Starting phenix.real_space_refine on Fri Mar 6 11:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n57_0348/03_2026/6n57_0348_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n57_0348/03_2026/6n57_0348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n57_0348/03_2026/6n57_0348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n57_0348/03_2026/6n57_0348.map" model { file = "/net/cci-nas-00/data/ceres_data/6n57_0348/03_2026/6n57_0348_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n57_0348/03_2026/6n57_0348_trim.cif" } resolution = 3.7 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 Mg 1 5.21 5 S 136 5.16 5 C 18961 2.51 5 N 5327 2.21 5 O 5805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30233 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10479 Classifications: {'peptide': 1347} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1290} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 4423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4423 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 2, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "L" 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: "M" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20313 SG CYS J 814 25.504 89.870 82.477 1.00 34.14 S ATOM 20878 SG CYS J 888 28.493 88.510 84.421 1.00 38.06 S ATOM 20929 SG CYS J 895 27.462 87.320 81.418 1.00 21.90 S ATOM 20950 SG CYS J 898 28.060 90.381 80.150 1.00 24.08 S ATOM 14479 SG CYS J 70 50.502 39.237 119.673 1.00 46.89 S ATOM 14493 SG CYS J 72 52.431 37.499 122.064 1.00 47.01 S ATOM 14601 SG CYS J 85 48.798 37.822 122.466 1.00 68.08 S ATOM 14625 SG CYS J 88 51.793 41.223 122.111 1.00 58.98 S ATOM 29831 SG CYS M 37 76.970 129.893 81.580 1.00 66.53 S ATOM 29851 SG CYS M 40 79.508 131.735 83.020 1.00 64.05 S ATOM 29988 SG CYS M 58 80.825 128.222 80.883 1.00 49.44 S Time building chain proxies: 6.48, per 1000 atoms: 0.21 Number of scatterers: 30233 At special positions: 0 Unit cell: (153.4, 163.8, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 136 16.00 Mg 1 11.99 O 5805 8.00 N 5327 7.00 C 18961 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 72 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 58 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 40 " Number of angles added : 12 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7138 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 49 sheets defined 41.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.680A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.937A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.692A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.558A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.516A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 4.730A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) 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 removed outlier: 3.684A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 88 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.103A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 222 Processing helix chain 'I' and resid 270 through 279 removed outlier: 3.588A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.131A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (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 389 removed outlier: 4.494A 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: 3.851A pdb=" N GLY I 438 " --> pdb=" O ASP I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.984A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.252A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 525 Processing helix chain 'I' and resid 544 through 548 removed outlier: 3.550A pdb=" N VAL I 547 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.693A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 819 through 825 removed outlier: 3.889A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 980 removed outlier: 3.844A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.680A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.543A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 removed outlier: 4.400A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1201 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.646A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.568A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1321 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 removed outlier: 3.507A pdb=" N GLU J 100 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.573A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.562A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 342 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 403 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.195A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 458 removed outlier: 4.394A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.515A pdb=" N ASN J 488 " --> pdb=" O MET J 485 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 485 through 489' Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 removed outlier: 3.619A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.953A pdb=" N ALA J 577 " --> pdb=" O THR J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.897A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY J 613 " --> pdb=" O TYR J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.006A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 669 removed outlier: 3.767A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA J 662 " --> pdb=" O GLU J 658 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 787 removed outlier: 3.836A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 787 through 792 removed outlier: 3.586A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 794 through 804 removed outlier: 3.638A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.707A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.729A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1070 through 1074 Processing helix chain 'J' and resid 1138 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 4.196A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.283A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.601A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.355A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.603A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 20 removed outlier: 3.554A pdb=" N GLY L 20 " --> pdb=" O GLY L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 31 Processing helix chain 'L' and resid 39 through 51 Processing helix chain 'L' and resid 76 through 90 Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 115 through 137 Processing helix chain 'L' and resid 137 through 154 removed outlier: 3.708A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU L 154 " --> pdb=" O ARG L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.589A pdb=" N LEU L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 233 Processing helix chain 'L' and resid 244 through 257 Processing helix chain 'L' and resid 262 through 296 removed outlier: 4.003A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 removed outlier: 4.815A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 321 removed outlier: 4.266A pdb=" N ALA L 319 " --> pdb=" O TRP L 315 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA L 321 " --> pdb=" O ASN L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 329 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 392 removed outlier: 4.872A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 4.859A 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 418 Processing helix chain 'L' and resid 419 through 424 removed outlier: 6.929A pdb=" N ARG L 422 " --> pdb=" O PHE L 419 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.856A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 474 Processing helix chain 'L' and resid 479 through 487 removed outlier: 4.069A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.731A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 552 through 562 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 584 through 600 removed outlier: 3.869A pdb=" N ARG L 588 " --> pdb=" O ARG L 584 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'M' and resid 5 through 27 removed outlier: 3.761A pdb=" N ILE M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 52 Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.515A pdb=" N GLN M 62 " --> pdb=" O CYS M 58 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.985A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 102 through 105 Processing sheet with id=AA3, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.593A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 188 through 189 Processing sheet with id=AA5, first strand: chain 'H' and resid 16 through 17 removed outlier: 3.627A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 53 through 61 removed outlier: 3.753A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA8, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'H' and resid 187 through 190 Processing sheet with id=AB1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.933A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 66 through 69 removed outlier: 3.769A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 73 through 75 removed outlier: 4.363A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'I' and resid 155 through 157 removed outlier: 3.701A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 238 through 239 Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.163A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR I 262 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 599 through 603 removed outlier: 5.195A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC4, first strand: chain 'I' and resid 732 through 736 removed outlier: 6.544A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.723A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE I 765 " --> pdb=" O THR I 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1097 through 1098 removed outlier: 3.623A pdb=" N GLN I 798 " --> pdb=" O MET I1232 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 832 through 833 Processing sheet with id=AD1, first strand: chain 'I' and resid 836 through 838 removed outlier: 3.909A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AD3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.792A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD5, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'I' and resid 1209 through 1210 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1335 through 1339 removed outlier: 3.629A pdb=" N LYS J 21 " --> pdb=" O GLU I1338 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 103 through 112 removed outlier: 3.727A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE2, first strand: chain 'J' and resid 252 through 254 removed outlier: 4.169A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 365 through 369 removed outlier: 7.073A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 548 through 549 Processing sheet with id=AE5, first strand: chain 'J' and resid 553 through 556 removed outlier: 3.891A pdb=" N GLU J 554 " --> pdb=" O LYS J 566 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS J 566 " --> pdb=" O GLU J 554 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU J 556 " --> pdb=" O VAL J 564 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE7, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.635A pdb=" N MET J 822 " --> pdb=" O VAL J 880 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.025A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.573A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1049 Processing sheet with id=AF2, first strand: chain 'J' and resid 1077 through 1079 Processing sheet with id=AF3, first strand: chain 'J' and resid 1187 through 1191 Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 1209 hydrogen bonds defined for protein. 3426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10356 1.34 - 1.46: 6246 1.46 - 1.59: 13818 1.59 - 1.72: 14 1.72 - 1.84: 245 Bond restraints: 30679 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.841 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C19 1N7 M 102 " pdb=" C3 1N7 M 102 " ideal model delta sigma weight residual 1.532 1.815 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.738 -0.206 2.00e-02 2.50e+03 1.07e+02 ... (remaining 30674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.10: 41313 6.10 - 12.21: 121 12.21 - 18.31: 10 18.31 - 24.41: 1 24.41 - 30.52: 2 Bond angle restraints: 41447 Sorted by residual: angle pdb=" N GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta sigma weight residual 110.49 141.01 -30.52 1.69e+00 3.50e-01 3.26e+02 angle pdb=" C PHE J 437 " pdb=" N GLU J 438 " pdb=" CA GLU J 438 " ideal model delta sigma weight residual 121.92 104.59 17.33 1.60e+00 3.91e-01 1.17e+02 angle pdb=" N GLU L 58 " pdb=" CA GLU L 58 " pdb=" C GLU L 58 " ideal model delta sigma weight residual 110.80 90.84 19.96 2.13e+00 2.20e-01 8.78e+01 angle pdb=" C GLU H 29 " pdb=" N PRO H 30 " pdb=" CD PRO H 30 " ideal model delta sigma weight residual 120.60 136.83 -16.23 2.20e+00 2.07e-01 5.44e+01 angle pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CD PRO I 58 " ideal model delta sigma weight residual 120.60 136.16 -15.56 2.20e+00 2.07e-01 5.00e+01 ... (remaining 41442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 18472 19.50 - 39.00: 636 39.00 - 58.50: 47 58.50 - 78.00: 26 78.00 - 97.50: 2 Dihedral angle restraints: 19183 sinusoidal: 8114 harmonic: 11069 Sorted by residual: dihedral pdb=" N GLU L 58 " pdb=" C GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta harmonic sigma weight residual 122.80 146.50 -23.70 0 2.50e+00 1.60e-01 8.99e+01 dihedral pdb=" CA THR J 853 " pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta harmonic sigma weight residual 180.00 135.88 44.12 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -139.53 -40.47 0 5.00e+00 4.00e-02 6.55e+01 ... (remaining 19180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4683 0.149 - 0.298: 63 0.298 - 0.448: 3 0.448 - 0.597: 1 0.597 - 0.746: 1 Chirality restraints: 4751 Sorted by residual: chirality pdb=" CA GLU L 58 " pdb=" N GLU L 58 " pdb=" C GLU L 58 " pdb=" CB GLU L 58 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA GLU G 29 " pdb=" N GLU G 29 " pdb=" C GLU G 29 " pdb=" CB GLU G 29 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4748 not shown) Planarity restraints: 5415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 96 " -0.124 5.00e-02 4.00e+02 2.00e-01 6.43e+01 pdb=" N PRO L 97 " 0.347 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " -0.125 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " -0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 59 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO L 60 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 438 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO J 439 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO J 439 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO J 439 " 0.048 5.00e-02 4.00e+02 ... (remaining 5412 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 15 2.07 - 2.78: 7355 2.78 - 3.49: 43260 3.49 - 4.19: 67851 4.19 - 4.90: 120552 Nonbonded interactions: 239033 Sorted by model distance: nonbonded pdb=" NH1 ARG J 933 " pdb=" OD2 ASP L 63 " model vdw 1.366 3.120 nonbonded pdb=" O ASP L 63 " pdb=" N LEU L 65 " model vdw 1.570 3.120 nonbonded pdb=" OH TYR L 148 " pdb=" OE2 GLU L 152 " model vdw 1.824 3.040 nonbonded pdb=" O THR I 539 " pdb=" O ALA I 543 " model vdw 1.884 3.040 nonbonded pdb=" OD1 ASP L 96 " pdb=" N PRO L 97 " model vdw 1.956 3.120 ... (remaining 239028 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 8 through 158 or resid 171 through 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 8 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.920 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.013 0.552 30691 Z= 0.578 Angle : 1.230 57.947 41459 Z= 0.615 Chirality : 0.060 0.746 4751 Planarity : 0.007 0.200 5415 Dihedral : 10.444 97.497 12045 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 38.98 Ramachandran Plot: Outliers : 0.60 % Allowed : 15.43 % Favored : 83.97 % Rotamer: Outliers : 0.37 % Allowed : 3.46 % Favored : 96.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.67 % Twisted General : 0.22 % 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: -4.55 (0.11), residues: 3817 helix: -2.11 (0.11), residues: 1526 sheet: -3.68 (0.23), residues: 349 loop : -3.76 (0.12), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I1223 TYR 0.037 0.003 TYR G 177 PHE 0.036 0.004 PHE J 437 TRP 0.030 0.004 TRP I1276 HIS 0.014 0.003 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.01230 (30679) covalent geometry : angle 1.13546 (41447) hydrogen bonds : bond 0.16908 ( 1209) hydrogen bonds : angle 7.46875 ( 3426) metal coordination : bond 0.25726 ( 11) metal coordination : angle 27.86686 ( 12) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 801 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: G 200 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8434 (ttmm) REVERT: H 51 MET cc_start: 0.8338 (mmm) cc_final: 0.7877 (mmm) REVERT: H 95 LYS cc_start: 0.8560 (tptm) cc_final: 0.8350 (tppt) REVERT: H 197 ASP cc_start: 0.7505 (p0) cc_final: 0.7204 (p0) REVERT: H 199 ASP cc_start: 0.8146 (m-30) cc_final: 0.7787 (m-30) REVERT: H 200 LYS cc_start: 0.9362 (tttt) cc_final: 0.9126 (tttp) REVERT: H 211 ILE cc_start: 0.8189 (tp) cc_final: 0.7776 (tp) REVERT: I 14 ASP cc_start: 0.7997 (t70) cc_final: 0.7796 (t0) REVERT: I 59 ILE cc_start: 0.7451 (mt) cc_final: 0.7043 (mt) REVERT: I 422 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7696 (mtmm) REVERT: I 545 PHE cc_start: 0.7142 (t80) cc_final: 0.6824 (t80) REVERT: I 684 ASN cc_start: 0.8650 (t0) cc_final: 0.8325 (t0) REVERT: I 699 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9256 (tm) REVERT: I 702 THR cc_start: 0.9187 (p) cc_final: 0.8916 (p) REVERT: I 717 VAL cc_start: 0.9486 (t) cc_final: 0.9187 (m) REVERT: I 976 ARG cc_start: 0.6453 (tpt-90) cc_final: 0.6215 (ttt90) REVERT: I 1040 ASP cc_start: 0.8045 (m-30) cc_final: 0.7836 (m-30) REVERT: I 1273 MET cc_start: 0.8379 (mtm) cc_final: 0.8024 (mtp) REVERT: I 1290 MET cc_start: 0.8528 (tpp) cc_final: 0.8221 (tpp) REVERT: J 21 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8521 (tttp) REVERT: J 130 MET cc_start: 0.8355 (ttt) cc_final: 0.7563 (ttp) REVERT: J 157 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7651 (mm-40) REVERT: J 325 LYS cc_start: 0.8869 (tttt) cc_final: 0.8492 (mtmt) REVERT: J 429 LEU cc_start: 0.9171 (mm) cc_final: 0.8872 (mt) REVERT: J 466 MET cc_start: 0.8289 (mtp) cc_final: 0.8081 (mtp) REVERT: J 683 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8807 (tt) REVERT: J 725 MET cc_start: 0.8839 (mtm) cc_final: 0.8570 (mtp) REVERT: J 821 MET cc_start: 0.8487 (tpp) cc_final: 0.8170 (tpt) REVERT: J 982 LEU cc_start: 0.8489 (tp) cc_final: 0.8267 (tp) REVERT: J 1286 LYS cc_start: 0.8303 (tmmt) cc_final: 0.8074 (ttpp) REVERT: J 1291 GLU cc_start: 0.8054 (pt0) cc_final: 0.7749 (pp20) REVERT: J 1316 THR cc_start: 0.8986 (m) cc_final: 0.8750 (p) REVERT: K 55 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7763 (tm-30) REVERT: L 21 TYR cc_start: 0.7256 (p90) cc_final: 0.6707 (p90) REVERT: L 46 GLN cc_start: 0.6467 (tp-100) cc_final: 0.6007 (mm110) REVERT: L 117 ILE cc_start: 0.5984 (mp) cc_final: 0.5780 (mp) REVERT: L 273 MET cc_start: 0.5297 (mtt) cc_final: 0.4974 (tpt) REVERT: L 276 MET cc_start: 0.5528 (tpp) cc_final: 0.4941 (mmt) REVERT: L 339 ARG cc_start: 0.5151 (mtp85) cc_final: 0.4227 (mmp-170) REVERT: M 61 CYS cc_start: 0.8005 (m) cc_final: 0.7273 (m) outliers start: 12 outliers final: 3 residues processed: 810 average time/residue: 0.2226 time to fit residues: 272.7517 Evaluate side-chains 434 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 428 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 683 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS G 147 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 69 GLN I 133 ASN I 343 HIS I 620 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS I1209 GLN J 489 ASN J 680 ASN J 720 ASN J 910 ASN J1010 GLN J1197 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1268 ASN J1295 ASN ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 70 GLN L 40 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN L 346 GLN L 383 ASN L 518 HIS L 568 ASN M 21 ASN M 68 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138852 restraints weight = 44740.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138814 restraints weight = 39059.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140235 restraints weight = 35174.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140488 restraints weight = 25178.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140692 restraints weight = 22953.372| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30691 Z= 0.153 Angle : 0.752 13.494 41459 Z= 0.382 Chirality : 0.047 0.408 4751 Planarity : 0.006 0.128 5415 Dihedral : 6.437 79.720 4511 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.73 % Favored : 91.98 % Rotamer: Outliers : 2.73 % Allowed : 10.05 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.01 (0.12), residues: 3817 helix: -0.45 (0.13), residues: 1528 sheet: -3.31 (0.24), residues: 338 loop : -3.16 (0.12), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 322 TYR 0.026 0.002 TYR J 349 PHE 0.020 0.002 PHE I 38 TRP 0.020 0.001 TRP I 807 HIS 0.012 0.001 HIS I 273 Details of bonding type rmsd covalent geometry : bond 0.00347 (30679) covalent geometry : angle 0.74799 (41447) hydrogen bonds : bond 0.04424 ( 1209) hydrogen bonds : angle 5.16248 ( 3426) metal coordination : bond 0.00997 ( 11) metal coordination : angle 4.62805 ( 12) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 585 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8552 (tt) REVERT: G 185 TYR cc_start: 0.8886 (p90) cc_final: 0.8420 (p90) REVERT: G 200 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8589 (ttmm) REVERT: G 207 THR cc_start: 0.8585 (m) cc_final: 0.8150 (p) REVERT: H 211 ILE cc_start: 0.8143 (tp) cc_final: 0.7754 (tp) REVERT: I 272 ARG cc_start: 0.7300 (tmt170) cc_final: 0.6909 (ttt-90) REVERT: I 470 ARG cc_start: 0.7400 (ppp80) cc_final: 0.6826 (tpm170) REVERT: I 717 VAL cc_start: 0.9297 (t) cc_final: 0.8929 (m) REVERT: I 817 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8259 (tt) REVERT: I 1240 ASP cc_start: 0.7717 (p0) cc_final: 0.7333 (p0) REVERT: I 1290 MET cc_start: 0.8349 (tpp) cc_final: 0.8144 (tpp) REVERT: J 130 MET cc_start: 0.8446 (ttt) cc_final: 0.7580 (ttp) REVERT: J 180 MET cc_start: 0.7156 (ptm) cc_final: 0.6467 (ptm) REVERT: J 325 LYS cc_start: 0.8468 (tttt) cc_final: 0.8152 (mptt) REVERT: J 429 LEU cc_start: 0.9003 (mm) cc_final: 0.8594 (mt) REVERT: J 466 MET cc_start: 0.8209 (mtp) cc_final: 0.7936 (mtp) REVERT: J 701 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8781 (tm) REVERT: J 725 MET cc_start: 0.8721 (mtm) cc_final: 0.8510 (mtp) REVERT: J 849 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7453 (mt) REVERT: J 1020 TRP cc_start: 0.7392 (p90) cc_final: 0.6332 (p90) REVERT: J 1208 ASP cc_start: 0.7022 (m-30) cc_final: 0.6778 (m-30) REVERT: J 1275 LEU cc_start: 0.8277 (tp) cc_final: 0.7966 (tt) REVERT: J 1330 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7841 (ttp80) REVERT: K 3 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8064 (ttm170) REVERT: K 55 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8092 (tm-30) REVERT: L 21 TYR cc_start: 0.6973 (p90) cc_final: 0.6580 (p90) REVERT: L 24 TYR cc_start: 0.6568 (m-80) cc_final: 0.5048 (t80) REVERT: L 46 GLN cc_start: 0.6371 (tp-100) cc_final: 0.5897 (mm-40) REVERT: L 121 LYS cc_start: 0.7901 (tppt) cc_final: 0.7252 (tptt) REVERT: L 266 PHE cc_start: 0.4137 (OUTLIER) cc_final: 0.3879 (t80) REVERT: L 273 MET cc_start: 0.5145 (mtt) cc_final: 0.4841 (tpp) REVERT: L 288 MET cc_start: 0.0558 (ttt) cc_final: 0.0037 (ptt) REVERT: L 339 ARG cc_start: 0.4912 (mtp85) cc_final: 0.4131 (mmp-170) REVERT: M 61 CYS cc_start: 0.7991 (m) cc_final: 0.7776 (m) outliers start: 89 outliers final: 32 residues processed: 640 average time/residue: 0.1978 time to fit residues: 199.0832 Evaluate side-chains 457 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 419 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 2 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 365 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS I 69 GLN I 219 GLN I 613 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 31 GLN L 129 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138163 restraints weight = 44783.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138286 restraints weight = 40436.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139913 restraints weight = 35724.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139970 restraints weight = 23655.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140171 restraints weight = 21737.108| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30691 Z= 0.141 Angle : 0.678 14.412 41459 Z= 0.341 Chirality : 0.045 0.308 4751 Planarity : 0.005 0.095 5415 Dihedral : 5.697 49.934 4502 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.52 % Favored : 92.25 % Rotamer: Outliers : 3.09 % Allowed : 12.68 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -2.34 (0.13), residues: 3817 helix: 0.16 (0.13), residues: 1552 sheet: -2.94 (0.26), residues: 329 loop : -2.87 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 148 TYR 0.018 0.001 TYR I 367 PHE 0.021 0.001 PHE I 389 TRP 0.016 0.001 TRP I 807 HIS 0.009 0.001 HIS I 273 Details of bonding type rmsd covalent geometry : bond 0.00325 (30679) covalent geometry : angle 0.67629 (41447) hydrogen bonds : bond 0.03920 ( 1209) hydrogen bonds : angle 4.73306 ( 3426) metal coordination : bond 0.00588 ( 11) metal coordination : angle 3.16754 ( 12) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 502 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8604 (tt) REVERT: G 185 TYR cc_start: 0.8858 (p90) cc_final: 0.8291 (p90) REVERT: G 200 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8601 (ttmm) REVERT: G 207 THR cc_start: 0.8484 (m) cc_final: 0.8047 (p) REVERT: H 28 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8342 (mt) REVERT: I 66 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8113 (p) REVERT: I 429 MET cc_start: 0.7836 (mtt) cc_final: 0.7477 (mtm) REVERT: I 470 ARG cc_start: 0.7420 (ppp80) cc_final: 0.6891 (tpm170) REVERT: I 515 MET cc_start: 0.8222 (ttp) cc_final: 0.7898 (ttp) REVERT: I 642 SER cc_start: 0.8806 (p) cc_final: 0.8598 (p) REVERT: I 717 VAL cc_start: 0.9193 (t) cc_final: 0.8843 (m) REVERT: I 870 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8706 (mm) REVERT: I 1088 ASP cc_start: 0.8161 (p0) cc_final: 0.7876 (p0) REVERT: I 1253 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9080 (tm) REVERT: I 1290 MET cc_start: 0.8406 (tpp) cc_final: 0.8064 (tpp) REVERT: J 180 MET cc_start: 0.7047 (ptm) cc_final: 0.6433 (ptm) REVERT: J 325 LYS cc_start: 0.8506 (tttt) cc_final: 0.8178 (mptt) REVERT: J 398 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8161 (ttmt) REVERT: J 466 MET cc_start: 0.8186 (mtp) cc_final: 0.7897 (mtp) REVERT: J 725 MET cc_start: 0.8689 (mtm) cc_final: 0.8481 (mtp) REVERT: J 823 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7782 (m) REVERT: J 849 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7435 (mt) REVERT: J 1208 ASP cc_start: 0.7400 (m-30) cc_final: 0.7178 (m-30) REVERT: J 1330 ARG cc_start: 0.7995 (tmm-80) cc_final: 0.7784 (ttm110) REVERT: K 55 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8112 (tm-30) REVERT: L 21 TYR cc_start: 0.7016 (p90) cc_final: 0.6643 (p90) REVERT: L 24 TYR cc_start: 0.6731 (m-80) cc_final: 0.6530 (m-80) REVERT: L 46 GLN cc_start: 0.6558 (tp-100) cc_final: 0.6161 (mm110) REVERT: L 121 LYS cc_start: 0.7904 (tppt) cc_final: 0.7173 (tptt) REVERT: L 224 LEU cc_start: 0.4281 (tt) cc_final: 0.3535 (mm) REVERT: L 266 PHE cc_start: 0.4311 (OUTLIER) cc_final: 0.4039 (t80) REVERT: L 273 MET cc_start: 0.5296 (mtt) cc_final: 0.4259 (tpp) REVERT: L 339 ARG cc_start: 0.4836 (mtp85) cc_final: 0.3968 (mmp-170) REVERT: M 61 CYS cc_start: 0.7777 (m) cc_final: 0.7186 (m) outliers start: 101 outliers final: 47 residues processed: 575 average time/residue: 0.1867 time to fit residues: 172.5083 Evaluate side-chains 461 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 405 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 935 PHE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 2 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 230 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS H 128 HIS I 613 ASN I 620 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1017 GLN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN J 951 GLN J 979 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 568 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131574 restraints weight = 44499.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131662 restraints weight = 42698.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133233 restraints weight = 37022.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133299 restraints weight = 26041.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133588 restraints weight = 23701.543| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30691 Z= 0.251 Angle : 0.748 14.753 41459 Z= 0.377 Chirality : 0.047 0.267 4751 Planarity : 0.005 0.076 5415 Dihedral : 5.826 48.522 4502 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.80 % Favored : 90.99 % Rotamer: Outliers : 3.65 % Allowed : 14.92 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -2.14 (0.13), residues: 3817 helix: 0.27 (0.13), residues: 1531 sheet: -2.82 (0.28), residues: 287 loop : -2.69 (0.12), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 312 TYR 0.018 0.002 TYR J 631 PHE 0.017 0.002 PHE I 80 TRP 0.019 0.002 TRP I 807 HIS 0.008 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00600 (30679) covalent geometry : angle 0.74567 (41447) hydrogen bonds : bond 0.04308 ( 1209) hydrogen bonds : angle 4.81978 ( 3426) metal coordination : bond 0.01156 ( 11) metal coordination : angle 3.53139 ( 12) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 412 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9200 (m-80) cc_final: 0.8826 (m-10) REVERT: G 185 TYR cc_start: 0.8875 (p90) cc_final: 0.8379 (p90) REVERT: G 200 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8685 (ttmm) REVERT: G 207 THR cc_start: 0.8536 (m) cc_final: 0.8077 (p) REVERT: I 239 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.5892 (tpp) REVERT: I 349 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: I 470 ARG cc_start: 0.7553 (ppp80) cc_final: 0.6971 (tpm170) REVERT: I 515 MET cc_start: 0.8307 (ttp) cc_final: 0.8018 (ttp) REVERT: I 717 VAL cc_start: 0.9273 (t) cc_final: 0.8926 (m) REVERT: I 870 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8753 (mm) REVERT: I 1085 MET cc_start: 0.8834 (mmp) cc_final: 0.8349 (mmp) REVERT: I 1088 ASP cc_start: 0.8302 (p0) cc_final: 0.8017 (p0) REVERT: I 1172 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8853 (tt) REVERT: I 1253 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9030 (tm) REVERT: I 1290 MET cc_start: 0.8574 (tpp) cc_final: 0.7938 (tpp) REVERT: J 130 MET cc_start: 0.8274 (ttt) cc_final: 0.7980 (ttt) REVERT: J 180 MET cc_start: 0.7252 (ptm) cc_final: 0.6624 (ptm) REVERT: J 325 LYS cc_start: 0.8510 (tttt) cc_final: 0.8255 (mptt) REVERT: J 342 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7842 (mp) REVERT: J 466 MET cc_start: 0.8249 (mtp) cc_final: 0.7973 (mtp) REVERT: J 478 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8650 (mt) REVERT: J 725 MET cc_start: 0.8723 (mtm) cc_final: 0.8437 (mtp) REVERT: J 849 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7423 (mt) REVERT: J 1293 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7488 (tm-30) REVERT: J 1330 ARG cc_start: 0.8088 (tmm-80) cc_final: 0.7801 (ttp80) REVERT: K 3 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: K 55 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8053 (tm-30) REVERT: L 21 TYR cc_start: 0.6926 (p90) cc_final: 0.6526 (p90) REVERT: L 46 GLN cc_start: 0.6612 (tp-100) cc_final: 0.6120 (mm110) REVERT: L 121 LYS cc_start: 0.7980 (tppt) cc_final: 0.7263 (tptt) REVERT: L 339 ARG cc_start: 0.4995 (mtp85) cc_final: 0.3770 (mmp-170) REVERT: L 508 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7125 (tm-30) REVERT: M 61 CYS cc_start: 0.7892 (m) cc_final: 0.7375 (m) REVERT: M 64 TYR cc_start: 0.8010 (t80) cc_final: 0.7777 (t80) REVERT: M 68 GLN cc_start: 0.7839 (mt0) cc_final: 0.7610 (mt0) outliers start: 119 outliers final: 75 residues processed: 499 average time/residue: 0.1810 time to fit residues: 147.4923 Evaluate side-chains 459 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 375 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1172 LEU 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 1289 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 16 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 3 optimal weight: 0.9990 chunk 242 optimal weight: 0.0010 chunk 297 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 376 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 361 optimal weight: 4.9990 chunk 366 optimal weight: 0.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 613 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136525 restraints weight = 44517.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136755 restraints weight = 36450.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137932 restraints weight = 34460.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138245 restraints weight = 22409.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138437 restraints weight = 19745.906| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30691 Z= 0.130 Angle : 0.642 11.597 41459 Z= 0.323 Chirality : 0.043 0.223 4751 Planarity : 0.004 0.067 5415 Dihedral : 5.346 48.838 4502 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.00 % Favored : 92.77 % Rotamer: Outliers : 3.09 % Allowed : 15.69 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.75 (0.13), residues: 3817 helix: 0.58 (0.13), residues: 1560 sheet: -2.22 (0.29), residues: 293 loop : -2.57 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 312 TYR 0.016 0.001 TYR I 5 PHE 0.012 0.001 PHE J1319 TRP 0.016 0.001 TRP I 807 HIS 0.008 0.001 HIS I 273 Details of bonding type rmsd covalent geometry : bond 0.00299 (30679) covalent geometry : angle 0.64029 (41447) hydrogen bonds : bond 0.03703 ( 1209) hydrogen bonds : angle 4.52550 ( 3426) metal coordination : bond 0.00426 ( 11) metal coordination : angle 2.71217 ( 12) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 435 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8427 (tt) REVERT: G 185 TYR cc_start: 0.8842 (p90) cc_final: 0.8248 (p90) REVERT: G 200 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8580 (ttmm) REVERT: G 207 THR cc_start: 0.8363 (m) cc_final: 0.7911 (p) REVERT: H 95 LYS cc_start: 0.8296 (tppt) cc_final: 0.7748 (mmtm) REVERT: I 14 ASP cc_start: 0.7811 (t0) cc_final: 0.7565 (t0) REVERT: I 239 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.5778 (tpp) REVERT: I 349 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: I 470 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7006 (tpm170) REVERT: I 515 MET cc_start: 0.8164 (ttp) cc_final: 0.7849 (ttp) REVERT: I 549 ASP cc_start: 0.7919 (t0) cc_final: 0.7687 (t0) REVERT: I 613 ASN cc_start: 0.7881 (m-40) cc_final: 0.7649 (m110) REVERT: I 717 VAL cc_start: 0.9150 (t) cc_final: 0.8775 (m) REVERT: I 870 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8539 (mt) REVERT: I 1088 ASP cc_start: 0.8164 (p0) cc_final: 0.7863 (p0) REVERT: I 1253 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9080 (tm) REVERT: I 1290 MET cc_start: 0.8472 (tpp) cc_final: 0.8063 (tpp) REVERT: J 97 VAL cc_start: 0.9611 (OUTLIER) cc_final: 0.9354 (p) REVERT: J 130 MET cc_start: 0.8253 (ttt) cc_final: 0.8005 (ttt) REVERT: J 180 MET cc_start: 0.6916 (ptm) cc_final: 0.6383 (ptm) REVERT: J 325 LYS cc_start: 0.8489 (tttt) cc_final: 0.8067 (mptt) REVERT: J 398 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8200 (ttmt) REVERT: J 478 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8579 (mt) REVERT: J 513 MET cc_start: 0.8048 (ttm) cc_final: 0.7668 (ttm) REVERT: J 725 MET cc_start: 0.8733 (mtm) cc_final: 0.8462 (mtp) REVERT: J 757 THR cc_start: 0.8690 (m) cc_final: 0.8200 (p) REVERT: J 823 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7776 (m) REVERT: J 849 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7402 (mt) REVERT: J 918 ILE cc_start: 0.8839 (pt) cc_final: 0.8143 (mt) REVERT: J 932 MET cc_start: 0.8844 (tmm) cc_final: 0.8619 (tmm) REVERT: K 3 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: K 12 LYS cc_start: 0.8542 (tppp) cc_final: 0.8171 (tppp) REVERT: K 55 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7910 (tm-30) REVERT: K 56 GLU cc_start: 0.8173 (tp30) cc_final: 0.7954 (tp30) REVERT: L 21 TYR cc_start: 0.6996 (p90) cc_final: 0.6696 (p90) REVERT: L 46 GLN cc_start: 0.6635 (tp-100) cc_final: 0.6176 (mm110) REVERT: L 105 MET cc_start: 0.7649 (ppp) cc_final: 0.7080 (ppp) REVERT: L 121 LYS cc_start: 0.7955 (tppt) cc_final: 0.7256 (tptt) REVERT: L 273 MET cc_start: 0.4815 (mtt) cc_final: 0.4529 (mtm) REVERT: L 339 ARG cc_start: 0.4853 (mtp85) cc_final: 0.3676 (mmp-170) REVERT: L 508 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7099 (tm-30) REVERT: M 61 CYS cc_start: 0.7863 (m) cc_final: 0.7344 (m) REVERT: M 64 TYR cc_start: 0.7955 (t80) cc_final: 0.7698 (t80) outliers start: 101 outliers final: 59 residues processed: 510 average time/residue: 0.1815 time to fit residues: 149.8859 Evaluate side-chains 452 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 381 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL 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 1289 GLU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 582 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 210 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 273 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 907 HIS K 31 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 437 GLN M 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134456 restraints weight = 44249.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133797 restraints weight = 42289.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135879 restraints weight = 35703.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135804 restraints weight = 23832.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136119 restraints weight = 22676.881| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30691 Z= 0.179 Angle : 0.669 11.458 41459 Z= 0.335 Chirality : 0.045 0.254 4751 Planarity : 0.005 0.067 5415 Dihedral : 5.333 48.721 4502 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.04 % Favored : 91.72 % Rotamer: Outliers : 3.34 % Allowed : 16.12 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.63 (0.13), residues: 3817 helix: 0.65 (0.13), residues: 1562 sheet: -2.22 (0.29), residues: 293 loop : -2.45 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 312 TYR 0.027 0.002 TYR I 367 PHE 0.015 0.002 PHE L 302 TRP 0.014 0.001 TRP I 807 HIS 0.006 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00429 (30679) covalent geometry : angle 0.66746 (41447) hydrogen bonds : bond 0.03834 ( 1209) hydrogen bonds : angle 4.56012 ( 3426) metal coordination : bond 0.00735 ( 11) metal coordination : angle 2.75119 ( 12) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 390 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8941 (tt) REVERT: G 185 TYR cc_start: 0.8889 (p90) cc_final: 0.8261 (p90) REVERT: G 200 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8623 (ttmm) REVERT: G 207 THR cc_start: 0.8443 (m) cc_final: 0.7983 (p) REVERT: G 231 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7021 (t80) REVERT: H 28 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8235 (mt) REVERT: H 95 LYS cc_start: 0.8231 (tppt) cc_final: 0.7710 (mmtm) REVERT: I 10 ARG cc_start: 0.8537 (ptt180) cc_final: 0.8276 (ptt180) REVERT: I 14 ASP cc_start: 0.7783 (t0) cc_final: 0.7483 (t0) REVERT: I 230 PHE cc_start: 0.8079 (m-80) cc_final: 0.7566 (m-10) REVERT: I 239 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.5895 (tpp) REVERT: I 349 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: I 454 ARG cc_start: 0.8713 (mtt90) cc_final: 0.8433 (mtt90) REVERT: I 470 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6995 (tpm170) REVERT: I 613 ASN cc_start: 0.7947 (m-40) cc_final: 0.7682 (m110) REVERT: I 717 VAL cc_start: 0.9234 (t) cc_final: 0.8858 (m) REVERT: I 1253 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9090 (tm) REVERT: I 1290 MET cc_start: 0.8603 (tpp) cc_final: 0.7976 (tpp) REVERT: J 97 VAL cc_start: 0.9659 (OUTLIER) cc_final: 0.9396 (p) REVERT: J 130 MET cc_start: 0.8250 (ttt) cc_final: 0.7989 (ttt) REVERT: J 169 LEU cc_start: 0.7433 (mm) cc_final: 0.7134 (mm) REVERT: J 180 MET cc_start: 0.6959 (ptm) cc_final: 0.6401 (ptm) REVERT: J 325 LYS cc_start: 0.8425 (tttt) cc_final: 0.8162 (mptt) REVERT: J 330 MET cc_start: 0.7421 (ptp) cc_final: 0.7008 (ptp) REVERT: J 342 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7781 (mp) REVERT: J 398 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8246 (ttmt) REVERT: J 478 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8598 (mt) REVERT: J 725 MET cc_start: 0.8760 (mtm) cc_final: 0.8499 (mtp) REVERT: J 757 THR cc_start: 0.8738 (m) cc_final: 0.8328 (p) REVERT: J 823 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7882 (m) REVERT: J 849 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7173 (mt) REVERT: J 918 ILE cc_start: 0.8891 (pt) cc_final: 0.8222 (mt) REVERT: K 3 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: K 55 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8057 (tm-30) REVERT: K 56 GLU cc_start: 0.8255 (tp30) cc_final: 0.8027 (tp30) REVERT: L 21 TYR cc_start: 0.6963 (p90) cc_final: 0.6699 (p90) REVERT: L 46 GLN cc_start: 0.6669 (tp-100) cc_final: 0.6305 (mm110) REVERT: L 105 MET cc_start: 0.7683 (ppp) cc_final: 0.7187 (ppp) REVERT: L 121 LYS cc_start: 0.7950 (tppt) cc_final: 0.7244 (tptt) REVERT: L 339 ARG cc_start: 0.4735 (mtp85) cc_final: 0.3495 (mmp-170) REVERT: L 508 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7081 (tm-30) REVERT: M 61 CYS cc_start: 0.7859 (m) cc_final: 0.7292 (m) outliers start: 109 outliers final: 77 residues processed: 471 average time/residue: 0.1829 time to fit residues: 140.3076 Evaluate side-chains 461 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 370 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1094 VAL 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 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 185 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 38 optimal weight: 0.0070 chunk 158 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 250 optimal weight: 0.0570 chunk 202 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 291 optimal weight: 9.9990 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135454 restraints weight = 44259.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135256 restraints weight = 36056.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136720 restraints weight = 32981.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136990 restraints weight = 22373.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137202 restraints weight = 20363.261| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30691 Z= 0.147 Angle : 0.641 11.364 41459 Z= 0.321 Chirality : 0.043 0.233 4751 Planarity : 0.004 0.069 5415 Dihedral : 5.152 48.220 4502 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 3.62 % Allowed : 16.82 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.42 (0.13), residues: 3817 helix: 0.79 (0.13), residues: 1563 sheet: -1.91 (0.30), residues: 290 loop : -2.34 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 49 TYR 0.023 0.001 TYR I 367 PHE 0.016 0.001 PHE G 231 TRP 0.015 0.001 TRP I 807 HIS 0.019 0.001 HIS J1023 Details of bonding type rmsd covalent geometry : bond 0.00347 (30679) covalent geometry : angle 0.63935 (41447) hydrogen bonds : bond 0.03602 ( 1209) hydrogen bonds : angle 4.43597 ( 3426) metal coordination : bond 0.00520 ( 11) metal coordination : angle 2.42061 ( 12) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 412 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8942 (tt) REVERT: G 185 TYR cc_start: 0.8787 (p90) cc_final: 0.8291 (p90) REVERT: G 200 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8546 (ttmm) REVERT: G 207 THR cc_start: 0.8387 (m) cc_final: 0.7909 (p) REVERT: G 231 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7061 (t80) REVERT: H 28 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8265 (mt) REVERT: I 14 ASP cc_start: 0.7759 (t0) cc_final: 0.7558 (t0) REVERT: I 239 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.5914 (tpp) REVERT: I 349 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: I 454 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8439 (mtt90) REVERT: I 470 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6986 (tpm170) REVERT: I 477 GLU cc_start: 0.7792 (tp30) cc_final: 0.7496 (tp30) REVERT: I 613 ASN cc_start: 0.7919 (m-40) cc_final: 0.7623 (m110) REVERT: I 717 VAL cc_start: 0.9191 (t) cc_final: 0.8831 (m) REVERT: I 870 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8606 (mt) REVERT: I 1253 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9146 (tm) REVERT: I 1290 MET cc_start: 0.8581 (tpp) cc_final: 0.7970 (tpp) REVERT: J 97 VAL cc_start: 0.9652 (OUTLIER) cc_final: 0.9391 (p) REVERT: J 130 MET cc_start: 0.8377 (ttt) cc_final: 0.8127 (ttt) REVERT: J 169 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7220 (mm) REVERT: J 180 MET cc_start: 0.6743 (ptm) cc_final: 0.6339 (ptm) REVERT: J 209 ASN cc_start: 0.7043 (m-40) cc_final: 0.5992 (p0) REVERT: J 325 LYS cc_start: 0.8421 (tttt) cc_final: 0.8098 (mptt) REVERT: J 330 MET cc_start: 0.7201 (ptp) cc_final: 0.6762 (ptp) REVERT: J 398 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8213 (ttmt) REVERT: J 478 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8590 (mt) REVERT: J 725 MET cc_start: 0.8738 (mtm) cc_final: 0.8509 (mtp) REVERT: J 757 THR cc_start: 0.8751 (m) cc_final: 0.8359 (p) REVERT: J 823 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7898 (m) REVERT: J 849 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7116 (mt) REVERT: J 918 ILE cc_start: 0.8857 (pt) cc_final: 0.8183 (mt) REVERT: K 3 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7518 (ttm170) REVERT: K 55 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7875 (tm-30) REVERT: K 56 GLU cc_start: 0.8182 (tp30) cc_final: 0.7932 (tp30) REVERT: L 21 TYR cc_start: 0.7123 (p90) cc_final: 0.6861 (p90) REVERT: L 46 GLN cc_start: 0.6510 (tp-100) cc_final: 0.6252 (mm-40) REVERT: L 105 MET cc_start: 0.7609 (ppp) cc_final: 0.7162 (ppp) REVERT: L 121 LYS cc_start: 0.7930 (tppt) cc_final: 0.7343 (tptt) REVERT: L 273 MET cc_start: 0.4826 (mtt) cc_final: 0.4555 (mtm) REVERT: L 339 ARG cc_start: 0.4762 (mtp85) cc_final: 0.3488 (mmp-170) REVERT: M 61 CYS cc_start: 0.7870 (m) cc_final: 0.7299 (m) outliers start: 118 outliers final: 80 residues processed: 494 average time/residue: 0.1827 time to fit residues: 147.4992 Evaluate side-chains 469 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 374 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL 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 1289 GLU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 79 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 328 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 283 optimal weight: 30.0000 chunk 240 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135950 restraints weight = 44393.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135344 restraints weight = 43550.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137486 restraints weight = 37108.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137249 restraints weight = 25951.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137555 restraints weight = 23433.336| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30691 Z= 0.151 Angle : 0.643 11.707 41459 Z= 0.322 Chirality : 0.043 0.225 4751 Planarity : 0.004 0.069 5415 Dihedral : 5.111 47.931 4502 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.89 % Favored : 91.88 % Rotamer: Outliers : 3.43 % Allowed : 17.49 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.32 (0.13), residues: 3817 helix: 0.85 (0.13), residues: 1564 sheet: -1.73 (0.29), residues: 319 loop : -2.29 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 49 TYR 0.022 0.001 TYR I 367 PHE 0.025 0.001 PHE I 80 TRP 0.014 0.001 TRP I 807 HIS 0.015 0.001 HIS J1023 Details of bonding type rmsd covalent geometry : bond 0.00358 (30679) covalent geometry : angle 0.64186 (41447) hydrogen bonds : bond 0.03589 ( 1209) hydrogen bonds : angle 4.40497 ( 3426) metal coordination : bond 0.00535 ( 11) metal coordination : angle 2.36190 ( 12) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 394 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8944 (tt) REVERT: G 185 TYR cc_start: 0.8813 (p90) cc_final: 0.8254 (p90) REVERT: G 200 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8560 (ttmm) REVERT: G 231 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.6974 (t80) REVERT: H 28 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8265 (mt) REVERT: H 84 ASN cc_start: 0.8879 (m110) cc_final: 0.8541 (m110) REVERT: H 199 ASP cc_start: 0.7825 (m-30) cc_final: 0.7495 (m-30) REVERT: H 232 VAL cc_start: 0.7685 (m) cc_final: 0.7472 (m) REVERT: I 14 ASP cc_start: 0.7675 (t0) cc_final: 0.7447 (t0) REVERT: I 239 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.5971 (tpp) REVERT: I 349 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: I 429 MET cc_start: 0.7610 (mtt) cc_final: 0.7395 (mtm) REVERT: I 470 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6992 (tpm170) REVERT: I 613 ASN cc_start: 0.7899 (m-40) cc_final: 0.7609 (m110) REVERT: I 717 VAL cc_start: 0.9207 (t) cc_final: 0.8842 (m) REVERT: I 862 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8332 (tp) REVERT: I 870 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8774 (mm) REVERT: I 1253 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9170 (tm) REVERT: I 1290 MET cc_start: 0.8591 (tpp) cc_final: 0.7973 (tpp) REVERT: J 97 VAL cc_start: 0.9634 (OUTLIER) cc_final: 0.9362 (p) REVERT: J 130 MET cc_start: 0.8381 (ttt) cc_final: 0.8119 (ttt) REVERT: J 169 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7278 (mm) REVERT: J 180 MET cc_start: 0.6733 (ptm) cc_final: 0.6232 (ptm) REVERT: J 200 GLN cc_start: 0.7391 (tt0) cc_final: 0.7092 (tm-30) REVERT: J 209 ASN cc_start: 0.7060 (m-40) cc_final: 0.6121 (p0) REVERT: J 325 LYS cc_start: 0.8441 (tttt) cc_final: 0.8071 (mptt) REVERT: J 330 MET cc_start: 0.7238 (ptp) cc_final: 0.6881 (ptp) REVERT: J 342 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7760 (mp) REVERT: J 398 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8225 (ttmt) REVERT: J 478 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8610 (mt) REVERT: J 701 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8797 (tm) REVERT: J 725 MET cc_start: 0.8783 (mtm) cc_final: 0.8560 (mtp) REVERT: J 757 THR cc_start: 0.8780 (m) cc_final: 0.8394 (p) REVERT: J 823 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7932 (m) REVERT: J 849 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6770 (mt) REVERT: J 918 ILE cc_start: 0.8853 (pt) cc_final: 0.8213 (mt) REVERT: K 3 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: K 55 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7908 (tm-30) REVERT: L 21 TYR cc_start: 0.7059 (p90) cc_final: 0.6828 (p90) REVERT: L 46 GLN cc_start: 0.6572 (tp-100) cc_final: 0.6325 (mm-40) REVERT: L 105 MET cc_start: 0.7713 (ppp) cc_final: 0.7283 (ppp) REVERT: L 121 LYS cc_start: 0.7883 (tppt) cc_final: 0.7211 (tptt) REVERT: L 273 MET cc_start: 0.4870 (mtt) cc_final: 0.4620 (mtm) REVERT: L 339 ARG cc_start: 0.4870 (mtp85) cc_final: 0.3534 (mmp-170) REVERT: M 61 CYS cc_start: 0.7883 (m) cc_final: 0.7279 (m) outliers start: 112 outliers final: 82 residues processed: 471 average time/residue: 0.1857 time to fit residues: 142.7160 Evaluate side-chains 470 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 370 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL 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 1289 GLU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 642 ASP Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 72 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 246 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN L 19 GLN L 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113434 restraints weight = 44760.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111526 restraints weight = 70334.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112716 restraints weight = 66064.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113366 restraints weight = 42621.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113507 restraints weight = 38218.862| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30691 Z= 0.151 Angle : 0.647 11.735 41459 Z= 0.324 Chirality : 0.043 0.234 4751 Planarity : 0.004 0.069 5415 Dihedral : 5.067 47.610 4502 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.83 % Favored : 91.93 % Rotamer: Outliers : 3.34 % Allowed : 17.62 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.23 (0.13), residues: 3817 helix: 0.90 (0.13), residues: 1564 sheet: -1.63 (0.29), residues: 318 loop : -2.22 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 49 TYR 0.021 0.001 TYR I1229 PHE 0.021 0.001 PHE I 80 TRP 0.014 0.001 TRP I 807 HIS 0.011 0.001 HIS J1023 Details of bonding type rmsd covalent geometry : bond 0.00358 (30679) covalent geometry : angle 0.64576 (41447) hydrogen bonds : bond 0.03579 ( 1209) hydrogen bonds : angle 4.37344 ( 3426) metal coordination : bond 0.00528 ( 11) metal coordination : angle 2.27266 ( 12) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 390 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8533 (m-80) REVERT: G 102 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8961 (tt) REVERT: G 185 TYR cc_start: 0.8967 (p90) cc_final: 0.8326 (p90) REVERT: G 200 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8481 (ttmm) REVERT: G 207 THR cc_start: 0.8575 (m) cc_final: 0.8016 (p) REVERT: G 231 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6886 (t80) REVERT: H 28 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8217 (mt) REVERT: H 84 ASN cc_start: 0.9027 (m110) cc_final: 0.8627 (m110) REVERT: H 199 ASP cc_start: 0.7873 (m-30) cc_final: 0.7554 (m-30) REVERT: I 14 ASP cc_start: 0.7931 (t0) cc_final: 0.7593 (t0) REVERT: I 239 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.5881 (tpp) REVERT: I 349 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: I 429 MET cc_start: 0.7740 (mtt) cc_final: 0.7540 (mtm) REVERT: I 470 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6863 (tpm170) REVERT: I 613 ASN cc_start: 0.8192 (m-40) cc_final: 0.7955 (m110) REVERT: I 717 VAL cc_start: 0.9318 (t) cc_final: 0.8970 (m) REVERT: I 723 VAL cc_start: 0.9217 (t) cc_final: 0.9010 (m) REVERT: I 870 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8526 (mt) REVERT: I 1241 ASP cc_start: 0.8115 (m-30) cc_final: 0.7813 (t0) REVERT: I 1253 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9267 (tm) REVERT: I 1290 MET cc_start: 0.8714 (tpp) cc_final: 0.8145 (tpp) REVERT: I 1329 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7729 (mm-30) REVERT: J 97 VAL cc_start: 0.9638 (OUTLIER) cc_final: 0.9369 (p) REVERT: J 130 MET cc_start: 0.8442 (ttt) cc_final: 0.8184 (ttt) REVERT: J 180 MET cc_start: 0.6805 (ptm) cc_final: 0.6457 (ptm) REVERT: J 200 GLN cc_start: 0.7495 (tt0) cc_final: 0.7084 (tm-30) REVERT: J 209 ASN cc_start: 0.7058 (m-40) cc_final: 0.6149 (p0) REVERT: J 325 LYS cc_start: 0.8381 (tttt) cc_final: 0.7834 (mptt) REVERT: J 330 MET cc_start: 0.7301 (ptp) cc_final: 0.6978 (ptp) REVERT: J 342 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7928 (mp) REVERT: J 398 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8218 (ttmt) REVERT: J 478 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8494 (mt) REVERT: J 513 MET cc_start: 0.8374 (ttm) cc_final: 0.8158 (ttm) REVERT: J 525 MET cc_start: 0.8542 (ptt) cc_final: 0.8303 (ptt) REVERT: J 725 MET cc_start: 0.8851 (mtm) cc_final: 0.8599 (mtp) REVERT: J 757 THR cc_start: 0.8855 (m) cc_final: 0.8453 (p) REVERT: J 822 MET cc_start: 0.8484 (mmt) cc_final: 0.7979 (mmt) REVERT: J 823 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8098 (m) REVERT: J 849 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6678 (mt) REVERT: J 918 ILE cc_start: 0.8741 (pt) cc_final: 0.8142 (mt) REVERT: K 3 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: K 55 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7888 (tm-30) REVERT: K 56 GLU cc_start: 0.8278 (tp30) cc_final: 0.7974 (tp30) REVERT: L 21 TYR cc_start: 0.7199 (p90) cc_final: 0.6787 (p90) REVERT: L 46 GLN cc_start: 0.6832 (tp-100) cc_final: 0.6490 (mm-40) REVERT: L 105 MET cc_start: 0.7762 (ppp) cc_final: 0.7354 (ppp) REVERT: L 121 LYS cc_start: 0.7877 (tppt) cc_final: 0.7193 (tptt) REVERT: L 268 TYR cc_start: 0.5524 (t80) cc_final: 0.4870 (t80) REVERT: L 273 MET cc_start: 0.5093 (mtt) cc_final: 0.4780 (mtm) REVERT: L 339 ARG cc_start: 0.4909 (mtp85) cc_final: 0.3536 (mmp-170) REVERT: M 61 CYS cc_start: 0.7883 (m) cc_final: 0.7180 (m) outliers start: 109 outliers final: 81 residues processed: 464 average time/residue: 0.1796 time to fit residues: 136.0815 Evaluate side-chains 478 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 381 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1155 VAL 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 1289 GLU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 60 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 281 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 345 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114144 restraints weight = 44763.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112628 restraints weight = 66885.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113654 restraints weight = 63691.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114053 restraints weight = 42394.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114301 restraints weight = 38881.017| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30691 Z= 0.155 Angle : 0.649 15.119 41459 Z= 0.324 Chirality : 0.043 0.233 4751 Planarity : 0.004 0.067 5415 Dihedral : 5.044 47.451 4502 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.83 % Favored : 91.93 % Rotamer: Outliers : 3.25 % Allowed : 18.20 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.17 (0.13), residues: 3817 helix: 0.92 (0.13), residues: 1564 sheet: -1.46 (0.30), residues: 308 loop : -2.19 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 49 TYR 0.021 0.001 TYR I1229 PHE 0.024 0.001 PHE I 80 TRP 0.013 0.001 TRP I 807 HIS 0.010 0.001 HIS J1023 Details of bonding type rmsd covalent geometry : bond 0.00369 (30679) covalent geometry : angle 0.64761 (41447) hydrogen bonds : bond 0.03567 ( 1209) hydrogen bonds : angle 4.36714 ( 3426) metal coordination : bond 0.00563 ( 11) metal coordination : angle 2.28992 ( 12) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 389 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: G 102 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8967 (tt) REVERT: G 185 TYR cc_start: 0.8945 (p90) cc_final: 0.8333 (p90) REVERT: G 200 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8487 (ttmm) REVERT: G 207 THR cc_start: 0.8545 (m) cc_final: 0.7978 (p) REVERT: G 231 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6888 (t80) REVERT: H 28 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8209 (mt) REVERT: H 84 ASN cc_start: 0.9034 (m110) cc_final: 0.8629 (m110) REVERT: H 199 ASP cc_start: 0.7905 (m-30) cc_final: 0.7557 (m-30) REVERT: I 14 ASP cc_start: 0.7935 (t0) cc_final: 0.7580 (t0) REVERT: I 239 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.5911 (tpp) REVERT: I 349 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: I 470 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6935 (tpm170) REVERT: I 613 ASN cc_start: 0.8174 (m-40) cc_final: 0.7939 (m110) REVERT: I 674 ASP cc_start: 0.8821 (m-30) cc_final: 0.8533 (m-30) REVERT: I 717 VAL cc_start: 0.9300 (t) cc_final: 0.8962 (m) REVERT: I 723 VAL cc_start: 0.9189 (t) cc_final: 0.8977 (m) REVERT: I 862 LEU cc_start: 0.8239 (tp) cc_final: 0.7996 (tp) REVERT: I 870 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8688 (mm) REVERT: I 1241 ASP cc_start: 0.8088 (m-30) cc_final: 0.7877 (t0) REVERT: I 1290 MET cc_start: 0.8696 (tpp) cc_final: 0.8140 (tpp) REVERT: I 1329 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7713 (mm-30) REVERT: J 97 VAL cc_start: 0.9644 (OUTLIER) cc_final: 0.9370 (p) REVERT: J 130 MET cc_start: 0.8472 (ttt) cc_final: 0.8214 (ttt) REVERT: J 180 MET cc_start: 0.6754 (ptm) cc_final: 0.6446 (ptm) REVERT: J 200 GLN cc_start: 0.7475 (tt0) cc_final: 0.7100 (tm-30) REVERT: J 209 ASN cc_start: 0.7003 (m-40) cc_final: 0.6129 (p0) REVERT: J 325 LYS cc_start: 0.8401 (tttt) cc_final: 0.7876 (mptt) REVERT: J 330 MET cc_start: 0.7270 (ptp) cc_final: 0.6950 (ptp) REVERT: J 342 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7914 (mp) REVERT: J 398 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8220 (ttmt) REVERT: J 478 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8536 (mt) REVERT: J 525 MET cc_start: 0.8528 (ptt) cc_final: 0.8282 (ptt) REVERT: J 701 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8439 (tp) REVERT: J 725 MET cc_start: 0.8896 (mtm) cc_final: 0.8679 (mtp) REVERT: J 757 THR cc_start: 0.8854 (m) cc_final: 0.8457 (p) REVERT: J 822 MET cc_start: 0.8529 (mmt) cc_final: 0.8058 (mmt) REVERT: J 823 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (m) REVERT: J 849 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6526 (mt) REVERT: J 918 ILE cc_start: 0.8785 (pt) cc_final: 0.8078 (mt) REVERT: J 1189 MET cc_start: 0.7352 (pmm) cc_final: 0.7102 (pmm) REVERT: K 3 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7796 (ttm170) REVERT: K 55 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7942 (tm-30) REVERT: K 75 GLN cc_start: 0.7489 (tp40) cc_final: 0.7243 (tp40) REVERT: L 21 TYR cc_start: 0.6968 (p90) cc_final: 0.6697 (p90) REVERT: L 46 GLN cc_start: 0.6703 (tp-100) cc_final: 0.6302 (mm-40) REVERT: L 105 MET cc_start: 0.7655 (ppp) cc_final: 0.7267 (ppp) REVERT: L 121 LYS cc_start: 0.7919 (tppt) cc_final: 0.7179 (tptt) REVERT: L 268 TYR cc_start: 0.5500 (t80) cc_final: 0.4821 (t80) REVERT: L 273 MET cc_start: 0.5013 (mtt) cc_final: 0.4754 (mtm) REVERT: L 339 ARG cc_start: 0.4928 (mtp85) cc_final: 0.3519 (mmp-170) REVERT: M 61 CYS cc_start: 0.7892 (m) cc_final: 0.7179 (m) outliers start: 106 outliers final: 81 residues processed: 466 average time/residue: 0.1800 time to fit residues: 137.1536 Evaluate side-chains 469 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 372 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1155 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 364 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 342 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 951 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117460 restraints weight = 44782.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115899 restraints weight = 62642.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117407 restraints weight = 58245.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117379 restraints weight = 39251.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117826 restraints weight = 35237.098| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30691 Z= 0.127 Angle : 0.630 12.402 41459 Z= 0.315 Chirality : 0.043 0.224 4751 Planarity : 0.004 0.068 5415 Dihedral : 4.895 48.075 4502 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.97 % Favored : 92.85 % Rotamer: Outliers : 2.94 % Allowed : 18.69 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % 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: -1.03 (0.14), residues: 3817 helix: 1.06 (0.13), residues: 1552 sheet: -1.51 (0.29), residues: 322 loop : -2.09 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 49 TYR 0.019 0.001 TYR I 367 PHE 0.026 0.001 PHE I 80 TRP 0.013 0.001 TRP I 807 HIS 0.009 0.001 HIS J1023 Details of bonding type rmsd covalent geometry : bond 0.00295 (30679) covalent geometry : angle 0.62953 (41447) hydrogen bonds : bond 0.03383 ( 1209) hydrogen bonds : angle 4.27803 ( 3426) metal coordination : bond 0.00360 ( 11) metal coordination : angle 2.02607 ( 12) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4747.43 seconds wall clock time: 82 minutes 54.49 seconds (4974.49 seconds total)