Starting phenix.real_space_refine on Wed Feb 21 02:53:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf0_34707/02_2024/8hf0_34707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf0_34707/02_2024/8hf0_34707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf0_34707/02_2024/8hf0_34707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf0_34707/02_2024/8hf0_34707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf0_34707/02_2024/8hf0_34707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf0_34707/02_2024/8hf0_34707.pdb" } resolution = 3.72 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= 0.007 sd= 0.046 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: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 153 5.16 5 C 18503 2.51 5 N 5028 2.21 5 O 5729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1213": "OE1" <-> "OE2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A GLU 1534": "OE1" <-> "OE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 794": "OE1" <-> "OE2" Residue "D PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 941": "OE1" <-> "OE2" Residue "D PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 245": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29510 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1027 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "E" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1010 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1003 Classifications: {'RNA': 47} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 25, 'rna3p_pyr': 21} Link IDs: {'rna3p': 46} Chain: "N" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1058 Classifications: {'RNA': 50} Modifications used: {'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna3p': 49} Time building chain proxies: 15.96, per 1000 atoms: 0.54 Number of scatterers: 29510 At special positions: 0 Unit cell: (160.056, 174.02, 183.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 153 16.00 P 97 15.00 O 5729 8.00 N 5028 7.00 C 18503 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: 11.87 Conformation dependent library (CDL) restraints added in 4.7 seconds 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 26 sheets defined 55.3% alpha, 11.7% beta 42 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 10.34 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 Processing helix chain 'A' and resid 31 through 45 removed outlier: 4.082A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.588A pdb=" N PHE A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 50' Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.592A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.609A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.644A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 316 through 345 removed outlier: 3.642A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.606A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.858A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 removed outlier: 3.633A pdb=" N THR A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 608 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 4.303A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.661A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.802A pdb=" N ASN A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.604A pdb=" N LEU A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 916 through 930 removed outlier: 6.987A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 983 through 990 removed outlier: 4.574A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.734A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.764A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.926A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1266 Proline residue: A1263 - end of helix Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.725A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.581A pdb=" N LEU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1339 Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 6.030A pdb=" N PHE A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1387 removed outlier: 3.577A pdb=" N LEU A1370 " --> pdb=" O ILE A1366 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A1380 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1393 removed outlier: 4.136A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.778A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.572A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.860A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1547 Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.219A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix removed outlier: 4.009A pdb=" N ARG A1650 " --> pdb=" O GLN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1701 through 1721 Processing helix chain 'C' and resid 189 through 210 removed outlier: 4.057A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 4.591A pdb=" N PHE C 227 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 249 through 260 removed outlier: 3.512A pdb=" N LYS C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 removed outlier: 3.693A pdb=" N TYR C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.890A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.583A pdb=" N PHE D 49 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 50' Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 66 through 81 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 116 through 125 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 140 through 144 removed outlier: 3.530A pdb=" N HIS D 143 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.687A pdb=" N THR D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 removed outlier: 3.522A pdb=" N LEU D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.871A pdb=" N LYS D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.975A pdb=" N MET D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 250 removed outlier: 4.301A pdb=" N ARG D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 292 Processing helix chain 'D' and resid 292 through 314 removed outlier: 3.946A pdb=" N ILE D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 343 Processing helix chain 'D' and resid 344 through 348 removed outlier: 3.635A pdb=" N ASP D 347 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.916A pdb=" N ILE D 359 " --> pdb=" O THR D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 Processing helix chain 'D' and resid 382 through 386 removed outlier: 3.759A pdb=" N ILE D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 412 removed outlier: 3.517A pdb=" N CYS D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 4.332A pdb=" N VAL D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 510 through 535 Processing helix chain 'D' and resid 543 through 552 Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 570 through 582 removed outlier: 3.636A pdb=" N ILE D 582 " --> pdb=" O TYR D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 608 through 611 Processing helix chain 'D' and resid 637 through 656 Processing helix chain 'D' and resid 667 through 680 removed outlier: 3.906A pdb=" N ILE D 675 " --> pdb=" O ARG D 671 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP D 677 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 687 removed outlier: 3.628A pdb=" N LYS D 685 " --> pdb=" O HIS D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 697 Processing helix chain 'D' and resid 741 through 748 removed outlier: 3.856A pdb=" N LEU D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 810 Processing helix chain 'D' and resid 845 through 852 Processing helix chain 'D' and resid 862 through 866 Processing helix chain 'D' and resid 873 through 878 removed outlier: 3.551A pdb=" N PHE D 877 " --> pdb=" O ARG D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 930 removed outlier: 7.520A pdb=" N ASN D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG D 928 " --> pdb=" O LYS D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 965 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 982 through 1017 Proline residue: D 993 - end of helix Processing helix chain 'D' and resid 1018 through 1025 Proline residue: D1022 - end of helix Processing helix chain 'D' and resid 1174 through 1182 Processing helix chain 'D' and resid 1183 through 1186 Processing helix chain 'D' and resid 1190 through 1199 Processing helix chain 'D' and resid 1209 through 1232 removed outlier: 4.071A pdb=" N LEU D1215 " --> pdb=" O ARG D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1248 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 3.766A pdb=" N ASP D1259 " --> pdb=" O PHE D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1262 through 1266 removed outlier: 3.587A pdb=" N LEU D1266 " --> pdb=" O PRO D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1272 through 1277 removed outlier: 3.806A pdb=" N TRP D1277 " --> pdb=" O PRO D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1285 through 1295 Processing helix chain 'D' and resid 1297 through 1302 removed outlier: 3.506A pdb=" N LYS D1300 " --> pdb=" O GLU D1297 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D1301 " --> pdb=" O PHE D1298 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D1302 " --> pdb=" O ALA D1299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1297 through 1302' Processing helix chain 'D' and resid 1303 through 1308 Processing helix chain 'D' and resid 1313 through 1319 Processing helix chain 'D' and resid 1324 through 1337 Processing helix chain 'D' and resid 1338 through 1341 removed outlier: 3.538A pdb=" N SER D1341 " --> pdb=" O ASN D1338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1338 through 1341' Processing helix chain 'D' and resid 1348 through 1351 removed outlier: 3.598A pdb=" N GLU D1351 " --> pdb=" O PHE D1348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1348 through 1351' Processing helix chain 'D' and resid 1352 through 1357 removed outlier: 3.695A pdb=" N VAL D1356 " --> pdb=" O VAL D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1387 removed outlier: 8.005A pdb=" N LEU D1383 " --> pdb=" O LYS D1379 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLN D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS D1385 " --> pdb=" O TYR D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1387 through 1393 removed outlier: 4.117A pdb=" N GLU D1391 " --> pdb=" O PHE D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1403 through 1407 Processing helix chain 'D' and resid 1422 through 1428 Processing helix chain 'D' and resid 1432 through 1441 Processing helix chain 'D' and resid 1446 through 1455 removed outlier: 4.392A pdb=" N LEU D1450 " --> pdb=" O ASP D1446 " (cutoff:3.500A) Processing helix chain 'D' and resid 1468 through 1491 removed outlier: 3.805A pdb=" N ILE D1474 " --> pdb=" O GLU D1470 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D1477 " --> pdb=" O PHE D1473 " (cutoff:3.500A) Processing helix chain 'D' and resid 1495 through 1508 Processing helix chain 'D' and resid 1508 through 1519 Processing helix chain 'D' and resid 1521 through 1525 Processing helix chain 'D' and resid 1529 through 1546 Processing helix chain 'D' and resid 1609 through 1628 removed outlier: 4.340A pdb=" N GLY D1613 " --> pdb=" O PRO D1609 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D1616 " --> pdb=" O LEU D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1629 through 1651 Proline residue: D1643 - end of helix Processing helix chain 'D' and resid 1655 through 1663 Processing helix chain 'D' and resid 1701 through 1721 Processing helix chain 'E' and resid 189 through 210 removed outlier: 3.913A pdb=" N ARG E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 4.237A pdb=" N PHE E 227 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE E 230 " --> pdb=" O PHE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 243 removed outlier: 3.997A pdb=" N GLU E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 261 Processing helix chain 'E' and resid 295 through 310 removed outlier: 4.620A pdb=" N TYR E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.599A pdb=" N THR A 115 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLY A 24 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR A 172 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 26 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.259A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.540A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.568A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 771 removed outlier: 4.793A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.082A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 897 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 895 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1554 through 1558 removed outlier: 6.639A pdb=" N MET A1602 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A1603 " --> pdb=" O PHE A1698 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1554 through 1558 removed outlier: 6.639A pdb=" N MET A1602 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A1603 " --> pdb=" O PHE A1698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 268 through 270 removed outlier: 4.247A pdb=" N LEU C 278 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.549A pdb=" N VAL D 113 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 115 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA D 60 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY D 114 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE D 62 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG D 59 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 135 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 61 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER D 134 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL D 169 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 136 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU D 171 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 138 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 172 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE D 25 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 219 through 225 removed outlier: 6.595A pdb=" N VAL D 476 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE D 505 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE D 478 " --> pdb=" O PHE D 505 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ALA D 507 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS D 388 " --> pdb=" O MET D 458 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS D 460 " --> pdb=" O CYS D 388 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL D 390 " --> pdb=" O CYS D 460 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 422 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 260 through 261 removed outlier: 4.362A pdb=" N ARG D 260 " --> pdb=" O ARG D 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AB9, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC1, first strand: chain 'D' and resid 703 through 706 Processing sheet with id=AC2, first strand: chain 'D' and resid 768 through 771 Processing sheet with id=AC3, first strand: chain 'D' and resid 768 through 771 removed outlier: 3.585A pdb=" N ILE D 729 " --> pdb=" O TYR D 754 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR D 754 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 830 " --> pdb=" O LEU D 757 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 819 through 820 Processing sheet with id=AC5, first strand: chain 'D' and resid 970 through 971 removed outlier: 3.794A pdb=" N LEU D 971 " --> pdb=" O ILE D 940 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG D 943 " --> pdb=" O VAL D 895 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL D 895 " --> pdb=" O ARG D 943 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1554 through 1558 removed outlier: 7.347A pdb=" N MET D1602 " --> pdb=" O LEU D1557 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D1603 " --> pdb=" O PHE D1698 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1554 through 1558 removed outlier: 7.347A pdb=" N MET D1602 " --> pdb=" O LEU D1557 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D1603 " --> pdb=" O PHE D1698 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 267 through 270 removed outlier: 4.311A pdb=" N LEU E 278 " --> pdb=" O VAL E 270 " (cutoff:3.500A) 1392 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 15.47 Time building geometry restraints manager: 12.72 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: 9107 1.34 - 1.46: 5382 1.46 - 1.58: 15411 1.58 - 1.70: 192 1.70 - 1.82: 242 Bond restraints: 30334 Sorted by residual: bond pdb=" CG1 ILE D1258 " pdb=" CD1 ILE D1258 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 bond pdb=" CG LEU C 193 " pdb=" CD1 LEU C 193 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB GLU A1371 " pdb=" CG GLU A1371 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" C ILE D1262 " pdb=" N PRO D1263 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" CA MET A 967 " pdb=" CB MET A 967 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.21e-02 6.83e+03 1.26e+00 ... (remaining 30329 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.16: 787 104.16 - 111.63: 13976 111.63 - 119.10: 10795 119.10 - 126.57: 15344 126.57 - 134.04: 586 Bond angle restraints: 41488 Sorted by residual: angle pdb=" N GLY D 957 " pdb=" CA GLY D 957 " pdb=" C GLY D 957 " ideal model delta sigma weight residual 111.35 116.42 -5.07 1.20e+00 6.94e-01 1.79e+01 angle pdb=" CB MET A 620 " pdb=" CG MET A 620 " pdb=" SD MET A 620 " ideal model delta sigma weight residual 112.70 125.37 -12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CG ARG B 346 " pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " ideal model delta sigma weight residual 112.00 119.73 -7.73 2.20e+00 2.07e-01 1.24e+01 angle pdb=" CA ALA C 286 " pdb=" C ALA C 286 " pdb=" N PHE C 287 " ideal model delta sigma weight residual 118.27 113.51 4.76 1.59e+00 3.96e-01 8.98e+00 angle pdb=" N ILE D 582 " pdb=" CA ILE D 582 " pdb=" C ILE D 582 " ideal model delta sigma weight residual 108.88 115.26 -6.38 2.16e+00 2.14e-01 8.72e+00 ... (remaining 41483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.45: 17791 31.45 - 62.90: 596 62.90 - 94.34: 146 94.34 - 125.79: 1 125.79 - 157.24: 1 Dihedral angle restraints: 18535 sinusoidal: 8537 harmonic: 9998 Sorted by residual: dihedral pdb=" CA CYS C 285 " pdb=" C CYS C 285 " pdb=" N ALA C 286 " pdb=" CA ALA C 286 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N TRP D 102 " pdb=" CA TRP D 102 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG A 427 " pdb=" C ARG A 427 " pdb=" N ASN A 428 " pdb=" CA ASN A 428 " ideal model delta harmonic sigma weight residual 180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 18532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3260 0.035 - 0.070: 1026 0.070 - 0.105: 342 0.105 - 0.140: 97 0.140 - 0.175: 8 Chirality restraints: 4733 Sorted by residual: chirality pdb=" C3' C N 27 " pdb=" C4' C N 27 " pdb=" O3' C N 27 " pdb=" C2' C N 27 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ILE A1654 " pdb=" N ILE A1654 " pdb=" C ILE A1654 " pdb=" CB ILE A1654 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CG LEU D 992 " pdb=" CB LEU D 992 " pdb=" CD1 LEU D 992 " pdb=" CD2 LEU D 992 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 4730 not shown) Planarity restraints: 4953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 370 " 0.015 2.00e-02 2.50e+03 1.65e-02 4.76e+00 pdb=" CG PHE A 370 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 370 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 370 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 370 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 370 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 903 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO D 904 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 904 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 904 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 101 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C MET D 101 " -0.032 2.00e-02 2.50e+03 pdb=" O MET D 101 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP D 102 " 0.011 2.00e-02 2.50e+03 ... (remaining 4950 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 895 2.71 - 3.25: 31454 3.25 - 3.80: 49744 3.80 - 4.35: 63108 4.35 - 4.90: 99879 Nonbonded interactions: 245080 Sorted by model distance: nonbonded pdb=" OG SER D 264 " pdb=" OE1 GLN D 266 " model vdw 2.157 2.440 nonbonded pdb=" OG SER E 244 " pdb=" OE1 GLU E 246 " model vdw 2.165 2.440 nonbonded pdb=" OG1 THR D 182 " pdb=" OP1 A N 18 " model vdw 2.175 2.440 nonbonded pdb=" OD1 ASP A 944 " pdb=" N LEU A 945 " model vdw 2.188 2.520 nonbonded pdb=" O LEU A 341 " pdb=" OG1 THR A 345 " model vdw 2.195 2.440 ... (remaining 245075 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' selection = chain 'D' } ncs_group { reference = (chain 'C' and resid 188 through 311) selection = chain 'E' } ncs_group { reference = (chain 'N' and resid 3 through 47) selection = (chain 'P' and resid 3 through 47) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.030 Extract box with map and model: 5.160 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 86.740 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30334 Z= 0.176 Angle : 0.574 12.674 41488 Z= 0.300 Chirality : 0.040 0.175 4733 Planarity : 0.004 0.053 4953 Dihedral : 15.853 157.241 12047 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.15), residues: 3370 helix: 0.87 (0.13), residues: 1591 sheet: -0.57 (0.26), residues: 363 loop : -0.18 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 814 HIS 0.014 0.001 HIS C 224 PHE 0.038 0.001 PHE A 370 TYR 0.014 0.001 TYR D1328 ARG 0.007 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.246 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 176 ILE cc_start: 0.7060 (mm) cc_final: 0.6686 (mm) REVERT: A 317 LEU cc_start: 0.8314 (tp) cc_final: 0.7983 (tp) REVERT: A 494 ARG cc_start: 0.6537 (mmp-170) cc_final: 0.6140 (mmm160) REVERT: A 531 TYR cc_start: 0.8574 (t80) cc_final: 0.8354 (t80) REVERT: C 223 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.7510 (ptt-90) REVERT: D 714 TYR cc_start: 0.8793 (t80) cc_final: 0.8513 (t80) REVERT: D 794 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8275 (pp20) REVERT: D 1209 MET cc_start: 0.7871 (mtm) cc_final: 0.7411 (mtm) REVERT: D 1333 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8916 (pt0) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3767 time to fit residues: 185.5991 Evaluate side-chains 223 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 3.9990 chunk 262 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 104 optimal weight: 0.0270 chunk 164 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS D 253 ASN D 287 GLN D 747 ASN ** D 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 960 ASN D1305 HIS ** D1605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30334 Z= 0.226 Angle : 0.597 10.596 41488 Z= 0.307 Chirality : 0.041 0.268 4733 Planarity : 0.004 0.048 4953 Dihedral : 14.165 157.146 5192 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 0.92 % Allowed : 6.88 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.15), residues: 3370 helix: 0.94 (0.13), residues: 1607 sheet: -0.62 (0.26), residues: 374 loop : -0.24 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 814 HIS 0.006 0.001 HIS D1185 PHE 0.019 0.002 PHE A1342 TYR 0.016 0.001 TYR A1468 ARG 0.005 0.000 ARG D 719 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8319 (mpp80) REVERT: A 531 TYR cc_start: 0.8673 (t80) cc_final: 0.8456 (t80) REVERT: A 589 PHE cc_start: 0.7590 (t80) cc_final: 0.7384 (t80) REVERT: A 620 MET cc_start: 0.8700 (mmm) cc_final: 0.8177 (mmm) REVERT: A 907 TYR cc_start: 0.7977 (m-80) cc_final: 0.7629 (m-80) REVERT: A 939 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6904 (mmp) REVERT: A 1417 MET cc_start: 0.1667 (tpt) cc_final: 0.1394 (tpt) REVERT: C 223 ARG cc_start: 0.7898 (ptt-90) cc_final: 0.7664 (ptm-80) REVERT: D 154 MET cc_start: 0.8902 (mmm) cc_final: 0.8548 (mmm) REVERT: D 156 LEU cc_start: 0.9100 (tp) cc_final: 0.8874 (tp) REVERT: D 238 ILE cc_start: 0.9506 (mt) cc_final: 0.9305 (mp) REVERT: D 747 ASN cc_start: 0.8403 (t0) cc_final: 0.8061 (t0) REVERT: D 794 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8265 (pp20) REVERT: D 992 LEU cc_start: 0.8412 (mm) cc_final: 0.8067 (mm) REVERT: D 1209 MET cc_start: 0.7828 (mtm) cc_final: 0.7386 (mtm) REVERT: D 1614 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8100 (t0) REVERT: D 1681 MET cc_start: 0.7710 (tmm) cc_final: 0.7446 (tmm) outliers start: 28 outliers final: 18 residues processed: 257 average time/residue: 0.4146 time to fit residues: 179.3824 Evaluate side-chains 240 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 261 optimal weight: 0.0980 chunk 213 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 314 optimal weight: 0.6980 chunk 340 optimal weight: 20.0000 chunk 280 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 734 GLN D 778 HIS D1191 GLN D1605 ASN D1704 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 30334 Z= 0.137 Angle : 0.534 10.798 41488 Z= 0.271 Chirality : 0.039 0.188 4733 Planarity : 0.004 0.043 4953 Dihedral : 14.051 158.005 5192 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 0.66 % Allowed : 9.44 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.15), residues: 3370 helix: 1.15 (0.13), residues: 1606 sheet: -0.54 (0.26), residues: 375 loop : -0.27 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 97 HIS 0.006 0.001 HIS A 335 PHE 0.016 0.001 PHE D 981 TYR 0.014 0.001 TYR A 519 ARG 0.005 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8164 (mmm) cc_final: 0.7696 (mmm) REVERT: A 362 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5805 (m-10) REVERT: A 589 PHE cc_start: 0.7552 (t80) cc_final: 0.7325 (t80) REVERT: A 829 TYR cc_start: 0.7759 (p90) cc_final: 0.6829 (p90) REVERT: A 907 TYR cc_start: 0.7901 (m-80) cc_final: 0.7680 (m-80) REVERT: A 939 MET cc_start: 0.7320 (tpp) cc_final: 0.7007 (mmp) REVERT: A 1417 MET cc_start: 0.1656 (tpt) cc_final: 0.1374 (tpt) REVERT: B 357 ILE cc_start: 0.8266 (mm) cc_final: 0.7969 (mm) REVERT: D 156 LEU cc_start: 0.9012 (tp) cc_final: 0.8804 (tp) REVERT: D 208 MET cc_start: 0.7444 (mmm) cc_final: 0.7121 (mmp) REVERT: D 344 MET cc_start: 0.7535 (ppp) cc_final: 0.7212 (ppp) REVERT: D 714 TYR cc_start: 0.8794 (t80) cc_final: 0.8519 (t80) REVERT: D 719 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8417 (mtm-85) REVERT: D 747 ASN cc_start: 0.8309 (t0) cc_final: 0.7965 (t0) REVERT: D 794 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8297 (pp20) REVERT: D 805 MET cc_start: 0.7711 (ppp) cc_final: 0.7095 (ppp) REVERT: D 922 MET cc_start: 0.7046 (mmt) cc_final: 0.6840 (mmt) REVERT: D 939 MET cc_start: 0.3771 (ppp) cc_final: 0.1671 (ptp) REVERT: D 992 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8127 (mm) REVERT: D 1002 LEU cc_start: 0.9009 (tt) cc_final: 0.8760 (tp) REVERT: D 1681 MET cc_start: 0.7797 (tmm) cc_final: 0.7487 (tmm) REVERT: E 309 MET cc_start: 0.8737 (mmp) cc_final: 0.8520 (mmp) outliers start: 20 outliers final: 12 residues processed: 264 average time/residue: 0.4042 time to fit residues: 178.6153 Evaluate side-chains 235 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 6.9990 chunk 236 optimal weight: 0.2980 chunk 163 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 211 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30334 Z= 0.193 Angle : 0.544 12.453 41488 Z= 0.278 Chirality : 0.039 0.212 4733 Planarity : 0.004 0.044 4953 Dihedral : 14.037 157.531 5192 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 10.71 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.15), residues: 3370 helix: 1.14 (0.13), residues: 1621 sheet: -0.57 (0.26), residues: 367 loop : -0.30 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 814 HIS 0.004 0.001 HIS D 682 PHE 0.015 0.001 PHE A1001 TYR 0.017 0.001 TYR A 531 ARG 0.004 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8328 (tp) cc_final: 0.7942 (tt) REVERT: A 344 MET cc_start: 0.8219 (mmm) cc_final: 0.7733 (mmm) REVERT: A 362 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.6066 (m-10) REVERT: A 589 PHE cc_start: 0.7604 (t80) cc_final: 0.7395 (t80) REVERT: A 620 MET cc_start: 0.8689 (mmm) cc_final: 0.8285 (mmm) REVERT: A 893 MET cc_start: 0.8056 (mpp) cc_final: 0.7790 (mpp) REVERT: A 907 TYR cc_start: 0.7957 (m-80) cc_final: 0.7658 (m-80) REVERT: A 908 MET cc_start: 0.6032 (mmm) cc_final: 0.5351 (mmt) REVERT: A 939 MET cc_start: 0.7441 (tpp) cc_final: 0.7162 (mmp) REVERT: A 1417 MET cc_start: 0.1837 (tpt) cc_final: 0.1588 (tpt) REVERT: B 357 ILE cc_start: 0.8274 (mm) cc_final: 0.8062 (mm) REVERT: C 219 ARG cc_start: 0.8308 (tpt-90) cc_final: 0.7897 (tpt-90) REVERT: D 156 LEU cc_start: 0.9051 (tp) cc_final: 0.8812 (tp) REVERT: D 208 MET cc_start: 0.7581 (mmm) cc_final: 0.7163 (mmp) REVERT: D 344 MET cc_start: 0.7779 (ppp) cc_final: 0.7391 (ppp) REVERT: D 719 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8384 (mtm-85) REVERT: D 747 ASN cc_start: 0.8366 (t0) cc_final: 0.8039 (t0) REVERT: D 805 MET cc_start: 0.7602 (ppp) cc_final: 0.7022 (ppp) REVERT: D 939 MET cc_start: 0.3758 (ppp) cc_final: 0.2031 (ptp) REVERT: D 992 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8091 (mm) REVERT: D 1002 LEU cc_start: 0.9059 (tt) cc_final: 0.8849 (tp) REVERT: D 1207 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8065 (p90) REVERT: D 1209 MET cc_start: 0.7823 (mtm) cc_final: 0.7454 (mtm) REVERT: D 1681 MET cc_start: 0.7844 (tmm) cc_final: 0.7492 (tmm) outliers start: 46 outliers final: 32 residues processed: 253 average time/residue: 0.3735 time to fit residues: 158.1010 Evaluate side-chains 245 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 460 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1207 PHE Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1607 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 4 optimal weight: 0.0060 chunk 249 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 285 optimal weight: 20.0000 chunk 231 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30334 Z= 0.132 Angle : 0.522 14.190 41488 Z= 0.263 Chirality : 0.039 0.240 4733 Planarity : 0.003 0.048 4953 Dihedral : 13.964 157.755 5192 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.28 % Allowed : 11.80 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.15), residues: 3370 helix: 1.21 (0.13), residues: 1627 sheet: -0.51 (0.26), residues: 374 loop : -0.33 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 814 HIS 0.004 0.001 HIS D 227 PHE 0.014 0.001 PHE D 370 TYR 0.022 0.001 TYR A 531 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8238 (mmm) cc_final: 0.7719 (mmm) REVERT: A 362 PHE cc_start: 0.6262 (OUTLIER) cc_final: 0.5889 (m-10) REVERT: A 589 PHE cc_start: 0.7566 (t80) cc_final: 0.7330 (t80) REVERT: A 893 MET cc_start: 0.8167 (mpp) cc_final: 0.7866 (mpp) REVERT: A 907 TYR cc_start: 0.7919 (m-80) cc_final: 0.7660 (m-80) REVERT: A 908 MET cc_start: 0.5953 (mmm) cc_final: 0.5379 (mmt) REVERT: A 939 MET cc_start: 0.7435 (tpp) cc_final: 0.7221 (mmp) REVERT: A 1417 MET cc_start: 0.1925 (tpt) cc_final: 0.1697 (tpt) REVERT: B 357 ILE cc_start: 0.8331 (mm) cc_final: 0.7832 (mm) REVERT: C 219 ARG cc_start: 0.8323 (tpt-90) cc_final: 0.7862 (tpt-90) REVERT: C 258 MET cc_start: 0.7922 (ppp) cc_final: 0.7704 (ppp) REVERT: C 263 ILE cc_start: 0.8028 (mm) cc_final: 0.7301 (mm) REVERT: D 156 LEU cc_start: 0.8970 (tp) cc_final: 0.8735 (tp) REVERT: D 208 MET cc_start: 0.7541 (mmm) cc_final: 0.7132 (mmp) REVERT: D 344 MET cc_start: 0.7702 (ppp) cc_final: 0.7260 (ppp) REVERT: D 714 TYR cc_start: 0.8806 (t80) cc_final: 0.8508 (t80) REVERT: D 719 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8236 (mtm-85) REVERT: D 779 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (p) REVERT: D 794 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8322 (pp20) REVERT: D 805 MET cc_start: 0.7579 (ppp) cc_final: 0.7020 (ppp) REVERT: D 939 MET cc_start: 0.3771 (ppp) cc_final: 0.2123 (ptp) REVERT: D 992 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8071 (mm) REVERT: D 1002 LEU cc_start: 0.8967 (tt) cc_final: 0.8759 (tp) REVERT: D 1207 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7903 (p90) REVERT: D 1333 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8855 (pt0) REVERT: D 1681 MET cc_start: 0.7897 (tmm) cc_final: 0.7600 (tmm) REVERT: E 309 MET cc_start: 0.8967 (mmp) cc_final: 0.8760 (mmp) outliers start: 39 outliers final: 22 residues processed: 264 average time/residue: 0.3998 time to fit residues: 178.1320 Evaluate side-chains 240 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1207 PHE Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 0.9990 chunk 301 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 334 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A1509 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30334 Z= 0.198 Angle : 0.552 14.241 41488 Z= 0.279 Chirality : 0.039 0.209 4733 Planarity : 0.004 0.049 4953 Dihedral : 13.957 157.337 5192 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.77 % Allowed : 12.19 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.15), residues: 3370 helix: 1.18 (0.13), residues: 1634 sheet: -0.55 (0.25), residues: 379 loop : -0.36 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 814 HIS 0.009 0.001 HIS C 224 PHE 0.018 0.001 PHE A 153 TYR 0.022 0.001 TYR A 519 ARG 0.004 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8339 (tp) cc_final: 0.7964 (tt) REVERT: A 344 MET cc_start: 0.8182 (mmm) cc_final: 0.7697 (mmm) REVERT: A 589 PHE cc_start: 0.7604 (t80) cc_final: 0.7370 (t80) REVERT: A 907 TYR cc_start: 0.8075 (m-80) cc_final: 0.7742 (m-80) REVERT: A 908 MET cc_start: 0.6286 (mmm) cc_final: 0.5748 (mmt) REVERT: C 219 ARG cc_start: 0.8311 (tpt-90) cc_final: 0.7799 (tpt-90) REVERT: C 225 ASN cc_start: 0.8011 (t0) cc_final: 0.7617 (t0) REVERT: C 266 LYS cc_start: 0.8381 (mppt) cc_final: 0.8064 (mppt) REVERT: D 156 LEU cc_start: 0.9044 (tp) cc_final: 0.8806 (tp) REVERT: D 208 MET cc_start: 0.7694 (mmm) cc_final: 0.7261 (mmp) REVERT: D 344 MET cc_start: 0.7910 (ppp) cc_final: 0.7450 (ppp) REVERT: D 719 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8289 (mtm-85) REVERT: D 794 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8330 (pp20) REVERT: D 805 MET cc_start: 0.7533 (ppp) cc_final: 0.6963 (ppp) REVERT: D 992 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8055 (mm) REVERT: D 1029 MET cc_start: 0.7837 (mmm) cc_final: 0.7466 (mmm) REVERT: D 1209 MET cc_start: 0.7835 (mtm) cc_final: 0.7463 (mtm) REVERT: D 1333 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8850 (pt0) REVERT: D 1681 MET cc_start: 0.7924 (tmm) cc_final: 0.7636 (tmm) outliers start: 54 outliers final: 36 residues processed: 261 average time/residue: 0.3796 time to fit residues: 166.3473 Evaluate side-chains 254 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1607 ASP Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 333 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 841 GLN D 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30334 Z= 0.337 Angle : 0.651 12.888 41488 Z= 0.333 Chirality : 0.042 0.274 4733 Planarity : 0.004 0.050 4953 Dihedral : 14.121 156.893 5192 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.31 % Rotamer: Outliers : 2.00 % Allowed : 12.75 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.14), residues: 3370 helix: 0.88 (0.13), residues: 1614 sheet: -0.87 (0.25), residues: 369 loop : -0.50 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 205 HIS 0.013 0.001 HIS C 224 PHE 0.016 0.002 PHE A 938 TYR 0.024 0.002 TYR A 531 ARG 0.005 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8431 (mpp80) REVERT: A 322 MET cc_start: 0.8960 (ttp) cc_final: 0.8721 (ttp) REVERT: A 344 MET cc_start: 0.8169 (mmm) cc_final: 0.7650 (mmm) REVERT: A 424 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8265 (ppp) REVERT: A 849 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8135 (mtp) REVERT: A 908 MET cc_start: 0.6785 (mmm) cc_final: 0.6262 (mmt) REVERT: C 258 MET cc_start: 0.8057 (ppp) cc_final: 0.7821 (ppp) REVERT: D 208 MET cc_start: 0.7836 (mmm) cc_final: 0.7372 (mmp) REVERT: D 344 MET cc_start: 0.8142 (ppp) cc_final: 0.7681 (ppp) REVERT: D 768 MET cc_start: 0.8717 (tpt) cc_final: 0.8441 (tpt) REVERT: D 805 MET cc_start: 0.7585 (ppp) cc_final: 0.7020 (ppp) REVERT: D 992 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8111 (mm) REVERT: D 1029 MET cc_start: 0.7724 (mmm) cc_final: 0.7377 (mmm) REVERT: D 1209 MET cc_start: 0.8048 (mtm) cc_final: 0.7670 (mtm) REVERT: D 1333 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8963 (pt0) REVERT: D 1681 MET cc_start: 0.7934 (tmm) cc_final: 0.7606 (tmm) outliers start: 61 outliers final: 50 residues processed: 248 average time/residue: 0.3829 time to fit residues: 159.1393 Evaluate side-chains 257 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 203 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 247 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 460 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 940 ILE Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1607 ASP Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A1685 GLN C 301 HIS D 287 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1543 GLN D1656 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 30334 Z= 0.155 Angle : 0.566 15.725 41488 Z= 0.283 Chirality : 0.040 0.314 4733 Planarity : 0.004 0.046 4953 Dihedral : 13.959 156.854 5192 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 1.67 % Allowed : 13.56 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.15), residues: 3370 helix: 1.07 (0.13), residues: 1630 sheet: -0.73 (0.25), residues: 369 loop : -0.40 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1634 HIS 0.007 0.001 HIS C 224 PHE 0.022 0.001 PHE A 370 TYR 0.028 0.001 TYR A 519 ARG 0.004 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 227 time to evaluate : 3.531 Fit side-chains REVERT: A 236 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8415 (mpp80) REVERT: A 322 MET cc_start: 0.8933 (ttp) cc_final: 0.8449 (ttp) REVERT: A 344 MET cc_start: 0.8232 (mmm) cc_final: 0.7660 (mmm) REVERT: A 362 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6314 (m-10) REVERT: A 372 MET cc_start: 0.8139 (mpp) cc_final: 0.7334 (mpp) REVERT: A 805 MET cc_start: 0.8867 (tmm) cc_final: 0.8365 (tmm) REVERT: A 849 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: A 907 TYR cc_start: 0.8031 (m-80) cc_final: 0.7679 (m-80) REVERT: A 908 MET cc_start: 0.6474 (mmm) cc_final: 0.5848 (mmt) REVERT: C 219 ARG cc_start: 0.8247 (tpt-90) cc_final: 0.7814 (tpp80) REVERT: C 258 MET cc_start: 0.8007 (ppp) cc_final: 0.7792 (ppp) REVERT: C 266 LYS cc_start: 0.8222 (mppt) cc_final: 0.8019 (mppt) REVERT: D 42 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8106 (tt) REVERT: D 208 MET cc_start: 0.7738 (mmm) cc_final: 0.7310 (mmp) REVERT: D 344 MET cc_start: 0.7883 (ppp) cc_final: 0.7472 (ppp) REVERT: D 360 MET cc_start: 0.8522 (tpt) cc_final: 0.8109 (tpt) REVERT: D 465 GLU cc_start: 0.6875 (pt0) cc_final: 0.6667 (pt0) REVERT: D 719 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8117 (mtm-85) REVERT: D 794 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8314 (pp20) REVERT: D 805 MET cc_start: 0.7579 (ppp) cc_final: 0.7024 (ppp) REVERT: D 939 MET cc_start: 0.4164 (ppp) cc_final: 0.2210 (mmm) REVERT: D 992 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7897 (mm) REVERT: D 1029 MET cc_start: 0.7749 (mmm) cc_final: 0.7333 (mmm) REVERT: D 1333 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8824 (pt0) REVERT: D 1681 MET cc_start: 0.7943 (tmm) cc_final: 0.7634 (tmm) outliers start: 51 outliers final: 38 residues processed: 264 average time/residue: 0.3829 time to fit residues: 169.6205 Evaluate side-chains 261 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1495 ASN Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 247 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 291 optimal weight: 0.6980 chunk 310 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 309 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 30334 Z= 0.153 Angle : 0.562 17.267 41488 Z= 0.279 Chirality : 0.039 0.312 4733 Planarity : 0.004 0.046 4953 Dihedral : 13.847 156.999 5192 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.64 % Allowed : 13.79 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.15), residues: 3370 helix: 1.15 (0.13), residues: 1632 sheet: -0.62 (0.26), residues: 371 loop : -0.35 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1634 HIS 0.008 0.001 HIS C 224 PHE 0.029 0.001 PHE A 370 TYR 0.022 0.001 TYR A 531 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 3.331 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.8914 (ttp) cc_final: 0.8431 (ttp) REVERT: A 344 MET cc_start: 0.8228 (mmm) cc_final: 0.7635 (mmm) REVERT: A 360 MET cc_start: 0.8036 (tpt) cc_final: 0.7598 (mmt) REVERT: A 362 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: A 372 MET cc_start: 0.8170 (mpp) cc_final: 0.7855 (mpp) REVERT: A 805 MET cc_start: 0.8855 (tmm) cc_final: 0.8388 (tmm) REVERT: A 849 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7812 (mtp) REVERT: A 907 TYR cc_start: 0.8074 (m-80) cc_final: 0.7782 (m-80) REVERT: A 908 MET cc_start: 0.6657 (mmm) cc_final: 0.6044 (mmt) REVERT: A 939 MET cc_start: 0.6968 (mmp) cc_final: 0.6592 (mmm) REVERT: C 219 ARG cc_start: 0.8200 (tpt-90) cc_final: 0.7785 (tpp80) REVERT: C 223 ARG cc_start: 0.7704 (tmm-80) cc_final: 0.7472 (ptt-90) REVERT: D 208 MET cc_start: 0.7772 (mmm) cc_final: 0.7312 (mmp) REVERT: D 344 MET cc_start: 0.7894 (ppp) cc_final: 0.7455 (ppp) REVERT: D 714 TYR cc_start: 0.8846 (t80) cc_final: 0.8617 (t80) REVERT: D 719 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8088 (mtm-85) REVERT: D 794 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8329 (pp20) REVERT: D 805 MET cc_start: 0.7480 (ppp) cc_final: 0.6942 (ppp) REVERT: D 939 MET cc_start: 0.4366 (ppp) cc_final: 0.2990 (ptp) REVERT: D 992 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7897 (mm) REVERT: D 1029 MET cc_start: 0.7618 (mmm) cc_final: 0.7273 (mmm) REVERT: D 1209 MET cc_start: 0.7829 (mtm) cc_final: 0.7620 (mtm) REVERT: D 1333 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8811 (pt0) REVERT: D 1681 MET cc_start: 0.7960 (tmm) cc_final: 0.7613 (tmm) outliers start: 50 outliers final: 43 residues processed: 260 average time/residue: 0.3809 time to fit residues: 165.7060 Evaluate side-chains 266 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1495 ASN Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1474 ILE Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1607 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 200 optimal weight: 0.0010 chunk 155 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 317 optimal weight: 0.9990 chunk 274 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30334 Z= 0.234 Angle : 0.607 17.361 41488 Z= 0.302 Chirality : 0.041 0.284 4733 Planarity : 0.004 0.043 4953 Dihedral : 13.874 156.868 5192 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.57 % Allowed : 14.06 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.15), residues: 3370 helix: 1.07 (0.13), residues: 1630 sheet: -0.69 (0.25), residues: 371 loop : -0.40 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 814 HIS 0.010 0.001 HIS C 224 PHE 0.022 0.001 PHE A 153 TYR 0.022 0.001 TYR A 531 ARG 0.005 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 3.266 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.8921 (ttp) cc_final: 0.8432 (ttp) REVERT: A 344 MET cc_start: 0.8148 (mmm) cc_final: 0.7539 (mmm) REVERT: A 360 MET cc_start: 0.7972 (tpt) cc_final: 0.7512 (mmt) REVERT: A 362 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: A 372 MET cc_start: 0.8065 (mpp) cc_final: 0.7764 (mpp) REVERT: A 805 MET cc_start: 0.8902 (tmm) cc_final: 0.8373 (tmm) REVERT: A 849 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: A 907 TYR cc_start: 0.8153 (m-80) cc_final: 0.7870 (m-80) REVERT: A 908 MET cc_start: 0.6747 (mmm) cc_final: 0.6504 (mmt) REVERT: A 939 MET cc_start: 0.6862 (mmp) cc_final: 0.6451 (mmm) REVERT: A 1417 MET cc_start: 0.1212 (tpt) cc_final: 0.0755 (tpt) REVERT: C 219 ARG cc_start: 0.8249 (tpt-90) cc_final: 0.7810 (tpp80) REVERT: D 208 MET cc_start: 0.7757 (mmm) cc_final: 0.7287 (mmp) REVERT: D 344 MET cc_start: 0.8063 (ppp) cc_final: 0.7630 (ppp) REVERT: D 719 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.8047 (mtm-85) REVERT: D 794 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8299 (pp20) REVERT: D 805 MET cc_start: 0.7517 (ppp) cc_final: 0.6962 (ppp) REVERT: D 814 TRP cc_start: 0.7580 (OUTLIER) cc_final: 0.7357 (t-100) REVERT: D 939 MET cc_start: 0.4661 (ppp) cc_final: 0.3025 (ptp) REVERT: D 992 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (mm) REVERT: D 1029 MET cc_start: 0.7609 (mmm) cc_final: 0.7375 (mmm) REVERT: D 1209 MET cc_start: 0.7918 (mtm) cc_final: 0.7532 (mtm) REVERT: D 1333 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8942 (pt0) REVERT: D 1681 MET cc_start: 0.7964 (tmm) cc_final: 0.7623 (tmm) outliers start: 48 outliers final: 39 residues processed: 249 average time/residue: 0.3970 time to fit residues: 166.4096 Evaluate side-chains 256 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 213 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1495 ASN Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 247 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 814 TRP Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1607 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 5.9990 chunk 292 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 253 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 282 optimal weight: 0.2980 chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 HIS ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.087397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064477 restraints weight = 127526.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067124 restraints weight = 71858.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.067312 restraints weight = 43792.065| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 30334 Z= 0.150 Angle : 0.575 17.327 41488 Z= 0.282 Chirality : 0.039 0.302 4733 Planarity : 0.004 0.044 4953 Dihedral : 13.790 156.952 5192 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.44 % Allowed : 14.15 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.15), residues: 3370 helix: 1.23 (0.13), residues: 1620 sheet: -0.52 (0.26), residues: 367 loop : -0.29 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1634 HIS 0.005 0.001 HIS D1656 PHE 0.028 0.001 PHE A 370 TYR 0.021 0.001 TYR A 531 ARG 0.015 0.000 ARG C 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4946.60 seconds wall clock time: 92 minutes 27.50 seconds (5547.50 seconds total)