Starting phenix.real_space_refine on Mon Feb 19 22:56:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0j_13745/02_2024/7q0j_13745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0j_13745/02_2024/7q0j_13745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0j_13745/02_2024/7q0j_13745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0j_13745/02_2024/7q0j_13745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0j_13745/02_2024/7q0j_13745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0j_13745/02_2024/7q0j_13745.pdb" } resolution = 4.3 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= 0.006 sd= 0.049 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 53 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16157 2.51 5 N 4612 2.21 5 O 5125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "C ASP 1341": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1254": "OE1" <-> "OE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26056 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "C" Number of atoms: 10533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10533 Classifications: {'peptide': 1335} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 1 Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "N" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14451 SG CYS D 72 20.063 57.094 97.238 1.00224.23 S ATOM 14559 SG CYS D 85 17.293 58.484 98.864 1.00251.88 S ATOM 14583 SG CYS D 88 21.411 60.565 98.673 1.00247.24 S ATOM 20271 SG CYS D 814 41.053 125.934 90.059 1.00198.64 S ATOM 20836 SG CYS D 888 42.411 121.476 90.808 1.00192.05 S ATOM 20887 SG CYS D 895 41.450 123.208 87.760 1.00177.56 S Time building chain proxies: 14.24, per 1000 atoms: 0.55 Number of scatterers: 26056 At special positions: 0 Unit cell: (132, 168.3, 168.3, 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 53 15.00 Mg 1 11.99 O 5125 8.00 N 4612 7.00 C 16157 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: 10.62 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 43 sheets defined 37.6% alpha, 13.6% beta 24 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 9.23 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.032A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.517A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.909A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.676A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.507A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.628A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.540A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.529A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.277A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 353 removed outlier: 4.107A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.898A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.577A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.803A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.812A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 661 " --> pdb=" O GLN C 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 864 removed outlier: 4.542A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 942 through 979 removed outlier: 4.406A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 4.196A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1038 removed outlier: 3.589A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.075A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.503A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 4.261A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1175 removed outlier: 3.794A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.642A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.662A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C1279 " --> pdb=" O VAL C1275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 removed outlier: 3.707A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C1293 " --> pdb=" O GLU C1289 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.932A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.704A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU C1329 " --> pdb=" O VAL C1325 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C1330 " --> pdb=" O LEU C1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.813A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.829A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 171 Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.532A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 283 removed outlier: 3.790A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.645A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.786A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 4.126A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.764A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.701A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.667A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.660A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.239A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.899A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.513A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 885 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.257A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 4.090A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 4.152A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.656A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D1236 " --> pdb=" O TYR D1232 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.820A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.155A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 30 removed outlier: 4.091A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.713A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 72 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 3.877A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 26 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 28 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 7.150A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 57 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 53 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.766A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.518A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 60 removed outlier: 3.667A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 5.943A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.538A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.463A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 155 through 158 removed outlier: 3.531A pdb=" N ASP C 158 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 195 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.720A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.613A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.842A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 3.939A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.815A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.848A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 838 removed outlier: 4.009A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.035A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1245 removed outlier: 3.609A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 437 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1245 removed outlier: 7.631A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.958A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.616A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 9.904A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.567A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP D 558 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 3.503A pdb=" N THR D 810 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 819 through 822 removed outlier: 3.552A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 7.017A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.698A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.618A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1034 through 1035 removed outlier: 3.512A pdb=" N VAL D1113 " --> pdb=" O VAL D1035 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.367A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 12.74 Time building geometry restraints manager: 11.47 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: 8682 1.34 - 1.46: 5130 1.46 - 1.58: 12451 1.58 - 1.70: 103 1.70 - 1.83: 184 Bond restraints: 26550 Sorted by residual: bond pdb=" C VAL C1103 " pdb=" N PRO C1104 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.30e-02 5.92e+03 5.52e+00 bond pdb=" CG PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 1.503 1.559 -0.056 3.40e-02 8.65e+02 2.76e+00 bond pdb=" CD GLU D 873 " pdb=" OE1 GLU D 873 " ideal model delta sigma weight residual 1.249 1.218 0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" CG GLU E 55 " pdb=" CD GLU E 55 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.19e+00 bond pdb=" CG GLU D 873 " pdb=" CD GLU D 873 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.18e+00 ... (remaining 26545 not shown) Histogram of bond angle deviations from ideal: 97.42 - 104.76: 632 104.76 - 112.10: 12893 112.10 - 119.44: 9702 119.44 - 126.78: 12506 126.78 - 134.12: 349 Bond angle restraints: 36082 Sorted by residual: angle pdb=" N VAL C 714 " pdb=" CA VAL C 714 " pdb=" C VAL C 714 " ideal model delta sigma weight residual 111.88 104.60 7.28 1.06e+00 8.90e-01 4.72e+01 angle pdb=" C GLU A 163 " pdb=" N ASP A 164 " pdb=" CA ASP A 164 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C GLU A 165 " pdb=" N ARG A 166 " pdb=" CA ARG A 166 " ideal model delta sigma weight residual 123.21 117.45 5.76 1.19e+00 7.06e-01 2.34e+01 angle pdb=" C GLU E 55 " pdb=" N GLU E 56 " pdb=" CA GLU E 56 " ideal model delta sigma weight residual 121.58 113.13 8.45 1.95e+00 2.63e-01 1.88e+01 angle pdb=" N GLU D 658 " pdb=" CA GLU D 658 " pdb=" CB GLU D 658 " ideal model delta sigma weight residual 110.39 117.28 -6.89 1.66e+00 3.63e-01 1.72e+01 ... (remaining 36077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 15476 28.13 - 56.27: 681 56.27 - 84.40: 100 84.40 - 112.54: 2 112.54 - 140.67: 2 Dihedral angle restraints: 16261 sinusoidal: 7107 harmonic: 9154 Sorted by residual: dihedral pdb=" CA GLN E 72 " pdb=" C GLN E 72 " pdb=" N GLN E 73 " pdb=" CA GLN E 73 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLY C 162 " pdb=" C GLY C 162 " pdb=" N LYS C 163 " pdb=" CA LYS C 163 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ARG D 47 " pdb=" C ARG D 47 " pdb=" N THR D 48 " pdb=" CA THR D 48 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 16258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3331 0.061 - 0.121: 714 0.121 - 0.182: 69 0.182 - 0.242: 8 0.242 - 0.303: 2 Chirality restraints: 4124 Sorted by residual: chirality pdb=" CG LEU A 171 " pdb=" CB LEU A 171 " pdb=" CD1 LEU A 171 " pdb=" CD2 LEU A 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL D 661 " pdb=" CA VAL D 661 " pdb=" CG1 VAL D 661 " pdb=" CG2 VAL D 661 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL D1353 " pdb=" CA VAL D1353 " pdb=" CG1 VAL D1353 " pdb=" CG2 VAL D1353 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4121 not shown) Planarity restraints: 4543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " 0.018 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP C1276 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1331 " -0.300 9.50e-02 1.11e+02 1.35e-01 1.13e+01 pdb=" NE ARG C1331 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C1331 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C1331 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C1331 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 846 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO C 847 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 847 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 847 " 0.040 5.00e-02 4.00e+02 ... (remaining 4540 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 513 2.65 - 3.21: 25203 3.21 - 3.77: 41540 3.77 - 4.34: 53693 4.34 - 4.90: 82981 Nonbonded interactions: 203930 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1503 " model vdw 2.083 2.170 nonbonded pdb=" O GLN C1288 " pdb=" OG1 THR C1292 " model vdw 2.148 2.440 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1503 " model vdw 2.151 2.170 nonbonded pdb=" O TYR C 810 " pdb=" OG SER C 815 " model vdw 2.170 2.440 nonbonded pdb=" OH TYR D1186 " pdb=" OE2 GLU D1188 " model vdw 2.196 2.440 ... (remaining 203925 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 'A' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 6.090 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 83.730 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 0.056 26550 Z= 0.237 Angle : 0.790 12.680 36082 Z= 0.414 Chirality : 0.048 0.303 4124 Planarity : 0.006 0.135 4543 Dihedral : 15.005 140.671 10373 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.25 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3172 helix: -0.20 (0.16), residues: 1023 sheet: -1.62 (0.27), residues: 321 loop : -1.94 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP C1276 HIS 0.007 0.001 HIS C 150 PHE 0.024 0.002 PHE C 186 TYR 0.029 0.002 TYR C1281 ARG 0.010 0.001 ARG D1242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9146 (ptm) cc_final: 0.8728 (ppp) REVERT: B 142 MET cc_start: 0.8487 (mmp) cc_final: 0.8090 (mmp) REVERT: C 160 ASP cc_start: 0.8296 (m-30) cc_final: 0.8026 (m-30) REVERT: C 370 MET cc_start: 0.8826 (tpt) cc_final: 0.8370 (tpp) REVERT: C 542 ARG cc_start: 0.9138 (mmp80) cc_final: 0.8852 (mmp80) REVERT: C 685 MET cc_start: 0.9143 (mtm) cc_final: 0.8817 (mtt) REVERT: C 741 MET cc_start: 0.8860 (ptp) cc_final: 0.8653 (ptt) REVERT: C 794 LEU cc_start: 0.9372 (tp) cc_final: 0.9031 (pp) REVERT: C 1025 PHE cc_start: 0.9379 (t80) cc_final: 0.9078 (t80) REVERT: C 1170 MET cc_start: 0.9373 (mmp) cc_final: 0.9130 (mmm) REVERT: C 1232 MET cc_start: 0.9332 (mmp) cc_final: 0.9079 (mmm) REVERT: C 1304 MET cc_start: 0.9475 (ttp) cc_final: 0.9136 (ptm) REVERT: D 130 MET cc_start: 0.8507 (mpp) cc_final: 0.8274 (mpp) REVERT: D 330 MET cc_start: 0.8891 (mmp) cc_final: 0.8249 (mmp) REVERT: D 372 MET cc_start: 0.9285 (mmm) cc_final: 0.8985 (mmp) REVERT: D 458 ASN cc_start: 0.9737 (t0) cc_final: 0.9454 (p0) REVERT: D 485 MET cc_start: 0.9173 (tpt) cc_final: 0.8898 (tpp) REVERT: D 608 CYS cc_start: 0.9350 (t) cc_final: 0.9124 (t) REVERT: D 625 MET cc_start: 0.9556 (tmm) cc_final: 0.9336 (tmm) REVERT: D 644 MET cc_start: 0.8997 (mpp) cc_final: 0.8749 (mpp) REVERT: D 822 MET cc_start: 0.9504 (mmp) cc_final: 0.8965 (mmm) REVERT: D 915 ILE cc_start: 0.9556 (pt) cc_final: 0.9355 (mt) REVERT: D 1025 MET cc_start: 0.8497 (tpt) cc_final: 0.8269 (tpt) REVERT: D 1239 ASP cc_start: 0.9136 (m-30) cc_final: 0.8871 (m-30) REVERT: D 1326 GLN cc_start: 0.8277 (mt0) cc_final: 0.7853 (mt0) REVERT: E 30 MET cc_start: 0.9046 (mmp) cc_final: 0.8813 (mmm) REVERT: E 36 ASP cc_start: 0.8932 (p0) cc_final: 0.8601 (p0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.3771 time to fit residues: 128.1388 Evaluate side-chains 141 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 290 optimal weight: 3.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 771 GLN D 921 GLN D1238 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26550 Z= 0.318 Angle : 0.665 9.568 36082 Z= 0.353 Chirality : 0.043 0.173 4124 Planarity : 0.005 0.101 4543 Dihedral : 13.643 145.149 4127 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3172 helix: 0.01 (0.15), residues: 1070 sheet: -1.52 (0.26), residues: 345 loop : -1.99 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C1276 HIS 0.006 0.001 HIS B 37 PHE 0.019 0.002 PHE A 231 TYR 0.018 0.002 TYR C1149 ARG 0.006 0.001 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9488 (ptm) cc_final: 0.8871 (ppp) REVERT: B 51 MET cc_start: 0.9215 (mmm) cc_final: 0.8468 (mmm) REVERT: B 142 MET cc_start: 0.8614 (mmp) cc_final: 0.8200 (mmp) REVERT: C 160 ASP cc_start: 0.8298 (m-30) cc_final: 0.8025 (m-30) REVERT: C 370 MET cc_start: 0.9159 (tpt) cc_final: 0.8914 (tpp) REVERT: C 685 MET cc_start: 0.9198 (mtm) cc_final: 0.8765 (mtt) REVERT: C 741 MET cc_start: 0.8891 (ptp) cc_final: 0.8667 (ptt) REVERT: C 794 LEU cc_start: 0.9288 (tp) cc_final: 0.9063 (pp) REVERT: C 1025 PHE cc_start: 0.9315 (t80) cc_final: 0.9039 (t80) REVERT: C 1066 MET cc_start: 0.9240 (mmp) cc_final: 0.8844 (mmm) REVERT: C 1107 MET cc_start: 0.8885 (pmm) cc_final: 0.8663 (pmm) REVERT: C 1119 MET cc_start: 0.9427 (mmp) cc_final: 0.9145 (mmp) REVERT: C 1170 MET cc_start: 0.9482 (mmp) cc_final: 0.9230 (mmm) REVERT: C 1304 MET cc_start: 0.9405 (ttp) cc_final: 0.9184 (ptm) REVERT: C 1319 MET cc_start: 0.9161 (tmm) cc_final: 0.8910 (tmm) REVERT: D 245 LEU cc_start: 0.9274 (tp) cc_final: 0.9028 (tp) REVERT: D 330 MET cc_start: 0.8952 (mmp) cc_final: 0.8428 (mmp) REVERT: D 372 MET cc_start: 0.9258 (mmm) cc_final: 0.9012 (mmp) REVERT: D 604 MET cc_start: 0.9471 (mmm) cc_final: 0.8974 (mmm) REVERT: D 608 CYS cc_start: 0.9348 (t) cc_final: 0.9127 (t) REVERT: D 625 MET cc_start: 0.9595 (tmm) cc_final: 0.9303 (tmm) REVERT: D 644 MET cc_start: 0.8923 (mpp) cc_final: 0.8652 (mpp) REVERT: D 697 MET cc_start: 0.9307 (tmm) cc_final: 0.9060 (tmm) REVERT: D 698 MET cc_start: 0.9371 (mmm) cc_final: 0.8679 (mmm) REVERT: D 822 MET cc_start: 0.9394 (mmp) cc_final: 0.8921 (mmm) REVERT: D 915 ILE cc_start: 0.9475 (pt) cc_final: 0.9129 (mt) REVERT: D 1025 MET cc_start: 0.8322 (tpt) cc_final: 0.8046 (tpt) REVERT: D 1189 MET cc_start: 0.8732 (tpt) cc_final: 0.8354 (tpp) REVERT: D 1250 ASP cc_start: 0.9522 (m-30) cc_final: 0.9085 (p0) REVERT: D 1326 GLN cc_start: 0.8322 (mt0) cc_final: 0.7898 (mt0) REVERT: E 36 ASP cc_start: 0.9126 (p0) cc_final: 0.8751 (p0) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.3631 time to fit residues: 110.5949 Evaluate side-chains 132 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 291 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 465 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1126 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26550 Z= 0.210 Angle : 0.599 11.359 36082 Z= 0.314 Chirality : 0.042 0.219 4124 Planarity : 0.004 0.052 4543 Dihedral : 13.580 145.325 4127 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.49 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3172 helix: 0.15 (0.16), residues: 1077 sheet: -1.51 (0.25), residues: 366 loop : -1.87 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C1276 HIS 0.004 0.001 HIS D 777 PHE 0.016 0.001 PHE A 231 TYR 0.015 0.001 TYR D 679 ARG 0.004 0.000 ARG C1331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9526 (ptm) cc_final: 0.8884 (ppp) REVERT: B 142 MET cc_start: 0.8518 (mmp) cc_final: 0.8083 (mmp) REVERT: C 160 ASP cc_start: 0.8204 (m-30) cc_final: 0.7929 (m-30) REVERT: C 370 MET cc_start: 0.9118 (tpt) cc_final: 0.8905 (tpp) REVERT: C 488 MET cc_start: 0.8155 (ppp) cc_final: 0.7943 (ppp) REVERT: C 685 MET cc_start: 0.9261 (mtm) cc_final: 0.8814 (mtt) REVERT: C 741 MET cc_start: 0.8818 (ptp) cc_final: 0.8560 (ptt) REVERT: C 1025 PHE cc_start: 0.9284 (t80) cc_final: 0.9024 (t80) REVERT: C 1066 MET cc_start: 0.9252 (mmp) cc_final: 0.8863 (mmm) REVERT: C 1084 ASP cc_start: 0.9287 (m-30) cc_final: 0.9057 (m-30) REVERT: C 1107 MET cc_start: 0.8895 (pmm) cc_final: 0.8639 (pmm) REVERT: C 1170 MET cc_start: 0.9451 (mmp) cc_final: 0.9193 (mmm) REVERT: C 1273 MET cc_start: 0.9369 (mmm) cc_final: 0.8811 (mmm) REVERT: C 1304 MET cc_start: 0.9389 (ttp) cc_final: 0.9172 (ptm) REVERT: D 245 LEU cc_start: 0.9243 (tp) cc_final: 0.9022 (tp) REVERT: D 330 MET cc_start: 0.8976 (mmp) cc_final: 0.8510 (mmp) REVERT: D 458 ASN cc_start: 0.9740 (t0) cc_final: 0.9360 (p0) REVERT: D 479 GLU cc_start: 0.8858 (tt0) cc_final: 0.8634 (tt0) REVERT: D 608 CYS cc_start: 0.9291 (t) cc_final: 0.9078 (t) REVERT: D 625 MET cc_start: 0.9592 (tmm) cc_final: 0.9391 (tmm) REVERT: D 644 MET cc_start: 0.8884 (mpp) cc_final: 0.8676 (mpp) REVERT: D 697 MET cc_start: 0.9278 (tmm) cc_final: 0.8786 (tmm) REVERT: D 698 MET cc_start: 0.9377 (mmm) cc_final: 0.8677 (mmm) REVERT: D 822 MET cc_start: 0.9263 (mmp) cc_final: 0.8980 (mmm) REVERT: D 915 ILE cc_start: 0.9449 (pt) cc_final: 0.9098 (mt) REVERT: D 932 MET cc_start: 0.8763 (tmm) cc_final: 0.8517 (tmm) REVERT: D 1025 MET cc_start: 0.8270 (tpt) cc_final: 0.8005 (tpt) REVERT: D 1189 MET cc_start: 0.8741 (tpt) cc_final: 0.8257 (tpp) REVERT: D 1326 GLN cc_start: 0.8261 (mt0) cc_final: 0.7869 (mt0) REVERT: E 5 THR cc_start: 0.9261 (p) cc_final: 0.8721 (p) REVERT: E 36 ASP cc_start: 0.9042 (p0) cc_final: 0.8629 (p0) REVERT: E 53 GLU cc_start: 0.9504 (mt-10) cc_final: 0.8921 (mm-30) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.3702 time to fit residues: 119.8273 Evaluate side-chains 142 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 276 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26550 Z= 0.331 Angle : 0.682 10.656 36082 Z= 0.357 Chirality : 0.043 0.195 4124 Planarity : 0.005 0.058 4543 Dihedral : 13.686 148.781 4127 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3172 helix: 0.03 (0.15), residues: 1084 sheet: -1.57 (0.26), residues: 351 loop : -1.92 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C1276 HIS 0.007 0.002 HIS B 37 PHE 0.016 0.002 PHE A 231 TYR 0.022 0.002 TYR C1149 ARG 0.007 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9494 (ptm) cc_final: 0.8867 (ppp) REVERT: B 51 MET cc_start: 0.9312 (mmm) cc_final: 0.8958 (mmt) REVERT: B 142 MET cc_start: 0.8626 (mmp) cc_final: 0.8085 (mmp) REVERT: B 177 TYR cc_start: 0.5968 (m-80) cc_final: 0.5734 (m-80) REVERT: C 160 ASP cc_start: 0.8211 (m-30) cc_final: 0.7934 (m-30) REVERT: C 685 MET cc_start: 0.9331 (mtm) cc_final: 0.8831 (mtt) REVERT: C 741 MET cc_start: 0.8841 (ptp) cc_final: 0.8624 (ptt) REVERT: C 1025 PHE cc_start: 0.9300 (t80) cc_final: 0.9037 (t80) REVERT: C 1084 ASP cc_start: 0.9285 (m-30) cc_final: 0.9082 (m-30) REVERT: C 1170 MET cc_start: 0.9382 (mmp) cc_final: 0.9136 (mmm) REVERT: C 1290 MET cc_start: 0.9432 (mmp) cc_final: 0.9148 (mmp) REVERT: C 1304 MET cc_start: 0.9418 (ttp) cc_final: 0.9189 (ptm) REVERT: D 130 MET cc_start: 0.8806 (mmp) cc_final: 0.8546 (mmm) REVERT: D 237 MET cc_start: 0.9176 (ttt) cc_final: 0.8585 (tpt) REVERT: D 245 LEU cc_start: 0.9367 (tp) cc_final: 0.9093 (tp) REVERT: D 330 MET cc_start: 0.9081 (mmp) cc_final: 0.8641 (mmp) REVERT: D 372 MET cc_start: 0.9115 (mmp) cc_final: 0.8799 (mmt) REVERT: D 458 ASN cc_start: 0.9764 (t0) cc_final: 0.9527 (t0) REVERT: D 479 GLU cc_start: 0.8886 (tt0) cc_final: 0.8614 (tt0) REVERT: D 625 MET cc_start: 0.9592 (tmm) cc_final: 0.9309 (tmm) REVERT: D 644 MET cc_start: 0.8992 (mpp) cc_final: 0.8784 (mpp) REVERT: D 697 MET cc_start: 0.9263 (tmm) cc_final: 0.8789 (tmm) REVERT: D 698 MET cc_start: 0.9366 (mmm) cc_final: 0.8699 (mmm) REVERT: D 821 MET cc_start: 0.9034 (mmp) cc_final: 0.8820 (tpp) REVERT: D 915 ILE cc_start: 0.9362 (pt) cc_final: 0.8954 (mt) REVERT: D 932 MET cc_start: 0.8787 (tmm) cc_final: 0.8490 (tmm) REVERT: D 1025 MET cc_start: 0.8302 (tpt) cc_final: 0.8017 (tpt) REVERT: D 1099 TYR cc_start: 0.9544 (m-80) cc_final: 0.9329 (m-80) REVERT: D 1189 MET cc_start: 0.8752 (tpt) cc_final: 0.8221 (tpp) REVERT: D 1250 ASP cc_start: 0.9481 (m-30) cc_final: 0.9191 (p0) REVERT: D 1326 GLN cc_start: 0.8495 (mt0) cc_final: 0.8109 (mt0) REVERT: E 36 ASP cc_start: 0.9227 (p0) cc_final: 0.8855 (p0) REVERT: E 53 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9120 (mm-30) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.3686 time to fit residues: 103.9410 Evaluate side-chains 138 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 263 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 277 optimal weight: 50.0000 chunk 78 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN C 462 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26550 Z= 0.256 Angle : 0.624 11.347 36082 Z= 0.325 Chirality : 0.043 0.167 4124 Planarity : 0.004 0.055 4543 Dihedral : 13.680 147.568 4127 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3172 helix: 0.11 (0.15), residues: 1095 sheet: -1.43 (0.26), residues: 345 loop : -1.95 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1276 HIS 0.005 0.001 HIS D 777 PHE 0.013 0.001 PHE A 231 TYR 0.020 0.002 TYR C1018 ARG 0.004 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9426 (p0) cc_final: 0.9197 (p0) REVERT: A 205 MET cc_start: 0.9443 (ptm) cc_final: 0.9134 (ppp) REVERT: B 51 MET cc_start: 0.9289 (mmm) cc_final: 0.8930 (mmt) REVERT: B 177 TYR cc_start: 0.6220 (m-80) cc_final: 0.5909 (m-80) REVERT: C 160 ASP cc_start: 0.8205 (m-30) cc_final: 0.7939 (m-30) REVERT: C 492 MET cc_start: 0.9503 (pmm) cc_final: 0.8733 (pmm) REVERT: C 685 MET cc_start: 0.9317 (mtm) cc_final: 0.8793 (mtt) REVERT: C 741 MET cc_start: 0.8782 (ptp) cc_final: 0.8566 (ptt) REVERT: C 1025 PHE cc_start: 0.9279 (t80) cc_final: 0.9000 (t80) REVERT: C 1066 MET cc_start: 0.9311 (mmp) cc_final: 0.8883 (mmm) REVERT: C 1084 ASP cc_start: 0.9366 (m-30) cc_final: 0.9066 (m-30) REVERT: C 1085 MET cc_start: 0.9109 (mmt) cc_final: 0.8478 (mmp) REVERT: C 1170 MET cc_start: 0.9373 (mmp) cc_final: 0.9092 (mmm) REVERT: C 1290 MET cc_start: 0.9475 (mmp) cc_final: 0.9246 (mmp) REVERT: D 130 MET cc_start: 0.8845 (mmp) cc_final: 0.8587 (mmm) REVERT: D 180 MET cc_start: 0.7155 (mmm) cc_final: 0.6905 (mmm) REVERT: D 237 MET cc_start: 0.9151 (ttt) cc_final: 0.8637 (tpt) REVERT: D 245 LEU cc_start: 0.9323 (tp) cc_final: 0.9035 (tp) REVERT: D 330 MET cc_start: 0.9111 (mmp) cc_final: 0.8731 (mmp) REVERT: D 458 ASN cc_start: 0.9759 (t0) cc_final: 0.9502 (t0) REVERT: D 608 CYS cc_start: 0.9346 (t) cc_final: 0.9127 (t) REVERT: D 625 MET cc_start: 0.9598 (tmm) cc_final: 0.9372 (tmm) REVERT: D 697 MET cc_start: 0.9253 (tmm) cc_final: 0.8541 (tmm) REVERT: D 698 MET cc_start: 0.9386 (mmm) cc_final: 0.8665 (mmt) REVERT: D 821 MET cc_start: 0.9095 (mmp) cc_final: 0.8824 (tpp) REVERT: D 822 MET cc_start: 0.9228 (mmp) cc_final: 0.8957 (mmm) REVERT: D 915 ILE cc_start: 0.9374 (pt) cc_final: 0.8953 (mt) REVERT: D 1025 MET cc_start: 0.8280 (tpt) cc_final: 0.7985 (tpt) REVERT: D 1099 TYR cc_start: 0.9581 (m-80) cc_final: 0.9352 (m-80) REVERT: D 1189 MET cc_start: 0.8740 (tpt) cc_final: 0.8231 (tpp) REVERT: D 1250 ASP cc_start: 0.9444 (m-30) cc_final: 0.9154 (p0) REVERT: D 1326 GLN cc_start: 0.8671 (mt0) cc_final: 0.8318 (mt0) REVERT: E 36 ASP cc_start: 0.9208 (p0) cc_final: 0.8816 (p0) REVERT: E 53 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9144 (mm-30) outliers start: 2 outliers final: 1 residues processed: 181 average time/residue: 0.3669 time to fit residues: 108.6591 Evaluate side-chains 142 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 9.9990 chunk 278 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26550 Z= 0.334 Angle : 0.687 10.972 36082 Z= 0.359 Chirality : 0.044 0.393 4124 Planarity : 0.005 0.084 4543 Dihedral : 13.756 148.837 4127 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.70 % Favored : 91.20 % Rotamer: Outliers : 0.07 % Allowed : 3.94 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3172 helix: -0.04 (0.15), residues: 1100 sheet: -1.42 (0.26), residues: 339 loop : -2.03 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C1276 HIS 0.007 0.002 HIS B 37 PHE 0.019 0.002 PHE D 62 TYR 0.017 0.002 TYR C1149 ARG 0.018 0.001 ARG C1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9377 (ptm) cc_final: 0.9111 (ppp) REVERT: B 51 MET cc_start: 0.9320 (mmm) cc_final: 0.8949 (mmt) REVERT: C 160 ASP cc_start: 0.8256 (m-30) cc_final: 0.7978 (m-30) REVERT: C 681 MET cc_start: 0.8568 (ptp) cc_final: 0.8365 (ptp) REVERT: C 685 MET cc_start: 0.9287 (mtm) cc_final: 0.8786 (mtt) REVERT: C 741 MET cc_start: 0.8789 (ptp) cc_final: 0.8549 (ptt) REVERT: C 1025 PHE cc_start: 0.9300 (t80) cc_final: 0.9015 (t80) REVERT: C 1066 MET cc_start: 0.9352 (mmp) cc_final: 0.8691 (mmm) REVERT: C 1084 ASP cc_start: 0.9374 (m-30) cc_final: 0.9044 (m-30) REVERT: C 1085 MET cc_start: 0.9232 (mmt) cc_final: 0.8617 (mmp) REVERT: C 1170 MET cc_start: 0.9353 (mmp) cc_final: 0.9044 (mmm) REVERT: C 1232 MET cc_start: 0.9293 (mmm) cc_final: 0.8051 (mmt) REVERT: C 1290 MET cc_start: 0.9511 (mmp) cc_final: 0.9303 (mmp) REVERT: D 130 MET cc_start: 0.8792 (mmp) cc_final: 0.8478 (mmm) REVERT: D 237 MET cc_start: 0.9155 (ttt) cc_final: 0.8598 (tpt) REVERT: D 245 LEU cc_start: 0.9381 (tp) cc_final: 0.9097 (tp) REVERT: D 298 MET cc_start: 0.9326 (ttp) cc_final: 0.8759 (tmm) REVERT: D 330 MET cc_start: 0.9132 (mmp) cc_final: 0.8775 (mmp) REVERT: D 458 ASN cc_start: 0.9762 (t0) cc_final: 0.9481 (t0) REVERT: D 604 MET cc_start: 0.9542 (mmt) cc_final: 0.9076 (mmm) REVERT: D 608 CYS cc_start: 0.9297 (t) cc_final: 0.9073 (t) REVERT: D 625 MET cc_start: 0.9622 (tmm) cc_final: 0.9310 (tmm) REVERT: D 644 MET cc_start: 0.8888 (mpp) cc_final: 0.8604 (mpp) REVERT: D 697 MET cc_start: 0.9212 (tmm) cc_final: 0.8429 (tmm) REVERT: D 698 MET cc_start: 0.9342 (mmm) cc_final: 0.8562 (mmt) REVERT: D 747 MET cc_start: 0.9299 (mmp) cc_final: 0.8856 (mmp) REVERT: D 915 ILE cc_start: 0.9285 (pt) cc_final: 0.8797 (mt) REVERT: D 932 MET cc_start: 0.8490 (tmm) cc_final: 0.8219 (tmm) REVERT: D 1025 MET cc_start: 0.8314 (tpt) cc_final: 0.7972 (tpt) REVERT: D 1189 MET cc_start: 0.8704 (tpt) cc_final: 0.8265 (tpp) REVERT: D 1250 ASP cc_start: 0.9468 (m-30) cc_final: 0.9194 (p0) REVERT: D 1326 GLN cc_start: 0.8836 (mt0) cc_final: 0.8501 (mt0) REVERT: E 36 ASP cc_start: 0.9234 (p0) cc_final: 0.8843 (p0) REVERT: E 53 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9164 (mm-30) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.3579 time to fit residues: 101.8846 Evaluate side-chains 133 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 308 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 142 optimal weight: 0.2980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 737 ASN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26550 Z= 0.171 Angle : 0.613 12.691 36082 Z= 0.316 Chirality : 0.043 0.250 4124 Planarity : 0.004 0.049 4543 Dihedral : 13.671 146.847 4127 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.54 % Rotamer: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3172 helix: 0.19 (0.16), residues: 1089 sheet: -1.20 (0.26), residues: 341 loop : -1.89 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1276 HIS 0.006 0.001 HIS C 150 PHE 0.011 0.001 PHE A 231 TYR 0.019 0.001 TYR C1018 ARG 0.004 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9261 (mmm) cc_final: 0.8871 (mmt) REVERT: B 177 TYR cc_start: 0.6213 (m-80) cc_final: 0.5801 (m-80) REVERT: C 160 ASP cc_start: 0.8186 (m-30) cc_final: 0.7899 (m-30) REVERT: C 685 MET cc_start: 0.9260 (mtm) cc_final: 0.8714 (mtt) REVERT: C 741 MET cc_start: 0.8690 (ptp) cc_final: 0.8442 (ptt) REVERT: C 1025 PHE cc_start: 0.9259 (t80) cc_final: 0.8967 (t80) REVERT: C 1066 MET cc_start: 0.9348 (mmp) cc_final: 0.8840 (mmm) REVERT: C 1084 ASP cc_start: 0.9281 (m-30) cc_final: 0.8960 (m-30) REVERT: C 1085 MET cc_start: 0.9047 (mmt) cc_final: 0.8520 (mmp) REVERT: C 1170 MET cc_start: 0.9369 (mmp) cc_final: 0.9085 (mmm) REVERT: C 1232 MET cc_start: 0.9091 (mmm) cc_final: 0.8692 (mmm) REVERT: D 130 MET cc_start: 0.8734 (mmp) cc_final: 0.8432 (mmm) REVERT: D 180 MET cc_start: 0.7299 (mmm) cc_final: 0.7076 (mmm) REVERT: D 237 MET cc_start: 0.9133 (ttt) cc_final: 0.8474 (tpp) REVERT: D 245 LEU cc_start: 0.9376 (tp) cc_final: 0.9091 (tp) REVERT: D 298 MET cc_start: 0.9625 (ttp) cc_final: 0.9407 (ttp) REVERT: D 330 MET cc_start: 0.9079 (mmp) cc_final: 0.8679 (mmp) REVERT: D 449 LEU cc_start: 0.9361 (mm) cc_final: 0.9047 (tp) REVERT: D 454 CYS cc_start: 0.9160 (m) cc_final: 0.8723 (m) REVERT: D 458 ASN cc_start: 0.9735 (t0) cc_final: 0.9477 (t0) REVERT: D 475 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8558 (mt-10) REVERT: D 479 GLU cc_start: 0.8900 (tt0) cc_final: 0.8170 (pt0) REVERT: D 604 MET cc_start: 0.9539 (mmt) cc_final: 0.9092 (mmm) REVERT: D 608 CYS cc_start: 0.9295 (t) cc_final: 0.9059 (t) REVERT: D 625 MET cc_start: 0.9583 (tmm) cc_final: 0.9211 (tmm) REVERT: D 644 MET cc_start: 0.9043 (mpp) cc_final: 0.8778 (mpp) REVERT: D 697 MET cc_start: 0.9166 (tmm) cc_final: 0.8469 (ppp) REVERT: D 698 MET cc_start: 0.9402 (mmm) cc_final: 0.8746 (mmt) REVERT: D 747 MET cc_start: 0.9288 (mmp) cc_final: 0.8843 (mmp) REVERT: D 822 MET cc_start: 0.9378 (mmp) cc_final: 0.8864 (mmm) REVERT: D 915 ILE cc_start: 0.9362 (pt) cc_final: 0.8913 (mt) REVERT: D 932 MET cc_start: 0.8434 (tmm) cc_final: 0.8195 (tmm) REVERT: D 982 LEU cc_start: 0.9760 (tp) cc_final: 0.9558 (pp) REVERT: D 1025 MET cc_start: 0.8323 (tpt) cc_final: 0.8066 (tpt) REVERT: D 1099 TYR cc_start: 0.9588 (m-80) cc_final: 0.9363 (m-80) REVERT: D 1189 MET cc_start: 0.8703 (tpt) cc_final: 0.8298 (tpp) REVERT: D 1326 GLN cc_start: 0.8770 (mt0) cc_final: 0.8386 (mt0) REVERT: E 36 ASP cc_start: 0.9222 (p0) cc_final: 0.8832 (p0) REVERT: E 53 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9123 (mm-30) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.3723 time to fit residues: 114.3738 Evaluate side-chains 141 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 0.0570 chunk 59 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 210 optimal weight: 0.0050 chunk 152 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 overall best weight: 1.9316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 ASN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 489 ASN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26550 Z= 0.177 Angle : 0.608 12.245 36082 Z= 0.311 Chirality : 0.043 0.186 4124 Planarity : 0.004 0.067 4543 Dihedral : 13.602 147.036 4127 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3172 helix: 0.18 (0.16), residues: 1091 sheet: -1.13 (0.27), residues: 331 loop : -1.85 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1276 HIS 0.004 0.001 HIS C 150 PHE 0.011 0.001 PHE A 231 TYR 0.030 0.001 TYR D 457 ARG 0.006 0.000 ARG C1269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9267 (mmm) cc_final: 0.8872 (mmt) REVERT: C 160 ASP cc_start: 0.8188 (m-30) cc_final: 0.7905 (m-30) REVERT: C 681 MET cc_start: 0.8758 (ptp) cc_final: 0.8408 (ptp) REVERT: C 685 MET cc_start: 0.9276 (mtm) cc_final: 0.8785 (mtp) REVERT: C 741 MET cc_start: 0.8693 (ptp) cc_final: 0.8433 (ptt) REVERT: C 1025 PHE cc_start: 0.9256 (t80) cc_final: 0.9007 (t80) REVERT: C 1066 MET cc_start: 0.9350 (mmp) cc_final: 0.8869 (mmm) REVERT: C 1084 ASP cc_start: 0.9228 (m-30) cc_final: 0.8867 (m-30) REVERT: C 1085 MET cc_start: 0.9049 (mmt) cc_final: 0.8517 (mmp) REVERT: C 1170 MET cc_start: 0.9370 (mmp) cc_final: 0.9076 (mmm) REVERT: C 1232 MET cc_start: 0.9079 (mmm) cc_final: 0.8766 (mmm) REVERT: D 130 MET cc_start: 0.8755 (mmp) cc_final: 0.8461 (mmm) REVERT: D 180 MET cc_start: 0.7252 (mmm) cc_final: 0.7017 (mmm) REVERT: D 237 MET cc_start: 0.9145 (ttt) cc_final: 0.8529 (tpp) REVERT: D 245 LEU cc_start: 0.9392 (tp) cc_final: 0.9112 (tp) REVERT: D 330 MET cc_start: 0.9041 (mmp) cc_final: 0.8723 (mmp) REVERT: D 449 LEU cc_start: 0.9407 (mm) cc_final: 0.9004 (tp) REVERT: D 454 CYS cc_start: 0.9067 (m) cc_final: 0.8477 (m) REVERT: D 458 ASN cc_start: 0.9714 (t0) cc_final: 0.9453 (t0) REVERT: D 475 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8470 (mt-10) REVERT: D 479 GLU cc_start: 0.9015 (tt0) cc_final: 0.8197 (pt0) REVERT: D 485 MET cc_start: 0.9037 (tpt) cc_final: 0.8820 (tpp) REVERT: D 604 MET cc_start: 0.9524 (mmt) cc_final: 0.9089 (mmm) REVERT: D 608 CYS cc_start: 0.9268 (t) cc_final: 0.9041 (t) REVERT: D 625 MET cc_start: 0.9588 (tmm) cc_final: 0.9182 (tmm) REVERT: D 644 MET cc_start: 0.8962 (mpp) cc_final: 0.8685 (mpp) REVERT: D 697 MET cc_start: 0.9159 (tmm) cc_final: 0.8473 (ppp) REVERT: D 698 MET cc_start: 0.9409 (mmm) cc_final: 0.8778 (mmt) REVERT: D 747 MET cc_start: 0.9269 (mmp) cc_final: 0.8845 (mmp) REVERT: D 821 MET cc_start: 0.8984 (mmp) cc_final: 0.8734 (tpp) REVERT: D 822 MET cc_start: 0.9269 (mmp) cc_final: 0.9033 (mmp) REVERT: D 915 ILE cc_start: 0.9330 (pt) cc_final: 0.8879 (mt) REVERT: D 982 LEU cc_start: 0.9754 (tp) cc_final: 0.9539 (pp) REVERT: D 1025 MET cc_start: 0.8331 (tpt) cc_final: 0.8058 (tpt) REVERT: D 1189 MET cc_start: 0.8671 (tpt) cc_final: 0.8163 (tpp) REVERT: D 1326 GLN cc_start: 0.8818 (mt0) cc_final: 0.8439 (mt0) REVERT: E 36 ASP cc_start: 0.9262 (p0) cc_final: 0.8866 (p0) REVERT: E 53 GLU cc_start: 0.9462 (mt-10) cc_final: 0.8928 (mm-30) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3541 time to fit residues: 102.9553 Evaluate side-chains 142 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 259 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1111 GLN C1257 GLN D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26550 Z= 0.190 Angle : 0.612 11.772 36082 Z= 0.313 Chirality : 0.043 0.187 4124 Planarity : 0.004 0.060 4543 Dihedral : 13.562 147.271 4127 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3172 helix: 0.19 (0.16), residues: 1091 sheet: -1.08 (0.27), residues: 336 loop : -1.84 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1276 HIS 0.004 0.001 HIS C 150 PHE 0.011 0.001 PHE A 231 TYR 0.018 0.001 TYR C1018 ARG 0.005 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9275 (mmm) cc_final: 0.8873 (mmt) REVERT: B 177 TYR cc_start: 0.6120 (m-80) cc_final: 0.5798 (m-80) REVERT: C 160 ASP cc_start: 0.8185 (m-30) cc_final: 0.7907 (m-30) REVERT: C 685 MET cc_start: 0.9292 (mtm) cc_final: 0.8829 (mtp) REVERT: C 741 MET cc_start: 0.8683 (ptp) cc_final: 0.8422 (ptt) REVERT: C 1066 MET cc_start: 0.9349 (mmp) cc_final: 0.8820 (mmm) REVERT: C 1084 ASP cc_start: 0.9255 (m-30) cc_final: 0.8901 (m-30) REVERT: C 1085 MET cc_start: 0.9054 (mmt) cc_final: 0.8494 (mmp) REVERT: C 1170 MET cc_start: 0.9365 (mmp) cc_final: 0.9071 (mmm) REVERT: C 1180 MET cc_start: 0.9157 (tpp) cc_final: 0.8792 (tpp) REVERT: C 1232 MET cc_start: 0.9062 (mmm) cc_final: 0.8755 (mmm) REVERT: C 1278 LEU cc_start: 0.9755 (tp) cc_final: 0.9550 (tp) REVERT: C 1281 TYR cc_start: 0.8342 (m-10) cc_final: 0.8048 (m-10) REVERT: C 1286 THR cc_start: 0.9720 (p) cc_final: 0.9489 (p) REVERT: D 130 MET cc_start: 0.8742 (mmp) cc_final: 0.8447 (mmm) REVERT: D 180 MET cc_start: 0.7305 (mmm) cc_final: 0.7044 (mmm) REVERT: D 237 MET cc_start: 0.9167 (ttt) cc_final: 0.8547 (tpp) REVERT: D 245 LEU cc_start: 0.9408 (tp) cc_final: 0.9128 (tp) REVERT: D 330 MET cc_start: 0.9068 (mmp) cc_final: 0.8748 (mmp) REVERT: D 449 LEU cc_start: 0.9411 (mm) cc_final: 0.9026 (tp) REVERT: D 454 CYS cc_start: 0.9110 (m) cc_final: 0.8584 (m) REVERT: D 458 ASN cc_start: 0.9733 (t0) cc_final: 0.9531 (t0) REVERT: D 475 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 479 GLU cc_start: 0.9039 (tt0) cc_final: 0.8425 (pt0) REVERT: D 485 MET cc_start: 0.9051 (tpt) cc_final: 0.8835 (tpp) REVERT: D 604 MET cc_start: 0.9521 (mmt) cc_final: 0.9085 (mmm) REVERT: D 608 CYS cc_start: 0.9256 (t) cc_final: 0.9037 (t) REVERT: D 625 MET cc_start: 0.9560 (tmm) cc_final: 0.9252 (tmm) REVERT: D 644 MET cc_start: 0.8961 (mpp) cc_final: 0.8663 (mpp) REVERT: D 697 MET cc_start: 0.9155 (tmm) cc_final: 0.8404 (tmm) REVERT: D 698 MET cc_start: 0.9410 (mmm) cc_final: 0.8700 (mmt) REVERT: D 747 MET cc_start: 0.9244 (mmp) cc_final: 0.8834 (mmp) REVERT: D 821 MET cc_start: 0.8964 (mmp) cc_final: 0.8733 (tpp) REVERT: D 915 ILE cc_start: 0.9321 (pt) cc_final: 0.8851 (mt) REVERT: D 982 LEU cc_start: 0.9752 (tp) cc_final: 0.9543 (pp) REVERT: D 1025 MET cc_start: 0.8364 (tpt) cc_final: 0.8091 (tpt) REVERT: D 1189 MET cc_start: 0.8745 (tpt) cc_final: 0.8336 (tpp) REVERT: D 1326 GLN cc_start: 0.8826 (mt0) cc_final: 0.8485 (mt0) REVERT: E 36 ASP cc_start: 0.9257 (p0) cc_final: 0.8858 (p0) REVERT: E 53 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9078 (mm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3703 time to fit residues: 107.7291 Evaluate side-chains 143 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 293 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 ASN C1111 GLN D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26550 Z= 0.189 Angle : 0.612 11.837 36082 Z= 0.315 Chirality : 0.043 0.193 4124 Planarity : 0.004 0.053 4543 Dihedral : 13.527 147.230 4127 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.19 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3172 helix: 0.18 (0.16), residues: 1090 sheet: -0.96 (0.27), residues: 341 loop : -1.81 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1276 HIS 0.004 0.001 HIS C 150 PHE 0.011 0.001 PHE A 231 TYR 0.016 0.001 TYR D 679 ARG 0.006 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.9278 (mmm) cc_final: 0.8891 (mmt) REVERT: B 177 TYR cc_start: 0.6182 (m-80) cc_final: 0.5821 (m-80) REVERT: C 160 ASP cc_start: 0.8174 (m-30) cc_final: 0.7902 (m-30) REVERT: C 685 MET cc_start: 0.9288 (mtm) cc_final: 0.8774 (mtt) REVERT: C 741 MET cc_start: 0.8656 (ptp) cc_final: 0.8394 (ptt) REVERT: C 1025 PHE cc_start: 0.9324 (t80) cc_final: 0.9072 (t80) REVERT: C 1066 MET cc_start: 0.9343 (mmp) cc_final: 0.8820 (mmm) REVERT: C 1084 ASP cc_start: 0.9243 (m-30) cc_final: 0.8889 (m-30) REVERT: C 1085 MET cc_start: 0.9003 (mmt) cc_final: 0.8475 (mmp) REVERT: C 1170 MET cc_start: 0.9368 (mmp) cc_final: 0.9107 (mmm) REVERT: C 1180 MET cc_start: 0.9046 (tpp) cc_final: 0.8771 (tpp) REVERT: C 1232 MET cc_start: 0.9061 (mmm) cc_final: 0.8800 (mmm) REVERT: C 1281 TYR cc_start: 0.8237 (m-10) cc_final: 0.8013 (m-10) REVERT: C 1286 THR cc_start: 0.9680 (p) cc_final: 0.9462 (p) REVERT: D 130 MET cc_start: 0.8746 (mmp) cc_final: 0.8469 (mmm) REVERT: D 237 MET cc_start: 0.9168 (ttt) cc_final: 0.8548 (tpp) REVERT: D 245 LEU cc_start: 0.9427 (tp) cc_final: 0.9161 (tp) REVERT: D 298 MET cc_start: 0.9240 (ttp) cc_final: 0.8738 (tmm) REVERT: D 329 ASP cc_start: 0.9510 (m-30) cc_final: 0.9240 (m-30) REVERT: D 330 MET cc_start: 0.9013 (mmp) cc_final: 0.8618 (mmp) REVERT: D 449 LEU cc_start: 0.9409 (mm) cc_final: 0.9034 (tp) REVERT: D 454 CYS cc_start: 0.9127 (m) cc_final: 0.8611 (m) REVERT: D 479 GLU cc_start: 0.9009 (tt0) cc_final: 0.8406 (pt0) REVERT: D 485 MET cc_start: 0.9005 (tpt) cc_final: 0.8802 (tpp) REVERT: D 604 MET cc_start: 0.9519 (mmt) cc_final: 0.9085 (mmm) REVERT: D 608 CYS cc_start: 0.9257 (t) cc_final: 0.9025 (t) REVERT: D 625 MET cc_start: 0.9549 (tmm) cc_final: 0.9264 (tmm) REVERT: D 644 MET cc_start: 0.8942 (mpp) cc_final: 0.8622 (mpp) REVERT: D 697 MET cc_start: 0.9150 (tmm) cc_final: 0.8407 (tmm) REVERT: D 698 MET cc_start: 0.9394 (mmm) cc_final: 0.8682 (mmt) REVERT: D 747 MET cc_start: 0.9264 (mmp) cc_final: 0.8877 (mmp) REVERT: D 821 MET cc_start: 0.9000 (mmp) cc_final: 0.8724 (tpp) REVERT: D 915 ILE cc_start: 0.9322 (pt) cc_final: 0.8846 (mt) REVERT: D 982 LEU cc_start: 0.9751 (tp) cc_final: 0.9549 (pp) REVERT: D 1025 MET cc_start: 0.8401 (tpt) cc_final: 0.8112 (tpt) REVERT: D 1189 MET cc_start: 0.8695 (tpt) cc_final: 0.8308 (tpp) REVERT: D 1326 GLN cc_start: 0.8766 (mt0) cc_final: 0.8379 (mt0) REVERT: E 36 ASP cc_start: 0.9258 (p0) cc_final: 0.8861 (p0) REVERT: E 53 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9062 (mm-30) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3523 time to fit residues: 101.4242 Evaluate side-chains 141 residues out of total 2717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 254 optimal weight: 9.9990 chunk 106 optimal weight: 0.0970 chunk 261 optimal weight: 7.9990 chunk 32 optimal weight: 0.0050 chunk 46 optimal weight: 8.9990 overall best weight: 2.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 ASN D 365 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.032845 restraints weight = 217297.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.033921 restraints weight = 132248.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034707 restraints weight = 93061.708| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26550 Z= 0.177 Angle : 0.605 11.790 36082 Z= 0.310 Chirality : 0.043 0.196 4124 Planarity : 0.004 0.052 4543 Dihedral : 13.468 146.877 4127 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 3172 helix: 0.22 (0.16), residues: 1091 sheet: -0.87 (0.27), residues: 340 loop : -1.77 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C1276 HIS 0.004 0.001 HIS C 150 PHE 0.012 0.001 PHE C 828 TYR 0.016 0.001 TYR C 367 ARG 0.007 0.000 ARG D 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.89 seconds wall clock time: 75 minutes 59.03 seconds (4559.03 seconds total)