Starting phenix.real_space_refine on Tue Feb 20 00:04:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh9_28144/02_2024/8eh9_28144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh9_28144/02_2024/8eh9_28144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh9_28144/02_2024/8eh9_28144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh9_28144/02_2024/8eh9_28144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh9_28144/02_2024/8eh9_28144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh9_28144/02_2024/8eh9_28144_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16251 2.51 5 N 4638 2.21 5 O 5173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I GLU 541": "OE1" <-> "OE2" Residue "I GLU 588": "OE1" <-> "OE2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J GLU 704": "OE1" <-> "OE2" Residue "J GLU 873": "OE1" <-> "OE2" Residue "J GLU 1202": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J GLU 1236": "OE1" <-> "OE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26234 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 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: "I" Number of atoms: 10372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10372 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 10524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10524 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15502 SG CYS J 70 104.968 101.810 90.315 1.00 75.93 S ATOM 15516 SG CYS J 72 104.937 105.378 91.491 1.00 83.55 S ATOM 15624 SG CYS J 85 107.256 102.920 93.205 1.00 78.54 S ATOM 15648 SG CYS J 88 103.529 102.631 93.752 1.00 80.03 S ATOM 21324 SG CYS J 814 87.665 36.514 86.912 1.00 49.61 S ATOM 21889 SG CYS J 888 86.502 40.194 87.195 1.00 40.44 S ATOM 21940 SG CYS J 895 87.305 38.777 83.766 1.00 36.22 S ATOM 21961 SG CYS J 898 84.355 37.480 85.534 1.00 33.77 S Time building chain proxies: 13.96, per 1000 atoms: 0.53 Number of scatterers: 26234 At special positions: 0 Unit cell: (140.4, 146.9, 163.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 63 15.00 Mg 1 11.99 O 5173 8.00 N 4638 7.00 C 16251 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.02 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 34 sheets defined 31.9% alpha, 10.8% beta 29 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 12.00 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 213 through 230 removed outlier: 4.190A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 87 removed outlier: 3.923A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 229 removed outlier: 3.906A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'I' and resid 43 through 45 No H-bonds generated for 'chain 'I' and resid 43 through 45' Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.577A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.752A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 328 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.822A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 479 Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 657 through 660 removed outlier: 3.685A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 657 through 660' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 676 through 687 removed outlier: 3.859A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY I 682 " --> pdb=" O ARG I 678 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 943 through 979 Processing helix chain 'I' and resid 987 through 991 removed outlier: 3.708A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS I 991 " --> pdb=" O LYS I 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 987 through 991' Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1170 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1279 removed outlier: 3.825A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 96 through 99 removed outlier: 3.676A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 96 through 99' Processing helix chain 'J' and resid 114 through 116 No H-bonds generated for 'chain 'J' and resid 114 through 116' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.916A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 402 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.739A pdb=" N ASP J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.642A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR J 457 " --> pdb=" O CYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 582 removed outlier: 3.799A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 615 through 633 removed outlier: 3.789A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 670 Processing helix chain 'J' and resid 675 through 703 removed outlier: 3.521A pdb=" N ASP J 684 " --> pdb=" O ASN J 680 " (cutoff:3.500A) Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 771 through 789 removed outlier: 3.894A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 803 removed outlier: 4.069A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 924 Processing helix chain 'J' and resid 927 through 931 Processing helix chain 'J' and resid 1070 through 1073 removed outlier: 4.130A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1070 through 1073' Processing helix chain 'J' and resid 1140 through 1146 Processing helix chain 'J' and resid 1219 through 1244 removed outlier: 7.817A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 removed outlier: 3.642A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1371 removed outlier: 4.006A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG J1371 " --> pdb=" O ASP J1368 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 77 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 17 removed outlier: 7.112A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G 188 " --> pdb=" O LYS G 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 99 removed outlier: 3.902A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 102 through 104 removed outlier: 3.625A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 140 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.569A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.022A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 12 through 15 removed outlier: 7.578A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.787A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.511A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 66 through 69 removed outlier: 3.742A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= K, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.605A pdb=" N ILE I 127 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 512 through 514 removed outlier: 3.968A pdb=" N ASN I 139 " --> pdb=" O THR I 141 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG I 143 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL I 137 " --> pdb=" O ARG I 143 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 154 through 158 Processing sheet with id= N, first strand: chain 'I' and resid 185 through 188 Processing sheet with id= O, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= P, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= Q, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.819A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 1096 through 1098 removed outlier: 3.530A pdb=" N GLN I 798 " --> pdb=" O MET I1232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.598A pdb=" N GLN I 834 " --> pdb=" O LEU I1054 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I1050 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.413A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.757A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.930A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'J' and resid 365 through 369 removed outlier: 6.306A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'J' and resid 421 through 424 Processing sheet with id= AA, first strand: chain 'J' and resid 548 through 552 Processing sheet with id= AB, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.717A pdb=" N LYS J 983 " --> pdb=" O LYS J 959 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AD, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.702A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 1162 through 1164 Processing sheet with id= AF, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.687A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.375A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 1026 through 1028 removed outlier: 3.915A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 10.59 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8704 1.34 - 1.46: 5281 1.46 - 1.58: 12457 1.58 - 1.70: 127 1.70 - 1.83: 187 Bond restraints: 26756 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.730 -0.198 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.707 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C19 1N7 I1401 " pdb=" C2 1N7 I1401 " ideal model delta sigma weight residual 1.551 1.400 0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C4 1N7 I1401 " pdb=" C5 1N7 I1401 " ideal model delta sigma weight residual 1.534 1.397 0.137 2.00e-02 2.50e+03 4.72e+01 ... (remaining 26751 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.72: 826 105.72 - 112.83: 14363 112.83 - 119.95: 9305 119.95 - 127.06: 11591 127.06 - 134.18: 335 Bond angle restraints: 36420 Sorted by residual: angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" N GLN J 504 " pdb=" CA GLN J 504 " pdb=" CB GLN J 504 " ideal model delta sigma weight residual 114.17 108.27 5.90 1.14e+00 7.69e-01 2.68e+01 angle pdb=" C PRO I 43 " pdb=" N GLU I 44 " pdb=" CA GLU I 44 " ideal model delta sigma weight residual 122.61 129.30 -6.69 1.56e+00 4.11e-01 1.84e+01 angle pdb=" C VAL J 518 " pdb=" N ASN J 519 " pdb=" CA ASN J 519 " ideal model delta sigma weight residual 122.19 131.77 -9.58 2.30e+00 1.89e-01 1.74e+01 angle pdb=" C MET I1290 " pdb=" N LEU I1291 " pdb=" CA LEU I1291 " ideal model delta sigma weight residual 122.08 115.63 6.45 1.59e+00 3.96e-01 1.64e+01 ... (remaining 36415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 15835 35.79 - 71.58: 514 71.58 - 107.37: 41 107.37 - 143.16: 1 143.16 - 178.95: 1 Dihedral angle restraints: 16392 sinusoidal: 7241 harmonic: 9151 Sorted by residual: dihedral pdb=" CA LEU J1138 " pdb=" C LEU J1138 " pdb=" N PRO J1139 " pdb=" CA PRO J1139 " ideal model delta harmonic sigma weight residual 180.00 145.64 34.36 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLU J 925 " pdb=" C GLU J 925 " pdb=" N PRO J 926 " pdb=" CA PRO J 926 " ideal model delta harmonic sigma weight residual 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA VAL I1309 " pdb=" C VAL I1309 " pdb=" N ASP I1310 " pdb=" CA ASP I1310 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 16389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3822 0.083 - 0.166: 341 0.166 - 0.248: 10 0.248 - 0.331: 2 0.331 - 0.414: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.95 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB ILE K 13 " pdb=" CA ILE K 13 " pdb=" CG1 ILE K 13 " pdb=" CG2 ILE K 13 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 1N7 I1401 " pdb=" C4 1N7 I1401 " pdb=" C6 1N7 I1401 " pdb=" C9 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.59 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4173 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 925 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO J 926 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO J 926 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 926 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO J1139 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 69 " 0.199 9.50e-02 1.11e+02 8.94e-02 5.80e+00 pdb=" NE ARG K 69 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG K 69 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG K 69 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG K 69 " 0.002 2.00e-02 2.50e+03 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 285 2.60 - 3.18: 22129 3.18 - 3.75: 41081 3.75 - 4.33: 54692 4.33 - 4.90: 90061 Nonbonded interactions: 208248 Sorted by model distance: nonbonded pdb=" O3' C R 18 " pdb="MG MG R 101 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R 101 " model vdw 2.079 2.170 nonbonded pdb=" O5' U R 19 " pdb="MG MG R 101 " model vdw 2.154 2.170 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.209 2.440 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG R 101 " model vdw 2.213 2.170 ... (remaining 208243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } 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: 0.690 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: 5.070 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 77.070 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.295 26756 Z= 0.294 Angle : 0.746 13.865 36420 Z= 0.407 Chirality : 0.046 0.414 4176 Planarity : 0.005 0.092 4541 Dihedral : 16.723 178.948 10508 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3174 helix: 0.09 (0.16), residues: 1081 sheet: -2.25 (0.26), residues: 362 loop : -1.96 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 236 HIS 0.007 0.001 HIS G 23 PHE 0.026 0.001 PHE I1025 TYR 0.027 0.001 TYR I 395 ARG 0.017 0.001 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 474 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8079 (t0) cc_final: 0.7417 (t0) REVERT: I 68 LEU cc_start: 0.8206 (tp) cc_final: 0.7983 (tt) REVERT: I 85 CYS cc_start: 0.8611 (m) cc_final: 0.8396 (m) REVERT: I 427 ASP cc_start: 0.7839 (m-30) cc_final: 0.7374 (m-30) REVERT: I 468 LEU cc_start: 0.8810 (tp) cc_final: 0.8370 (tp) REVERT: I 834 GLN cc_start: 0.8084 (pt0) cc_final: 0.7759 (pt0) REVERT: I 1248 THR cc_start: 0.8034 (t) cc_final: 0.7634 (t) REVERT: J 151 MET cc_start: 0.7165 (mpp) cc_final: 0.6710 (ppp) REVERT: J 382 TYR cc_start: 0.9024 (m-10) cc_final: 0.8778 (m-10) REVERT: J 679 TYR cc_start: 0.6983 (t80) cc_final: 0.6770 (t80) REVERT: J 697 MET cc_start: 0.6775 (tmm) cc_final: 0.6263 (tmm) REVERT: J 806 ASP cc_start: 0.7524 (p0) cc_final: 0.6726 (p0) REVERT: J 1258 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7604 (ttt90) REVERT: K 68 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8256 (mm-30) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.3714 time to fit residues: 282.7525 Evaluate side-chains 341 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 291 optimal weight: 0.0970 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 132 HIS I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN I1220 GLN J 424 ASN J1049 GLN J1197 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26756 Z= 0.285 Angle : 0.620 10.819 36420 Z= 0.319 Chirality : 0.043 0.251 4176 Planarity : 0.005 0.093 4541 Dihedral : 14.449 177.030 4311 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.67 % Allowed : 11.18 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3174 helix: 0.34 (0.16), residues: 1092 sheet: -1.84 (0.27), residues: 360 loop : -1.94 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 115 HIS 0.008 0.001 HIS I 165 PHE 0.022 0.001 PHE I 337 TYR 0.013 0.001 TYR I 105 ARG 0.006 0.000 ARG I 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 364 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8201 (ptmt) REVERT: H 86 LYS cc_start: 0.8791 (tptp) cc_final: 0.8378 (tptp) REVERT: H 185 TYR cc_start: 0.8869 (p90) cc_final: 0.8559 (p90) REVERT: I 85 CYS cc_start: 0.8639 (m) cc_final: 0.8385 (m) REVERT: I 427 ASP cc_start: 0.7949 (m-30) cc_final: 0.7536 (m-30) REVERT: I 472 GLU cc_start: 0.8167 (tp30) cc_final: 0.7694 (tp30) REVERT: I 1329 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7386 (mt-10) REVERT: J 124 ILE cc_start: 0.8596 (mm) cc_final: 0.8376 (mm) REVERT: J 133 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7779 (mmt90) REVERT: J 135 ILE cc_start: 0.9139 (mt) cc_final: 0.8801 (tt) REVERT: J 697 MET cc_start: 0.6820 (tmm) cc_final: 0.6233 (tmm) REVERT: J 788 LEU cc_start: 0.9068 (mm) cc_final: 0.8753 (tt) REVERT: J 806 ASP cc_start: 0.7630 (p0) cc_final: 0.6886 (p0) REVERT: J 1254 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7638 (mt-10) REVERT: J 1260 MET cc_start: 0.8605 (mtt) cc_final: 0.8386 (mtt) REVERT: K 75 GLN cc_start: 0.8032 (pp30) cc_final: 0.7819 (pp30) outliers start: 45 outliers final: 33 residues processed: 391 average time/residue: 0.3648 time to fit residues: 230.8671 Evaluate side-chains 355 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 322 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 120 GLN I 276 GLN I 554 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN J1049 GLN K 31 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26756 Z= 0.375 Angle : 0.652 12.825 36420 Z= 0.335 Chirality : 0.044 0.184 4176 Planarity : 0.005 0.092 4541 Dihedral : 14.280 176.789 4311 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.92 % Allowed : 14.88 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3174 helix: 0.38 (0.16), residues: 1063 sheet: -1.90 (0.25), residues: 396 loop : -1.91 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 115 HIS 0.007 0.001 HIS J 430 PHE 0.016 0.002 PHE J 437 TYR 0.014 0.002 TYR J 723 ARG 0.008 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 340 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8107 (ptmt) REVERT: G 205 MET cc_start: 0.8845 (ptp) cc_final: 0.8614 (ttp) REVERT: H 80 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7377 (mt-10) REVERT: I 85 CYS cc_start: 0.8676 (m) cc_final: 0.8435 (m) REVERT: J 124 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8707 (mm) REVERT: J 133 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7758 (mmt90) REVERT: J 135 ILE cc_start: 0.9246 (mt) cc_final: 0.8818 (tt) REVERT: J 697 MET cc_start: 0.6841 (tmm) cc_final: 0.6336 (tmm) REVERT: J 788 LEU cc_start: 0.9004 (mm) cc_final: 0.8705 (tt) REVERT: J 806 ASP cc_start: 0.7612 (p0) cc_final: 0.6889 (p0) REVERT: J 925 GLU cc_start: 0.8660 (pp20) cc_final: 0.8402 (pp20) REVERT: J 1040 MET cc_start: 0.6125 (ptp) cc_final: 0.5691 (mtm) REVERT: J 1254 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7609 (mt-10) outliers start: 79 outliers final: 60 residues processed: 391 average time/residue: 0.3655 time to fit residues: 232.9215 Evaluate side-chains 370 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 309 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 310 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN I 922 ASN J1049 GLN J1366 HIS K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26756 Z= 0.232 Angle : 0.578 13.560 36420 Z= 0.297 Chirality : 0.042 0.163 4176 Planarity : 0.004 0.093 4541 Dihedral : 14.179 177.150 4311 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.00 % Allowed : 16.85 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3174 helix: 0.46 (0.16), residues: 1071 sheet: -1.82 (0.26), residues: 383 loop : -1.82 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 115 HIS 0.005 0.001 HIS G 23 PHE 0.011 0.001 PHE J 437 TYR 0.018 0.001 TYR J 165 ARG 0.004 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 357 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7971 (ptmt) REVERT: H 80 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7348 (mt-10) REVERT: H 185 TYR cc_start: 0.9106 (p90) cc_final: 0.8734 (p90) REVERT: I 85 CYS cc_start: 0.8596 (m) cc_final: 0.8333 (m) REVERT: I 427 ASP cc_start: 0.7917 (m-30) cc_final: 0.7448 (m-30) REVERT: I 790 ASP cc_start: 0.8157 (t70) cc_final: 0.7946 (t0) REVERT: J 135 ILE cc_start: 0.9227 (mt) cc_final: 0.8841 (tt) REVERT: J 169 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7685 (tt) REVERT: J 180 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6686 (tmt) REVERT: J 330 MET cc_start: 0.7757 (ptp) cc_final: 0.7221 (ptp) REVERT: J 382 TYR cc_start: 0.9016 (m-10) cc_final: 0.8764 (m-10) REVERT: J 697 MET cc_start: 0.6934 (tmm) cc_final: 0.6437 (tmm) REVERT: J 788 LEU cc_start: 0.9221 (mm) cc_final: 0.8782 (tt) REVERT: J 806 ASP cc_start: 0.7551 (p0) cc_final: 0.7000 (p0) REVERT: J 925 GLU cc_start: 0.8587 (pp20) cc_final: 0.8283 (pp20) REVERT: J 1254 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7597 (mt-10) REVERT: K 55 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8117 (pt0) outliers start: 81 outliers final: 51 residues processed: 415 average time/residue: 0.3678 time to fit residues: 247.4879 Evaluate side-chains 377 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.0170 chunk 176 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 278 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN J1049 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26756 Z= 0.213 Angle : 0.576 14.974 36420 Z= 0.295 Chirality : 0.042 0.241 4176 Planarity : 0.004 0.090 4541 Dihedral : 14.120 176.734 4311 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.44 % Allowed : 17.81 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 3174 helix: 0.49 (0.16), residues: 1085 sheet: -1.80 (0.26), residues: 376 loop : -1.77 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J1193 HIS 0.007 0.001 HIS J1366 PHE 0.017 0.001 PHE J 668 TYR 0.016 0.001 TYR I 726 ARG 0.006 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 346 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7990 (ptmt) REVERT: H 80 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7358 (mt-10) REVERT: H 185 TYR cc_start: 0.9147 (p90) cc_final: 0.8792 (p90) REVERT: I 85 CYS cc_start: 0.8616 (m) cc_final: 0.8266 (m) REVERT: I 427 ASP cc_start: 0.8002 (m-30) cc_final: 0.7512 (m-30) REVERT: J 133 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7794 (mmt90) REVERT: J 135 ILE cc_start: 0.9203 (mt) cc_final: 0.8876 (tt) REVERT: J 169 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7540 (tt) REVERT: J 180 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6899 (tmt) REVERT: J 382 TYR cc_start: 0.8993 (m-10) cc_final: 0.8705 (m-10) REVERT: J 697 MET cc_start: 0.6886 (tmm) cc_final: 0.6415 (tmm) REVERT: J 788 LEU cc_start: 0.9216 (mm) cc_final: 0.8754 (tt) REVERT: J 806 ASP cc_start: 0.7569 (p0) cc_final: 0.6990 (p0) REVERT: J 925 GLU cc_start: 0.8571 (pp20) cc_final: 0.8226 (pp20) REVERT: K 55 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8131 (pt0) outliers start: 93 outliers final: 67 residues processed: 413 average time/residue: 0.3571 time to fit residues: 241.7552 Evaluate side-chains 395 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 325 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 61 optimal weight: 0.0050 chunk 182 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN I 808 ASN J 341 ASN J1049 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26756 Z= 0.159 Angle : 0.559 16.824 36420 Z= 0.286 Chirality : 0.041 0.208 4176 Planarity : 0.004 0.088 4541 Dihedral : 14.056 176.424 4311 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.85 % Allowed : 19.36 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3174 helix: 0.56 (0.16), residues: 1089 sheet: -1.66 (0.26), residues: 379 loop : -1.71 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 115 HIS 0.008 0.001 HIS I 165 PHE 0.018 0.001 PHE J 668 TYR 0.012 0.001 TYR J 165 ARG 0.006 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 363 time to evaluate : 2.556 Fit side-chains revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8148 (ptmt) REVERT: H 80 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7367 (mt-10) REVERT: H 185 TYR cc_start: 0.9123 (p90) cc_final: 0.8806 (p90) REVERT: I 85 CYS cc_start: 0.8577 (m) cc_final: 0.8181 (m) REVERT: I 315 MET cc_start: 0.7515 (ptp) cc_final: 0.7181 (ptp) REVERT: I 427 ASP cc_start: 0.7954 (m-30) cc_final: 0.7566 (m-30) REVERT: I 1119 MET cc_start: 0.8302 (tpp) cc_final: 0.8068 (tpp) REVERT: I 1291 LEU cc_start: 0.8716 (pp) cc_final: 0.8401 (pt) REVERT: J 133 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7889 (mmt90) REVERT: J 135 ILE cc_start: 0.9204 (mt) cc_final: 0.8875 (tt) REVERT: J 169 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7464 (tt) REVERT: J 382 TYR cc_start: 0.8956 (m-10) cc_final: 0.8687 (m-10) REVERT: J 697 MET cc_start: 0.6794 (tmm) cc_final: 0.6354 (tmm) REVERT: J 788 LEU cc_start: 0.9167 (mm) cc_final: 0.8680 (tt) REVERT: J 806 ASP cc_start: 0.7523 (p0) cc_final: 0.6808 (p0) REVERT: J 925 GLU cc_start: 0.8484 (pp20) cc_final: 0.8126 (pp20) REVERT: J 1260 MET cc_start: 0.8556 (mtt) cc_final: 0.8338 (mtt) REVERT: K 31 GLN cc_start: 0.7727 (tt0) cc_final: 0.7499 (tt0) REVERT: K 55 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: K 65 ASP cc_start: 0.8359 (p0) cc_final: 0.8140 (p0) outliers start: 77 outliers final: 58 residues processed: 420 average time/residue: 0.3075 time to fit residues: 208.7402 Evaluate side-chains 390 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 330 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 668 PHE Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1151 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 226 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 60 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J1049 GLN K 62 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26756 Z= 0.241 Angle : 0.587 15.234 36420 Z= 0.299 Chirality : 0.042 0.218 4176 Planarity : 0.004 0.088 4541 Dihedral : 14.073 175.601 4311 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.37 % Allowed : 19.33 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3174 helix: 0.52 (0.16), residues: 1091 sheet: -1.56 (0.27), residues: 382 loop : -1.70 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 236 HIS 0.022 0.001 HIS I 165 PHE 0.018 0.001 PHE J 668 TYR 0.011 0.001 TYR I 726 ARG 0.010 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 336 time to evaluate : 3.059 Fit side-chains revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8213 (ptmt) REVERT: H 185 TYR cc_start: 0.9273 (p90) cc_final: 0.9009 (p90) REVERT: I 85 CYS cc_start: 0.8643 (m) cc_final: 0.8247 (m) REVERT: I 315 MET cc_start: 0.7611 (ptp) cc_final: 0.7316 (ptp) REVERT: I 427 ASP cc_start: 0.7947 (m-30) cc_final: 0.7585 (m-30) REVERT: I 504 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7423 (tm-30) REVERT: I 1291 LEU cc_start: 0.8717 (pp) cc_final: 0.8399 (pt) REVERT: I 1329 GLU cc_start: 0.7969 (tt0) cc_final: 0.7674 (tt0) REVERT: J 133 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8006 (mmt90) REVERT: J 169 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7511 (tt) REVERT: J 382 TYR cc_start: 0.8970 (m-10) cc_final: 0.8766 (m-10) REVERT: J 697 MET cc_start: 0.6810 (tmm) cc_final: 0.6400 (tmm) REVERT: J 788 LEU cc_start: 0.9191 (mm) cc_final: 0.8728 (tt) REVERT: J 806 ASP cc_start: 0.7592 (p0) cc_final: 0.6879 (p0) REVERT: J 902 ASP cc_start: 0.8096 (t0) cc_final: 0.7836 (t70) REVERT: J 925 GLU cc_start: 0.8476 (pp20) cc_final: 0.8196 (pp20) REVERT: K 31 GLN cc_start: 0.7905 (tt0) cc_final: 0.7679 (tt0) REVERT: K 55 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: K 62 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8218 (tp40) outliers start: 91 outliers final: 74 residues processed: 400 average time/residue: 0.3619 time to fit residues: 237.4910 Evaluate side-chains 404 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 327 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 668 PHE Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 210 optimal weight: 0.0870 chunk 152 optimal weight: 0.9980 chunk 28 optimal weight: 0.0370 chunk 243 optimal weight: 5.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN J 341 ASN J1049 GLN K 62 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26756 Z= 0.154 Angle : 0.570 17.788 36420 Z= 0.289 Chirality : 0.041 0.351 4176 Planarity : 0.004 0.086 4541 Dihedral : 14.037 175.671 4311 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.96 % Allowed : 20.18 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3174 helix: 0.62 (0.16), residues: 1081 sheet: -1.45 (0.28), residues: 359 loop : -1.62 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 236 HIS 0.019 0.001 HIS I 165 PHE 0.020 0.001 PHE I 828 TYR 0.012 0.001 TYR H 68 ARG 0.010 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 364 time to evaluate : 2.970 Fit side-chains revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8183 (ptmt) REVERT: H 185 TYR cc_start: 0.9255 (p90) cc_final: 0.9033 (p90) REVERT: I 85 CYS cc_start: 0.8580 (m) cc_final: 0.8141 (m) REVERT: I 315 MET cc_start: 0.7564 (ptp) cc_final: 0.7188 (ptp) REVERT: I 427 ASP cc_start: 0.7912 (m-30) cc_final: 0.7513 (m-30) REVERT: I 504 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7427 (tm-30) REVERT: I 1108 ASN cc_start: 0.8836 (p0) cc_final: 0.8075 (p0) REVERT: I 1291 LEU cc_start: 0.8567 (pp) cc_final: 0.8226 (pt) REVERT: J 133 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.7996 (mmt90) REVERT: J 169 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7553 (tt) REVERT: J 684 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6148 (m-30) REVERT: J 697 MET cc_start: 0.6701 (tmm) cc_final: 0.6304 (tmm) REVERT: J 806 ASP cc_start: 0.7487 (p0) cc_final: 0.6820 (p0) REVERT: J 925 GLU cc_start: 0.8460 (pp20) cc_final: 0.8109 (pp20) REVERT: K 31 GLN cc_start: 0.7624 (tt0) cc_final: 0.7334 (tt0) REVERT: K 55 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8118 (pt0) outliers start: 80 outliers final: 57 residues processed: 415 average time/residue: 0.3626 time to fit residues: 244.9043 Evaluate side-chains 391 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 331 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 668 PHE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 287 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN J1049 GLN K 73 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26756 Z= 0.200 Angle : 0.590 17.192 36420 Z= 0.299 Chirality : 0.042 0.333 4176 Planarity : 0.004 0.087 4541 Dihedral : 14.037 174.865 4311 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.04 % Allowed : 20.33 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3174 helix: 0.57 (0.16), residues: 1095 sheet: -1.41 (0.27), residues: 364 loop : -1.64 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 236 HIS 0.011 0.001 HIS I 165 PHE 0.022 0.001 PHE I 828 TYR 0.016 0.001 TYR G 152 ARG 0.015 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 340 time to evaluate : 2.988 Fit side-chains revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8179 (ptmt) REVERT: I 85 CYS cc_start: 0.8604 (m) cc_final: 0.8163 (m) REVERT: I 315 MET cc_start: 0.7585 (ptp) cc_final: 0.7191 (ptp) REVERT: I 427 ASP cc_start: 0.7900 (m-30) cc_final: 0.7501 (m-30) REVERT: I 504 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7456 (tm-30) REVERT: I 518 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (p0) REVERT: I 1291 LEU cc_start: 0.8555 (pp) cc_final: 0.8225 (pt) REVERT: J 133 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8052 (mmt90) REVERT: J 169 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7569 (tt) REVERT: J 314 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.7282 (mmm160) REVERT: J 382 TYR cc_start: 0.8949 (m-10) cc_final: 0.8658 (m-10) REVERT: J 684 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6145 (m-30) REVERT: J 697 MET cc_start: 0.6745 (tmm) cc_final: 0.6326 (tmm) REVERT: J 806 ASP cc_start: 0.7500 (p0) cc_final: 0.6813 (p0) REVERT: J 821 MET cc_start: 0.8891 (mmm) cc_final: 0.8461 (mmt) REVERT: J 925 GLU cc_start: 0.8423 (pp20) cc_final: 0.8183 (pp20) REVERT: J 1188 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5592 (tm-30) REVERT: K 31 GLN cc_start: 0.7652 (tt0) cc_final: 0.7370 (tt0) REVERT: K 55 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: K 75 GLN cc_start: 0.8254 (pp30) cc_final: 0.8041 (pp30) outliers start: 82 outliers final: 66 residues processed: 400 average time/residue: 0.3583 time to fit residues: 236.9687 Evaluate side-chains 399 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 328 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 668 PHE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.4980 chunk 304 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 319 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN J1049 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26756 Z= 0.157 Angle : 0.576 17.350 36420 Z= 0.290 Chirality : 0.041 0.307 4176 Planarity : 0.004 0.085 4541 Dihedral : 14.008 174.270 4311 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.55 % Allowed : 20.96 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3174 helix: 0.71 (0.16), residues: 1071 sheet: -1.27 (0.28), residues: 357 loop : -1.54 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 236 HIS 0.005 0.001 HIS J 450 PHE 0.018 0.001 PHE J 668 TYR 0.015 0.001 TYR H 68 ARG 0.004 0.000 ARG I1269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 362 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8171 (ptmt) REVERT: I 85 CYS cc_start: 0.8605 (m) cc_final: 0.8158 (m) REVERT: I 315 MET cc_start: 0.7565 (ptp) cc_final: 0.7143 (ptp) REVERT: I 427 ASP cc_start: 0.7882 (m-30) cc_final: 0.7476 (m-30) REVERT: I 504 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7383 (tm-30) REVERT: J 133 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8064 (mmt90) REVERT: J 169 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7506 (tt) REVERT: J 314 ARG cc_start: 0.7349 (ttt-90) cc_final: 0.7118 (mmm160) REVERT: J 382 TYR cc_start: 0.8909 (m-10) cc_final: 0.8695 (m-10) REVERT: J 644 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5936 (mtp) REVERT: J 684 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: J 697 MET cc_start: 0.6675 (tmm) cc_final: 0.6290 (tmm) REVERT: J 806 ASP cc_start: 0.7397 (p0) cc_final: 0.6735 (p0) REVERT: J 925 GLU cc_start: 0.8397 (pp20) cc_final: 0.8183 (pp20) REVERT: J 1151 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7886 (tptp) REVERT: J 1260 MET cc_start: 0.8509 (mtt) cc_final: 0.8231 (mtt) REVERT: K 31 GLN cc_start: 0.7366 (tt0) cc_final: 0.7079 (tt0) REVERT: K 65 ASP cc_start: 0.8436 (p0) cc_final: 0.8193 (p0) outliers start: 69 outliers final: 56 residues processed: 408 average time/residue: 0.3777 time to fit residues: 251.2744 Evaluate side-chains 390 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 330 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 668 PHE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1151 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 255 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN I 834 GLN J1049 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098818 restraints weight = 50153.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099262 restraints weight = 31623.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099835 restraints weight = 25004.703| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26756 Z= 0.200 Angle : 0.596 16.865 36420 Z= 0.300 Chirality : 0.042 0.309 4176 Planarity : 0.004 0.086 4541 Dihedral : 14.008 173.716 4311 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.85 % Allowed : 21.44 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3174 helix: 0.69 (0.16), residues: 1079 sheet: -1.25 (0.27), residues: 359 loop : -1.55 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 236 HIS 0.009 0.001 HIS I 165 PHE 0.018 0.001 PHE J 668 TYR 0.024 0.001 TYR G 152 ARG 0.011 0.000 ARG K 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.09 seconds wall clock time: 97 minutes 38.46 seconds (5858.46 seconds total)