G 93 GLN cc_start: 0.8260 (tp40) cc_final: 0.8036 (tp-100) REVERT: G 125 LYS cc_start: 0.8351 (tttt) cc_final: 0.7790 (tppp) REVERT: G 129 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8595 (t) REVERT: G 147 GLN cc_start: 0.8701 (pt0) cc_final: 0.8416 (pt0) REVERT: G 150 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7577 (ptp90) REVERT: H 12 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6716 (ptt90) REVERT: H 48 LEU cc_start: 0.8327 (tt) cc_final: 0.8055 (tp) REVERT: H 78 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8056 (pp) REVERT: H 96 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6339 (p0) REVERT: H 199 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8027 (t70) REVERT: I 36 GLN cc_start: 0.8488 (tp40) cc_final: 0.8240 (tt0) REVERT: I 44 GLU cc_start: 0.7672 (pm20) cc_final: 0.7176 (tt0) REVERT: I 77 GLU cc_start: 0.8566 (pt0) cc_final: 0.8093 (pm20) REVERT: I 223 LEU cc_start: 0.8533 (mt) cc_final: 0.8280 (mp) REVERT: I 289 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (m) REVERT: I 319 LEU cc_start: 0.7921 (mp) cc_final: 0.7708 (mp) REVERT: I 337 PHE cc_start: 0.7947 (t80) cc_final: 0.7598 (t80) REVERT: I 525 THR cc_start: 0.9316 (t) cc_final: 0.9060 (p) REVERT: I 600 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8165 (p) REVERT: I 634 VAL cc_start: 0.8567 (m) cc_final: 0.8254 (p) REVERT: I 779 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7654 (ttm-80) REVERT: I 955 GLN cc_start: 0.8910 (tp40) cc_final: 0.8664 (tp-100) REVERT: I 963 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: I 1085 MET cc_start: 0.8961 (mmm) cc_final: 0.8650 (mmm) REVERT: I 1133 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (ptmt) REVERT: I 1160 ASP cc_start: 0.7969 (p0) cc_final: 0.7395 (p0) REVERT: J 83 VAL cc_start: 0.8287 (p) cc_final: 0.7910 (m) REVERT: J 94 GLN cc_start: 0.8591 (mt0) cc_final: 0.8337 (pt0) REVERT: J 97 VAL cc_start: 0.8824 (p) cc_final: 0.8323 (m) REVERT: J 126 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8792 (pp) REVERT: J 170 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: J 194 LEU cc_start: 0.8022 (mm) cc_final: 0.7747 (mt) REVERT: J 256 ASP cc_start: 0.6959 (m-30) cc_final: 0.6200 (p0) REVERT: J 594 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8017 (pp30) REVERT: J 648 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6840 (tm-30) REVERT: J 1146 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7332 (tp30) REVERT: J 1149 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7079 (mmm160) REVERT: J 1189 MET cc_start: 0.6033 (mmp) cc_final: 0.5632 (mmm) REVERT: J 1208 ASP cc_start: 0.7896 (t0) cc_final: 0.7545 (t70) REVERT: J 1253 ILE cc_start: 0.8747 (mm) cc_final: 0.8434 (mm) REVERT: J 1292 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5865 (mp) REVERT: J 1372 ARG cc_start: 0.6367 (mpp80) cc_final: 0.6139 (ptp-170) REVERT: L 117 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7921 (tp) REVERT: L 288 MET cc_start: 0.1801 (mmm) cc_final: 0.1138 (mmt) REVERT: L 341 LEU cc_start: 0.1252 (OUTLIER) cc_final: 0.0833 (tm) REVERT: L 357 GLN cc_start: 0.7118 (mt0) cc_final: 0.6293 (pp30) REVERT: L 386 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8560 (tp) REVERT: L 489 MET cc_start: 0.7746 (mpt) cc_final: 0.7044 (mmm) REVERT: L 511 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7238 (tp) REVERT: L 538 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8094 (tm-30) REVERT: L 546 ASP cc_start: 0.8096 (p0) cc_final: 0.7640 (t0) outliers start: 187 outliers final: 118 residues processed: 540 average time/residue: 0.6303 time to fit residues: 410.0262 Evaluate side-chains 497 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 359 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1133 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 26 optimal weight: 0.0170 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 932 GLN ** I1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.161647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120692 restraints weight = 42979.378| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.88 r_work: 0.3225 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32145 Z= 0.163 Angle : 0.688 16.432 43868 Z= 0.353 Chirality : 0.045 0.369 5031 Planarity : 0.005 0.100 5353 Dihedral : 17.840 177.770 5579 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 4.85 % Allowed : 28.75 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3698 helix: 0.95 (0.13), residues: 1600 sheet: -0.91 (0.27), residues: 353 loop : -1.44 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 272 TYR 0.019 0.001 TYR J 144 PHE 0.025 0.001 PHE L 259 TRP 0.012 0.001 TRP I 807 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (32133) covalent geometry : angle 0.68537 / 0.35 (43850) hydrogen bonds : bond 0.03984 / 3.83 ( 1465) hydrogen bonds : angle 4.62748 / 5.62 ( 4170) metal coordination : bond 0.00490 / 0.31 ( 12) metal coordination : angle 2.76993 / 1.59 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 362 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.9077 (m) cc_final: 0.8815 (p) REVERT: G 93 GLN cc_start: 0.8279 (tp40) cc_final: 0.8053 (tp-100) REVERT: G 125 LYS cc_start: 0.8337 (tttt) cc_final: 0.7814 (tppp) REVERT: G 129 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8597 (t) REVERT: G 147 GLN cc_start: 0.8704 (pt0) cc_final: 0.8409 (pt0) REVERT: G 150 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7591 (ptp90) REVERT: G 231 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6598 (t80) REVERT: H 48 LEU cc_start: 0.8390 (tt) cc_final: 0.8115 (tp) REVERT: H 78 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8030 (pp) REVERT: H 96 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6342 (p0) REVERT: H 199 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: I 36 GLN cc_start: 0.8477 (tp40) cc_final: 0.8226 (tt0) REVERT: I 44 GLU cc_start: 0.7609 (pm20) cc_final: 0.7149 (tt0) REVERT: I 77 GLU cc_start: 0.8546 (pt0) cc_final: 0.8070 (pm20) REVERT: I 223 LEU cc_start: 0.8495 (mt) cc_final: 0.8246 (mp) REVERT: I 289 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8123 (m) REVERT: I 319 LEU cc_start: 0.7871 (mp) cc_final: 0.7650 (mp) REVERT: I 337 PHE cc_start: 0.7982 (t80) cc_final: 0.7621 (t80) REVERT: I 600 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8251 (p) REVERT: I 634 VAL cc_start: 0.8599 (m) cc_final: 0.8269 (p) REVERT: I 779 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7628 (ttm-80) REVERT: I 790 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8364 (t0) REVERT: I 878 THR cc_start: 0.9029 (p) cc_final: 0.8826 (t) REVERT: I 955 GLN cc_start: 0.8922 (tp40) cc_final: 0.8670 (tp-100) REVERT: I 963 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7011 (pp20) REVERT: I 1085 MET cc_start: 0.8971 (mmm) cc_final: 0.8650 (mmm) REVERT: I 1160 ASP cc_start: 0.7978 (p0) cc_final: 0.7405 (p0) REVERT: J 83 VAL cc_start: 0.8308 (p) cc_final: 0.7938 (m) REVERT: J 94 GLN cc_start: 0.8600 (mt0) cc_final: 0.8348 (pt0) REVERT: J 97 VAL cc_start: 0.8850 (p) cc_final: 0.8342 (m) REVERT: J 170 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: J 194 LEU cc_start: 0.8057 (mm) cc_final: 0.7798 (mt) REVERT: J 256 ASP cc_start: 0.6942 (m-30) cc_final: 0.6202 (p0) REVERT: J 330 MET cc_start: 0.7967 (mtp) cc_final: 0.7683 (mtp) REVERT: J 594 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8080 (pp30) REVERT: J 648 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6874 (tm-30) REVERT: J 1146 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7338 (tp30) REVERT: J 1149 ARG cc_start: 0.7617 (tpp-160) cc_final: 0.7063 (mmm160) REVERT: J 1189 MET cc_start: 0.6132 (mmp) cc_final: 0.5696 (mmm) REVERT: J 1208 ASP cc_start: 0.7751 (t0) cc_final: 0.7391 (t70) REVERT: J 1292 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5864 (mp) REVERT: J 1372 ARG cc_start: 0.6360 (mpp80) cc_final: 0.6137 (ptp-170) REVERT: L 117 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7923 (tp) REVERT: L 288 MET cc_start: 0.2038 (mmm) cc_final: 0.1586 (mpp) REVERT: L 341 LEU cc_start: 0.1256 (OUTLIER) cc_final: 0.0845 (tm) REVERT: L 357 GLN cc_start: 0.7120 (mt0) cc_final: 0.6303 (pp30) REVERT: L 386 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8644 (tp) REVERT: L 511 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7308 (tp) REVERT: L 538 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8095 (tm-30) REVERT: L 546 ASP cc_start: 0.8097 (p0) cc_final: 0.7626 (t0) outliers start: 154 outliers final: 115 residues processed: 495 average time/residue: 0.6310 time to fit residues: 376.7733 Evaluate side-chains 483 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 350 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 150 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 790 ASP Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 473 GLU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 352 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 378 optimal weight: 0.4980 chunk 304 optimal weight: 2.9990 chunk 16 optimal weight: 40.0000 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 227 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 GLN H 186 ASN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN ** I1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.161858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120956 restraints weight = 43053.426| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.90 r_work: 0.3220 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 32145 Z= 0.175 Angle : 0.774 59.177 43868 Z= 0.420 Chirality : 0.046 0.414 5031 Planarity : 0.005 0.103 5353 Dihedral : 17.841 177.759 5575 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 4.97 % Allowed : 28.62 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3698 helix: 0.95 (0.13), residues: 1600 sheet: -0.92 (0.27), residues: 353 loop : -1.44 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 272 TYR 0.018 0.001 TYR J 144 PHE 0.021 0.001 PHE L 259 TRP 0.012 0.001 TRP I 807 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (32133) covalent geometry : angle 0.77192 / 0.42 (43850) hydrogen bonds : bond 0.04034 / 3.84 ( 1465) hydrogen bonds : angle 4.63055 / 5.63 ( 4170) metal coordination : bond 0.00475 / 0.30 ( 12) metal coordination : angle 2.76654 / 1.59 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13926.68 seconds wall clock time: 237 minutes 14.79 seconds (14234.79 seconds total)