Starting phenix.real_space_refine on Sat Jan 20 04:23:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6b_31741/01_2024/7v6b_31741.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6b_31741/01_2024/7v6b_31741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6b_31741/01_2024/7v6b_31741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6b_31741/01_2024/7v6b_31741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6b_31741/01_2024/7v6b_31741.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6b_31741/01_2024/7v6b_31741.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8758 2.51 5 N 2306 2.21 5 O 2489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 732": "OE1" <-> "OE2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A ARG 1041": "NH1" <-> "NH2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A GLU 1315": "OE1" <-> "OE2" Residue "A GLU 1472": "OE1" <-> "OE2" Residue "A GLU 1528": "OE1" <-> "OE2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "A ARG 1555": "NH1" <-> "NH2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1496, 12164 Classifications: {'peptide': 1496} Link IDs: {'PTRANS': 61, 'TRANS': 1434} Chain breaks: 14 Chain: "B" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1469 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 3 Time building chain proxies: 7.55, per 1000 atoms: 0.55 Number of scatterers: 13633 At special positions: 0 Unit cell: (93.375, 158.115, 140.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2489 8.00 N 2306 7.00 C 8758 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: 5.35 Conformation dependent library (CDL) restraints added in 2.4 seconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 54.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.845A pdb=" N GLY A 56 " --> pdb=" O ILE A 53 " (cutoff:3.500A) 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 removed outlier: 3.524A pdb=" N ILE A 106 " --> pdb=" O TRP A 102 " (cutoff:3.500A) 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 141 through 144 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.867A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 Processing helix chain 'A' and resid 292 through 313 removed outlier: 3.760A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 removed outlier: 3.513A pdb=" N LEU A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.834A pdb=" N ASN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.594A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.686A pdb=" N LYS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.573A pdb=" N ARG A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 removed outlier: 3.692A pdb=" N ARG A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 582A Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 638 through 656 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.714A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 4.175A pdb=" N TYR A 686 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.654A pdb=" N LEU A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.504A pdb=" N GLU A 797 " --> pdb=" O SER A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.503A pdb=" N MET A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 removed outlier: 3.849A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.874A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 Processing helix chain 'A' and resid 1087 through 1091 Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.860A pdb=" N LEU A1107 " --> pdb=" O TYR A1103 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A1108 " --> pdb=" O PRO A1104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.619A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 3.829A 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 1260 Processing helix chain 'A' and resid 1261 through 1265 removed outlier: 3.920A pdb=" N LYS A1264 " --> pdb=" O ASP A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1302 removed outlier: 3.783A pdb=" N ILE A1301 " --> pdb=" O GLU A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1309 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1324 through 1341 removed outlier: 3.908A pdb=" N GLY A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 4.265A pdb=" N PHE A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 4.161A pdb=" N ALA A1367 " --> pdb=" O ASN A1363 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 4.439A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 4.045A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1430 " --> pdb=" O ILE A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.510A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.680A pdb=" N PHE A1473 " --> pdb=" O GLN A1469 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1510 through 1519 removed outlier: 3.636A pdb=" N ILE A1515 " --> pdb=" O THR A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1525 removed outlier: 3.737A pdb=" N PHE A1524 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1525 " --> pdb=" O HIS A1522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1521 through 1525' Processing helix chain 'A' and resid 1529 through 1547 removed outlier: 3.545A pdb=" N SER A1545 " --> pdb=" O ASN A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1557 Processing helix chain 'A' and resid 1610 through 1628 removed outlier: 3.549A pdb=" N LEU A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 removed outlier: 3.593A pdb=" N VAL A1636 " --> pdb=" O ARG A1632 " (cutoff:3.500A) Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1701 through 1720 removed outlier: 3.574A pdb=" N LEU A1707 " --> pdb=" O ASP A1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 145 through 164 removed outlier: 3.845A pdb=" N ARG B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 198 removed outlier: 4.456A pdb=" N LEU B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.530A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.086A pdb=" N HIS B 224 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.584A pdb=" N ASP B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 removed outlier: 4.442A pdb=" N TYR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.810A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER A 134 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL A 169 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 136 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 171 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE A 25A" --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 223 removed outlier: 6.483A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS A 388 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 390 " --> pdb=" O CYS A 460 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.580A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768A through 770 Processing sheet with id=AA7, first strand: chain 'A' and resid 768A through 770 removed outlier: 4.598A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.918A pdb=" N LYS A 897 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1669 through 1670 removed outlier: 3.721A pdb=" N CYS A1688 " --> pdb=" O LYS A1691 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.543A pdb=" N CYS B 132 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.764A pdb=" N ALA B 293 " --> pdb=" O LEU B 279 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.54 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2239 1.31 - 1.44: 3671 1.44 - 1.57: 7884 1.57 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 13918 Sorted by residual: bond pdb=" C GLU A 530 " pdb=" O GLU A 530 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.46e+01 bond pdb=" C ARG A 395 " pdb=" O ARG A 395 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.19e-02 7.06e+03 2.58e+01 bond pdb=" CA SER A 46 " pdb=" CB SER A 46 " ideal model delta sigma weight residual 1.528 1.462 0.065 1.35e-02 5.49e+03 2.33e+01 bond pdb=" C ILE A1487 " pdb=" O ILE A1487 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.13e-02 7.83e+03 2.04e+01 bond pdb=" C ASN A 997 " pdb=" O ASN A 997 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.15e-02 7.56e+03 1.93e+01 ... (remaining 13913 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.64: 344 105.64 - 112.85: 6816 112.85 - 120.05: 6529 120.05 - 127.26: 5017 127.26 - 134.46: 107 Bond angle restraints: 18813 Sorted by residual: angle pdb=" N ILE A 995 " pdb=" CA ILE A 995 " pdb=" C ILE A 995 " ideal model delta sigma weight residual 110.82 104.03 6.79 9.70e-01 1.06e+00 4.90e+01 angle pdb=" N ILE A 528 " pdb=" CA ILE A 528 " pdb=" C ILE A 528 " ideal model delta sigma weight residual 110.62 103.85 6.77 1.02e+00 9.61e-01 4.41e+01 angle pdb=" N ILE B 302 " pdb=" CA ILE B 302 " pdb=" C ILE B 302 " ideal model delta sigma weight residual 110.42 104.24 6.18 9.60e-01 1.09e+00 4.14e+01 angle pdb=" N LYS B 251 " pdb=" CA LYS B 251 " pdb=" C LYS B 251 " ideal model delta sigma weight residual 113.30 105.00 8.30 1.34e+00 5.57e-01 3.83e+01 angle pdb=" C GLU A1472 " pdb=" CA GLU A1472 " pdb=" CB GLU A1472 " ideal model delta sigma weight residual 110.88 101.24 9.64 1.57e+00 4.06e-01 3.77e+01 ... (remaining 18808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 7657 17.60 - 35.21: 602 35.21 - 52.81: 132 52.81 - 70.41: 28 70.41 - 88.02: 7 Dihedral angle restraints: 8426 sinusoidal: 3467 harmonic: 4959 Sorted by residual: dihedral pdb=" C PHE A1001 " pdb=" N PHE A1001 " pdb=" CA PHE A1001 " pdb=" CB PHE A1001 " ideal model delta harmonic sigma weight residual -122.60 -133.97 11.37 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" CA GLY A1382 " pdb=" C GLY A1382 " pdb=" N LEU A1383 " pdb=" CA LEU A1383 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C GLU A1472 " pdb=" N GLU A1472 " pdb=" CA GLU A1472 " pdb=" CB GLU A1472 " ideal model delta harmonic sigma weight residual -122.60 -112.66 -9.94 0 2.50e+00 1.60e-01 1.58e+01 ... (remaining 8423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1067 0.065 - 0.129: 747 0.129 - 0.194: 262 0.194 - 0.259: 35 0.259 - 0.323: 7 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CA PHE A1001 " pdb=" N PHE A1001 " pdb=" C PHE A1001 " pdb=" CB PHE A1001 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ARG A 535 " pdb=" N ARG A 535 " pdb=" C ARG A 535 " pdb=" CB ARG A 535 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA TYR A1000 " pdb=" N TYR A1000 " pdb=" C TYR A1000 " pdb=" CB TYR A1000 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2115 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1000 " 0.058 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR A1000 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1000 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1000 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A1000 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A1000 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A1000 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1000 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1488 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PHE A1488 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE A1488 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU A1489 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1013 " 0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASN A1013 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN A1013 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A1014 " 0.021 2.00e-02 2.50e+03 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3598 2.83 - 3.35: 13155 3.35 - 3.86: 21385 3.86 - 4.38: 26921 4.38 - 4.90: 43830 Nonbonded interactions: 108889 Sorted by model distance: nonbonded pdb=" OG SER A1202 " pdb=" O THR A1268 " model vdw 2.312 2.440 nonbonded pdb=" O VAL A 77 " pdb=" OG1 THR A 81 " model vdw 2.397 2.440 nonbonded pdb=" O THR A1276 " pdb=" OG1 THR A1276 " model vdw 2.449 2.440 nonbonded pdb=" O GLN A 313 " pdb=" CB GLN A 313 " model vdw 2.477 2.752 nonbonded pdb=" O PRO A 751 " pdb=" CB PRO A 751 " model vdw 2.497 2.752 ... (remaining 108884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.010 Extract box with map and model: 1.880 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 43.500 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.068 13918 Z= 0.782 Angle : 1.651 9.641 18813 Z= 1.254 Chirality : 0.088 0.323 2118 Planarity : 0.006 0.038 2388 Dihedral : 13.687 88.017 5198 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.01 % Allowed : 8.38 % Favored : 86.61 % Cbeta Deviations : 0.19 % 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: -1.67 (0.19), residues: 1640 helix: -0.63 (0.16), residues: 812 sheet: -1.95 (0.37), residues: 164 loop : -1.30 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A1086 HIS 0.011 0.002 HIS A1456 PHE 0.032 0.005 PHE A 647 TYR 0.076 0.005 TYR A1000 ARG 0.011 0.001 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 377 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 128 VAL cc_start: 0.8367 (t) cc_final: 0.8055 (p) REVERT: A 174 VAL cc_start: 0.8255 (t) cc_final: 0.7895 (m) REVERT: A 183 ASN cc_start: 0.6130 (p0) cc_final: 0.5868 (p0) REVERT: A 217 LYS cc_start: 0.7323 (mtmm) cc_final: 0.7056 (mmtp) REVERT: A 289 LYS cc_start: 0.7776 (mttt) cc_final: 0.7224 (ttpp) REVERT: A 290 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7030 (tp30) REVERT: A 298 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 356 GLU cc_start: 0.5788 (tt0) cc_final: 0.5563 (pt0) REVERT: A 361 ASN cc_start: 0.6290 (t0) cc_final: 0.5638 (t0) REVERT: A 410 GLN cc_start: 0.5242 (tt0) cc_final: 0.4683 (tp40) REVERT: A 425 VAL cc_start: 0.8241 (m) cc_final: 0.7907 (m) REVERT: A 439 GLU cc_start: 0.7239 (tp30) cc_final: 0.6958 (tt0) REVERT: A 444 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7711 (mttt) REVERT: A 464 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4834 (mm) REVERT: A 483 LYS cc_start: 0.7496 (mttt) cc_final: 0.6730 (tptt) REVERT: A 519 TYR cc_start: 0.6611 (m-80) cc_final: 0.6382 (m-10) REVERT: A 527 ASP cc_start: 0.6711 (m-30) cc_final: 0.6463 (m-30) REVERT: A 531 TYR cc_start: 0.6168 (t80) cc_final: 0.5755 (t80) REVERT: A 625 MET cc_start: 0.6163 (mtp) cc_final: 0.5603 (mtp) REVERT: A 656 LEU cc_start: 0.6941 (mt) cc_final: 0.6578 (mp) REVERT: A 658 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 670 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 686 TYR cc_start: 0.7269 (m-80) cc_final: 0.6978 (m-80) REVERT: A 689 SER cc_start: 0.6904 (m) cc_final: 0.6332 (p) REVERT: A 708 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 719 ARG cc_start: 0.6772 (mtt180) cc_final: 0.6383 (mtt90) REVERT: A 728 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: A 792 ASN cc_start: 0.7004 (m-40) cc_final: 0.6493 (t0) REVERT: A 899 HIS cc_start: 0.5429 (m90) cc_final: 0.5225 (m170) REVERT: A 954 HIS cc_start: 0.5505 (t-90) cc_final: 0.4929 (p-80) REVERT: A 969 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6856 (t) REVERT: A 1029 MET cc_start: 0.8373 (tpp) cc_final: 0.7845 (tpp) REVERT: A 1091 GLU cc_start: 0.6400 (tt0) cc_final: 0.5898 (tp30) REVERT: A 1143 ASN cc_start: 0.7300 (m-40) cc_final: 0.6237 (p0) REVERT: A 1183 LYS cc_start: 0.6583 (mttt) cc_final: 0.6111 (mmmt) REVERT: A 1184 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7235 (tm-30) REVERT: A 1222 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 1223 SER cc_start: 0.8624 (t) cc_final: 0.8280 (p) REVERT: A 1269 ILE cc_start: 0.8008 (tt) cc_final: 0.7583 (pt) REVERT: A 1351 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6771 (mm-30) REVERT: A 1354 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6247 (p90) REVERT: A 1355 CYS cc_start: 0.6784 (m) cc_final: 0.6258 (m) REVERT: A 1389 MET cc_start: 0.7942 (mmp) cc_final: 0.7531 (mmp) REVERT: A 1404 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6232 (tp) REVERT: A 1425 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6862 (tt0) REVERT: A 1448 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7178 (ttm170) REVERT: A 1529 ASN cc_start: 0.7952 (t0) cc_final: 0.7638 (t0) REVERT: A 1531 LYS cc_start: 0.6686 (mtpt) cc_final: 0.5900 (mtmt) REVERT: A 1553 TYR cc_start: 0.5472 (m-80) cc_final: 0.5233 (m-10) REVERT: A 1560 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6317 (mm-30) REVERT: A 1651 LYS cc_start: 0.6228 (mttt) cc_final: 0.5652 (ttpp) REVERT: B 96 MET cc_start: 0.4525 (mmt) cc_final: 0.3985 (mmt) REVERT: B 107 ARG cc_start: 0.6988 (tpp-160) cc_final: 0.6578 (tpp-160) REVERT: B 190 MET cc_start: 0.5120 (mtp) cc_final: 0.4769 (mmt) REVERT: B 202 THR cc_start: 0.3771 (p) cc_final: 0.3463 (p) REVERT: B 218 MET cc_start: 0.5984 (mmt) cc_final: 0.5295 (ptt) REVERT: B 219 ARG cc_start: 0.6150 (mtt180) cc_final: 0.5814 (mtp180) REVERT: B 287 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.6007 (t80) REVERT: B 298 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7530 (pt) REVERT: B 303 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7180 (pt) outliers start: 76 outliers final: 14 residues processed: 427 average time/residue: 0.2884 time to fit residues: 173.3941 Evaluate side-chains 267 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1354 PHE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 303 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 142 HIS ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 570 ASN A 660 ASN A 743 HIS A 783 ASN A 795 GLN A 803 HIS A 827 ASN A 841 GLN A 857 GLN A1191 GLN A1250 ASN ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 ASN A1509 ASN A1546 GLN A1639 ASN ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 224 HIS B 225 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13918 Z= 0.236 Angle : 0.598 9.956 18813 Z= 0.322 Chirality : 0.042 0.199 2118 Planarity : 0.005 0.069 2388 Dihedral : 6.194 56.192 1861 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.83 % Allowed : 12.66 % Favored : 83.51 % 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: -0.40 (0.19), residues: 1640 helix: 0.60 (0.17), residues: 832 sheet: -1.26 (0.36), residues: 190 loop : -1.01 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 885 HIS 0.008 0.001 HIS A1019 PHE 0.033 0.002 PHE B 306 TYR 0.025 0.002 TYR A 925 ARG 0.004 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 245 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 VAL cc_start: 0.8040 (t) cc_final: 0.7722 (m) REVERT: A 183 ASN cc_start: 0.5328 (p0) cc_final: 0.4959 (p0) REVERT: A 190 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6295 (pt0) REVERT: A 217 LYS cc_start: 0.7332 (mtmm) cc_final: 0.6992 (mmtp) REVERT: A 286 TYR cc_start: 0.7789 (t80) cc_final: 0.7418 (t80) REVERT: A 361 ASN cc_start: 0.5884 (t0) cc_final: 0.5450 (t0) REVERT: A 393 GLU cc_start: 0.7507 (tp30) cc_final: 0.6612 (tt0) REVERT: A 410 GLN cc_start: 0.5705 (tt0) cc_final: 0.5473 (tp-100) REVERT: A 444 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7584 (mttt) REVERT: A 483 LYS cc_start: 0.8031 (mttt) cc_final: 0.7076 (tptt) REVERT: A 506 THR cc_start: 0.8132 (p) cc_final: 0.7906 (p) REVERT: A 589 PHE cc_start: 0.7806 (m-80) cc_final: 0.7539 (m-80) REVERT: A 635 MET cc_start: 0.6565 (mmm) cc_final: 0.6185 (mtp) REVERT: A 654 TYR cc_start: 0.7590 (t80) cc_final: 0.7375 (t80) REVERT: A 686 TYR cc_start: 0.7023 (m-80) cc_final: 0.6796 (m-80) REVERT: A 689 SER cc_start: 0.6447 (m) cc_final: 0.6026 (p) REVERT: A 708 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 719 ARG cc_start: 0.7177 (mtt180) cc_final: 0.6954 (mtt90) REVERT: A 768 MET cc_start: 0.8359 (ptp) cc_final: 0.8042 (ptp) REVERT: A 792 ASN cc_start: 0.6961 (m-40) cc_final: 0.6390 (t0) REVERT: A 805 MET cc_start: 0.8233 (tmm) cc_final: 0.7708 (tmm) REVERT: A 893 MET cc_start: 0.6342 (mtp) cc_final: 0.6120 (mmm) REVERT: A 984 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6437 (m-30) REVERT: A 1029 MET cc_start: 0.8184 (tpp) cc_final: 0.7664 (tpp) REVERT: A 1031 ARG cc_start: 0.8519 (mtp180) cc_final: 0.7550 (mtp85) REVERT: A 1143 ASN cc_start: 0.7326 (m-40) cc_final: 0.6184 (p0) REVERT: A 1183 LYS cc_start: 0.5645 (mttt) cc_final: 0.5314 (mmmt) REVERT: A 1184 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7103 (tm-30) REVERT: A 1213 GLU cc_start: 0.7294 (tt0) cc_final: 0.6929 (tm-30) REVERT: A 1222 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7594 (tp) REVERT: A 1269 ILE cc_start: 0.8017 (tt) cc_final: 0.7598 (pt) REVERT: A 1389 MET cc_start: 0.7922 (mmp) cc_final: 0.7498 (mmp) REVERT: A 1494 MET cc_start: 0.8514 (mtp) cc_final: 0.7817 (mtp) REVERT: A 1531 LYS cc_start: 0.6807 (mtpt) cc_final: 0.6124 (mtmt) REVERT: A 1560 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6312 (mm-30) REVERT: A 1651 LYS cc_start: 0.6026 (mttt) cc_final: 0.5505 (ttpt) REVERT: B 96 MET cc_start: 0.4536 (mmt) cc_final: 0.4037 (mmt) REVERT: B 107 ARG cc_start: 0.7495 (tpp-160) cc_final: 0.6992 (ttm-80) REVERT: B 109 MET cc_start: 0.6302 (mtt) cc_final: 0.6056 (mtt) REVERT: B 157 MET cc_start: 0.6020 (tpp) cc_final: 0.5492 (tpp) REVERT: B 190 MET cc_start: 0.4747 (mtp) cc_final: 0.4324 (mmt) REVERT: B 218 MET cc_start: 0.5900 (mmt) cc_final: 0.5431 (ptt) REVERT: B 263 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7379 (mt) REVERT: B 279 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5248 (mm) REVERT: B 298 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7211 (pt) outliers start: 58 outliers final: 36 residues processed: 283 average time/residue: 0.2726 time to fit residues: 112.9222 Evaluate side-chains 252 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1306 ASN Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 151 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A1287 ASN ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13918 Z= 0.156 Angle : 0.502 9.361 18813 Z= 0.265 Chirality : 0.039 0.196 2118 Planarity : 0.004 0.049 2388 Dihedral : 5.112 58.139 1840 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.23 % Allowed : 16.03 % Favored : 80.74 % 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: 0.22 (0.20), residues: 1640 helix: 1.15 (0.18), residues: 827 sheet: -0.79 (0.37), residues: 183 loop : -0.85 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 885 HIS 0.005 0.001 HIS A1019 PHE 0.019 0.001 PHE B 306 TYR 0.022 0.001 TYR A1000 ARG 0.006 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 1.651 Fit side-chains REVERT: A 174 VAL cc_start: 0.7965 (t) cc_final: 0.7644 (m) REVERT: A 183 ASN cc_start: 0.5574 (p0) cc_final: 0.5136 (p0) REVERT: A 190 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6711 (mt-10) REVERT: A 217 LYS cc_start: 0.7372 (mtmm) cc_final: 0.7022 (mmtp) REVERT: A 239 SER cc_start: 0.6856 (m) cc_final: 0.6439 (t) REVERT: A 286 TYR cc_start: 0.8089 (t80) cc_final: 0.7643 (t80) REVERT: A 361 ASN cc_start: 0.6183 (t0) cc_final: 0.5808 (t0) REVERT: A 393 GLU cc_start: 0.7604 (tp30) cc_final: 0.6741 (tt0) REVERT: A 407 ASN cc_start: 0.7222 (m-40) cc_final: 0.7009 (m-40) REVERT: A 410 GLN cc_start: 0.5754 (tt0) cc_final: 0.5536 (tp40) REVERT: A 424 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7307 (ptm) REVERT: A 444 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7332 (mtmt) REVERT: A 483 LYS cc_start: 0.7912 (mttt) cc_final: 0.6838 (tptt) REVERT: A 578 TYR cc_start: 0.5881 (t80) cc_final: 0.5581 (t80) REVERT: A 589 PHE cc_start: 0.7782 (m-80) cc_final: 0.7534 (m-80) REVERT: A 635 MET cc_start: 0.6618 (mmm) cc_final: 0.6122 (mtp) REVERT: A 654 TYR cc_start: 0.7627 (t80) cc_final: 0.7310 (t80) REVERT: A 658 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 670 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6466 (tm-30) REVERT: A 708 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 719 ARG cc_start: 0.6941 (mtt180) cc_final: 0.6519 (mtt90) REVERT: A 768 MET cc_start: 0.8285 (ptp) cc_final: 0.7904 (ptp) REVERT: A 792 ASN cc_start: 0.6651 (m-40) cc_final: 0.6212 (t0) REVERT: A 805 MET cc_start: 0.8259 (tmm) cc_final: 0.7791 (tmm) REVERT: A 984 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6266 (m-30) REVERT: A 1029 MET cc_start: 0.8167 (tpp) cc_final: 0.7621 (tpp) REVERT: A 1034 GLU cc_start: 0.7478 (pt0) cc_final: 0.7117 (mm-30) REVERT: A 1143 ASN cc_start: 0.7198 (m-40) cc_final: 0.6091 (p0) REVERT: A 1172 LYS cc_start: 0.7024 (pttm) cc_final: 0.6295 (mmtm) REVERT: A 1183 LYS cc_start: 0.5472 (mttt) cc_final: 0.5168 (mmmt) REVERT: A 1184 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7038 (tm-30) REVERT: A 1213 GLU cc_start: 0.7251 (tt0) cc_final: 0.6959 (tm-30) REVERT: A 1269 ILE cc_start: 0.8000 (tt) cc_final: 0.7566 (pt) REVERT: A 1389 MET cc_start: 0.7731 (mmp) cc_final: 0.7419 (mmp) REVERT: A 1494 MET cc_start: 0.8476 (mtp) cc_final: 0.7738 (mtp) REVERT: A 1531 LYS cc_start: 0.6853 (mtpt) cc_final: 0.6129 (mtmt) REVERT: A 1560 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6525 (mm-30) REVERT: A 1651 LYS cc_start: 0.5655 (mttt) cc_final: 0.5096 (ttpt) REVERT: A 1689 MET cc_start: 0.1421 (mmp) cc_final: 0.1102 (tmm) REVERT: B 107 ARG cc_start: 0.7256 (tpp-160) cc_final: 0.6734 (ttm-80) REVERT: B 157 MET cc_start: 0.6006 (tpp) cc_final: 0.5245 (tpp) REVERT: B 190 MET cc_start: 0.4642 (mtp) cc_final: 0.4265 (mmt) REVERT: B 218 MET cc_start: 0.5738 (mmt) cc_final: 0.5335 (ptt) outliers start: 49 outliers final: 28 residues processed: 266 average time/residue: 0.2618 time to fit residues: 101.3859 Evaluate side-chains 239 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1306 ASN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1472 GLU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 161 optimal weight: 0.0010 chunk 79 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 517 GLN A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN A1541 ASN ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13918 Z= 0.179 Angle : 0.503 9.283 18813 Z= 0.261 Chirality : 0.039 0.171 2118 Planarity : 0.004 0.040 2388 Dihedral : 4.695 57.069 1829 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.89 % Allowed : 16.16 % Favored : 79.95 % 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: 0.39 (0.20), residues: 1640 helix: 1.28 (0.18), residues: 827 sheet: -0.53 (0.38), residues: 183 loop : -0.81 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1292 HIS 0.006 0.001 HIS A1019 PHE 0.020 0.002 PHE A1342 TYR 0.023 0.001 TYR A1000 ARG 0.007 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 1.400 Fit side-chains REVERT: A 101 MET cc_start: 0.6146 (mtm) cc_final: 0.5858 (ttp) REVERT: A 174 VAL cc_start: 0.7992 (t) cc_final: 0.7689 (m) REVERT: A 190 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 217 LYS cc_start: 0.7368 (mtmm) cc_final: 0.7013 (mmtp) REVERT: A 239 SER cc_start: 0.6671 (m) cc_final: 0.6367 (t) REVERT: A 361 ASN cc_start: 0.6082 (t0) cc_final: 0.5672 (t0) REVERT: A 393 GLU cc_start: 0.7651 (tp30) cc_final: 0.6749 (tt0) REVERT: A 407 ASN cc_start: 0.7034 (m-40) cc_final: 0.6795 (m-40) REVERT: A 410 GLN cc_start: 0.5678 (tt0) cc_final: 0.5468 (tp40) REVERT: A 424 MET cc_start: 0.7970 (ttp) cc_final: 0.7521 (ptm) REVERT: A 444 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7352 (mtpt) REVERT: A 458 MET cc_start: 0.7957 (tpp) cc_final: 0.7139 (tpp) REVERT: A 483 LYS cc_start: 0.7925 (mttt) cc_final: 0.6778 (tptt) REVERT: A 589 PHE cc_start: 0.7822 (m-80) cc_final: 0.7585 (m-80) REVERT: A 654 TYR cc_start: 0.7444 (t80) cc_final: 0.7102 (t80) REVERT: A 670 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 686 TYR cc_start: 0.6931 (m-80) cc_final: 0.6729 (m-80) REVERT: A 719 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6923 (mtt90) REVERT: A 768 MET cc_start: 0.8305 (ptp) cc_final: 0.7914 (ptp) REVERT: A 792 ASN cc_start: 0.6764 (m-40) cc_final: 0.6364 (t0) REVERT: A 805 MET cc_start: 0.8269 (tmm) cc_final: 0.7747 (tmm) REVERT: A 893 MET cc_start: 0.6253 (mtp) cc_final: 0.5999 (mmm) REVERT: A 984 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6234 (m-30) REVERT: A 999 MET cc_start: 0.8128 (mtp) cc_final: 0.7882 (mtp) REVERT: A 1029 MET cc_start: 0.8204 (tpp) cc_final: 0.7721 (tpp) REVERT: A 1034 GLU cc_start: 0.7708 (pt0) cc_final: 0.7211 (mm-30) REVERT: A 1139 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5875 (ttp) REVERT: A 1143 ASN cc_start: 0.7361 (m-40) cc_final: 0.6235 (p0) REVERT: A 1172 LYS cc_start: 0.7088 (pttm) cc_final: 0.6424 (mmtm) REVERT: A 1183 LYS cc_start: 0.5561 (mttt) cc_final: 0.5248 (mmmt) REVERT: A 1184 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7107 (tm-30) REVERT: A 1213 GLU cc_start: 0.7290 (tt0) cc_final: 0.6998 (tm-30) REVERT: A 1269 ILE cc_start: 0.8015 (tt) cc_final: 0.7583 (pt) REVERT: A 1389 MET cc_start: 0.7735 (mmp) cc_final: 0.7413 (mmp) REVERT: A 1494 MET cc_start: 0.8466 (mtp) cc_final: 0.7759 (mtp) REVERT: A 1531 LYS cc_start: 0.6947 (mtpt) cc_final: 0.6143 (mtmt) REVERT: A 1651 LYS cc_start: 0.5678 (mttt) cc_final: 0.5077 (ttpt) REVERT: A 1689 MET cc_start: 0.1497 (mmp) cc_final: 0.1019 (tmm) REVERT: B 107 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6751 (ttm-80) REVERT: B 157 MET cc_start: 0.6247 (tpp) cc_final: 0.5487 (tpp) REVERT: B 190 MET cc_start: 0.4347 (mtp) cc_final: 0.3958 (mmt) REVERT: B 218 MET cc_start: 0.5609 (mmt) cc_final: 0.5266 (ptt) REVERT: B 266 LYS cc_start: 0.5879 (ttmt) cc_final: 0.5432 (tptt) outliers start: 59 outliers final: 44 residues processed: 257 average time/residue: 0.2454 time to fit residues: 93.5901 Evaluate side-chains 247 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1306 ASN Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN A1519 HIS ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13918 Z= 0.255 Angle : 0.554 13.420 18813 Z= 0.285 Chirality : 0.041 0.156 2118 Planarity : 0.004 0.039 2388 Dihedral : 4.854 56.815 1829 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.49 % Allowed : 16.42 % Favored : 79.09 % 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: 0.26 (0.20), residues: 1640 helix: 1.18 (0.18), residues: 816 sheet: -0.46 (0.38), residues: 183 loop : -0.88 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1292 HIS 0.006 0.001 HIS A1019 PHE 0.022 0.002 PHE A 423 TYR 0.028 0.002 TYR A1000 ARG 0.004 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 202 time to evaluate : 1.631 Fit side-chains REVERT: A 174 VAL cc_start: 0.8002 (t) cc_final: 0.7701 (m) REVERT: A 190 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6974 (mt-10) REVERT: A 217 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6736 (mmtp) REVERT: A 246 TYR cc_start: 0.5384 (m-80) cc_final: 0.5087 (m-80) REVERT: A 275 SER cc_start: 0.5105 (t) cc_final: 0.4808 (p) REVERT: A 282 ASN cc_start: 0.7138 (m-40) cc_final: 0.6283 (m110) REVERT: A 357 GLU cc_start: 0.5750 (mt-10) cc_final: 0.5318 (mp0) REVERT: A 361 ASN cc_start: 0.6116 (t0) cc_final: 0.5725 (t0) REVERT: A 393 GLU cc_start: 0.7803 (tp30) cc_final: 0.6872 (tt0) REVERT: A 443 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.5783 (tp40) REVERT: A 444 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7304 (mtmt) REVERT: A 464 LEU cc_start: 0.4458 (OUTLIER) cc_final: 0.4218 (mm) REVERT: A 483 LYS cc_start: 0.7930 (mttt) cc_final: 0.6698 (tptt) REVERT: A 527 ASP cc_start: 0.6567 (m-30) cc_final: 0.6286 (m-30) REVERT: A 589 PHE cc_start: 0.7881 (m-80) cc_final: 0.7638 (m-80) REVERT: A 654 TYR cc_start: 0.7296 (t80) cc_final: 0.6996 (t80) REVERT: A 670 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6545 (tm-30) REVERT: A 768 MET cc_start: 0.8358 (ptp) cc_final: 0.7945 (ptp) REVERT: A 792 ASN cc_start: 0.6779 (m-40) cc_final: 0.6297 (t0) REVERT: A 984 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: A 1029 MET cc_start: 0.8229 (tpp) cc_final: 0.7826 (tpp) REVERT: A 1031 ARG cc_start: 0.8539 (mtp180) cc_final: 0.7585 (mtp85) REVERT: A 1034 GLU cc_start: 0.7957 (pt0) cc_final: 0.7289 (mm-30) REVERT: A 1139 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5592 (ttp) REVERT: A 1143 ASN cc_start: 0.7579 (m-40) cc_final: 0.6457 (p0) REVERT: A 1172 LYS cc_start: 0.7123 (pttm) cc_final: 0.6447 (mmtm) REVERT: A 1183 LYS cc_start: 0.5636 (mttt) cc_final: 0.5176 (mttp) REVERT: A 1184 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7069 (tm-30) REVERT: A 1269 ILE cc_start: 0.8089 (tt) cc_final: 0.7610 (pt) REVERT: A 1389 MET cc_start: 0.7924 (mmp) cc_final: 0.7432 (mmp) REVERT: A 1494 MET cc_start: 0.8474 (mtp) cc_final: 0.7724 (mtp) REVERT: A 1531 LYS cc_start: 0.6874 (mtpt) cc_final: 0.6066 (mttp) REVERT: A 1651 LYS cc_start: 0.6020 (mttt) cc_final: 0.5302 (ttpt) REVERT: A 1689 MET cc_start: 0.1207 (mmp) cc_final: 0.0946 (tmm) REVERT: B 107 ARG cc_start: 0.7163 (tpp-160) cc_final: 0.6820 (ttm-80) REVERT: B 157 MET cc_start: 0.6302 (tpp) cc_final: 0.5566 (tpp) REVERT: B 190 MET cc_start: 0.4272 (mtp) cc_final: 0.3852 (mmt) REVERT: B 218 MET cc_start: 0.5573 (mmt) cc_final: 0.5318 (ptt) REVERT: B 266 LYS cc_start: 0.6032 (ttmt) cc_final: 0.5551 (tptt) outliers start: 68 outliers final: 54 residues processed: 248 average time/residue: 0.2517 time to fit residues: 92.2901 Evaluate side-chains 247 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1306 ASN Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 410 GLN A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13918 Z= 0.277 Angle : 0.560 15.701 18813 Z= 0.287 Chirality : 0.041 0.156 2118 Planarity : 0.004 0.040 2388 Dihedral : 4.823 57.371 1827 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.95 % Allowed : 16.49 % Favored : 78.56 % 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: 0.14 (0.20), residues: 1640 helix: 1.08 (0.18), residues: 817 sheet: -0.45 (0.39), residues: 178 loop : -0.97 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1292 HIS 0.006 0.001 HIS A1019 PHE 0.025 0.002 PHE B 306 TYR 0.031 0.002 TYR A1000 ARG 0.004 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 192 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: A 174 VAL cc_start: 0.7984 (t) cc_final: 0.7695 (m) REVERT: A 190 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6868 (mt-10) REVERT: A 217 LYS cc_start: 0.7158 (mtmm) cc_final: 0.6707 (mmtp) REVERT: A 275 SER cc_start: 0.4812 (t) cc_final: 0.4609 (p) REVERT: A 357 GLU cc_start: 0.5535 (mt-10) cc_final: 0.5039 (mp0) REVERT: A 361 ASN cc_start: 0.6123 (t0) cc_final: 0.5726 (t0) REVERT: A 393 GLU cc_start: 0.7904 (tp30) cc_final: 0.7155 (tt0) REVERT: A 444 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7350 (mtmt) REVERT: A 458 MET cc_start: 0.7999 (tpp) cc_final: 0.7540 (tpp) REVERT: A 464 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4457 (mm) REVERT: A 483 LYS cc_start: 0.8004 (mttt) cc_final: 0.6674 (tptt) REVERT: A 589 PHE cc_start: 0.7904 (m-80) cc_final: 0.7665 (m-80) REVERT: A 654 TYR cc_start: 0.7274 (t80) cc_final: 0.6946 (t80) REVERT: A 670 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6529 (tm-30) REVERT: A 768 MET cc_start: 0.8347 (ptp) cc_final: 0.7939 (ptp) REVERT: A 792 ASN cc_start: 0.6790 (m-40) cc_final: 0.6300 (t0) REVERT: A 984 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6349 (m-30) REVERT: A 1029 MET cc_start: 0.8238 (tpp) cc_final: 0.7820 (tpp) REVERT: A 1031 ARG cc_start: 0.8553 (mtp180) cc_final: 0.7616 (mtp85) REVERT: A 1143 ASN cc_start: 0.7422 (m-40) cc_final: 0.6591 (p0) REVERT: A 1172 LYS cc_start: 0.7120 (pttm) cc_final: 0.6453 (mmtm) REVERT: A 1183 LYS cc_start: 0.5704 (mttt) cc_final: 0.5473 (mtpt) REVERT: A 1184 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7124 (tm-30) REVERT: A 1269 ILE cc_start: 0.8107 (tt) cc_final: 0.7631 (pt) REVERT: A 1389 MET cc_start: 0.7941 (mmp) cc_final: 0.7434 (mmp) REVERT: A 1531 LYS cc_start: 0.6923 (mtpt) cc_final: 0.6159 (mtmt) REVERT: A 1651 LYS cc_start: 0.6116 (mttt) cc_final: 0.5348 (ttpt) REVERT: A 1689 MET cc_start: 0.1224 (mmp) cc_final: 0.1002 (tmm) REVERT: B 107 ARG cc_start: 0.7074 (tpp-160) cc_final: 0.6831 (ttm-80) REVERT: B 190 MET cc_start: 0.3672 (mtp) cc_final: 0.3361 (mmt) REVERT: B 218 MET cc_start: 0.5838 (mmt) cc_final: 0.5517 (mmt) REVERT: B 248 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5983 (pp20) REVERT: B 266 LYS cc_start: 0.5857 (ttmt) cc_final: 0.5409 (tptt) outliers start: 75 outliers final: 58 residues processed: 240 average time/residue: 0.2611 time to fit residues: 91.8791 Evaluate side-chains 247 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 13918 Z= 0.144 Angle : 0.477 9.520 18813 Z= 0.247 Chirality : 0.038 0.151 2118 Planarity : 0.003 0.041 2388 Dihedral : 4.554 58.194 1827 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.76 % Allowed : 17.61 % Favored : 78.63 % 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: 0.55 (0.21), residues: 1640 helix: 1.46 (0.18), residues: 816 sheet: -0.23 (0.39), residues: 177 loop : -0.85 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1292 HIS 0.005 0.001 HIS A1019 PHE 0.017 0.001 PHE A1342 TYR 0.023 0.001 TYR A1000 ARG 0.005 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.6144 (mtm) cc_final: 0.5889 (ttp) REVERT: A 174 VAL cc_start: 0.7905 (t) cc_final: 0.7631 (m) REVERT: A 190 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 217 LYS cc_start: 0.7173 (mtmm) cc_final: 0.6726 (mmtp) REVERT: A 246 TYR cc_start: 0.4514 (m-80) cc_final: 0.4190 (m-80) REVERT: A 282 ASN cc_start: 0.7155 (m-40) cc_final: 0.6349 (m-40) REVERT: A 357 GLU cc_start: 0.5599 (mt-10) cc_final: 0.5143 (mp0) REVERT: A 361 ASN cc_start: 0.6116 (t0) cc_final: 0.5736 (t0) REVERT: A 393 GLU cc_start: 0.7833 (tp30) cc_final: 0.6958 (tt0) REVERT: A 444 LYS cc_start: 0.7768 (ttpp) cc_final: 0.7317 (mtpt) REVERT: A 464 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4376 (mm) REVERT: A 483 LYS cc_start: 0.7994 (mttt) cc_final: 0.6658 (tptt) REVERT: A 589 PHE cc_start: 0.7870 (m-80) cc_final: 0.7627 (m-80) REVERT: A 654 TYR cc_start: 0.7262 (t80) cc_final: 0.6936 (t80) REVERT: A 670 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6498 (tm-30) REVERT: A 768 MET cc_start: 0.8271 (ptp) cc_final: 0.7869 (ptp) REVERT: A 792 ASN cc_start: 0.6752 (m-40) cc_final: 0.6366 (t0) REVERT: A 1029 MET cc_start: 0.8203 (tpp) cc_final: 0.7802 (tpp) REVERT: A 1031 ARG cc_start: 0.8541 (mtp180) cc_final: 0.7609 (mtp85) REVERT: A 1034 GLU cc_start: 0.7795 (pt0) cc_final: 0.7249 (mm-30) REVERT: A 1143 ASN cc_start: 0.7494 (m-40) cc_final: 0.6753 (p0) REVERT: A 1172 LYS cc_start: 0.7091 (pttm) cc_final: 0.6435 (mmtm) REVERT: A 1183 LYS cc_start: 0.5640 (mttt) cc_final: 0.5415 (mtpt) REVERT: A 1184 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7116 (tm-30) REVERT: A 1213 GLU cc_start: 0.7371 (tt0) cc_final: 0.7028 (tm-30) REVERT: A 1269 ILE cc_start: 0.8089 (tt) cc_final: 0.7611 (pt) REVERT: A 1389 MET cc_start: 0.7742 (mmp) cc_final: 0.7417 (mmp) REVERT: A 1494 MET cc_start: 0.8476 (mtp) cc_final: 0.7780 (mtp) REVERT: A 1531 LYS cc_start: 0.7029 (mtpt) cc_final: 0.6264 (mttp) REVERT: A 1651 LYS cc_start: 0.5592 (mttt) cc_final: 0.5155 (ttpt) REVERT: A 1689 MET cc_start: 0.1262 (mmp) cc_final: 0.1050 (tmm) REVERT: B 107 ARG cc_start: 0.7057 (tpp-160) cc_final: 0.6771 (ttm-80) REVERT: B 190 MET cc_start: 0.3819 (mtp) cc_final: 0.3531 (mmt) REVERT: B 248 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6188 (pp20) REVERT: B 266 LYS cc_start: 0.5684 (ttmt) cc_final: 0.5214 (tptt) outliers start: 57 outliers final: 40 residues processed: 227 average time/residue: 0.2508 time to fit residues: 84.1933 Evaluate side-chains 224 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 182 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 126 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13918 Z= 0.134 Angle : 0.466 9.058 18813 Z= 0.240 Chirality : 0.037 0.148 2118 Planarity : 0.003 0.040 2388 Dihedral : 4.356 58.563 1825 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.56 % Allowed : 17.48 % Favored : 78.96 % 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: 0.74 (0.21), residues: 1640 helix: 1.60 (0.18), residues: 821 sheet: -0.18 (0.39), residues: 177 loop : -0.74 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1292 HIS 0.007 0.001 HIS A1305 PHE 0.018 0.001 PHE A1342 TYR 0.022 0.001 TYR A1000 ARG 0.005 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 1.507 Fit side-chains REVERT: A 101 MET cc_start: 0.6181 (mtm) cc_final: 0.5968 (ttp) REVERT: A 174 VAL cc_start: 0.7888 (t) cc_final: 0.7625 (m) REVERT: A 190 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6931 (mt-10) REVERT: A 217 LYS cc_start: 0.7142 (mtmm) cc_final: 0.6693 (mmtp) REVERT: A 282 ASN cc_start: 0.7087 (m-40) cc_final: 0.6267 (m-40) REVERT: A 357 GLU cc_start: 0.5458 (mt-10) cc_final: 0.5015 (mp0) REVERT: A 361 ASN cc_start: 0.6120 (t0) cc_final: 0.5742 (t0) REVERT: A 393 GLU cc_start: 0.7790 (tp30) cc_final: 0.6858 (tt0) REVERT: A 444 LYS cc_start: 0.7780 (ttpp) cc_final: 0.7303 (mtpt) REVERT: A 464 LEU cc_start: 0.4072 (OUTLIER) cc_final: 0.3767 (mm) REVERT: A 483 LYS cc_start: 0.7992 (mttt) cc_final: 0.6644 (tptt) REVERT: A 589 PHE cc_start: 0.7802 (m-80) cc_final: 0.7547 (m-80) REVERT: A 635 MET cc_start: 0.6356 (mmm) cc_final: 0.5904 (mmm) REVERT: A 654 TYR cc_start: 0.7288 (t80) cc_final: 0.6949 (t80) REVERT: A 670 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6498 (tm-30) REVERT: A 756 ILE cc_start: 0.7294 (mt) cc_final: 0.7015 (tt) REVERT: A 768 MET cc_start: 0.8278 (ptp) cc_final: 0.7860 (ptp) REVERT: A 792 ASN cc_start: 0.6741 (m-40) cc_final: 0.6365 (t0) REVERT: A 845 ASP cc_start: 0.8130 (t0) cc_final: 0.7541 (t70) REVERT: A 1029 MET cc_start: 0.8237 (tpp) cc_final: 0.7826 (tpp) REVERT: A 1031 ARG cc_start: 0.8533 (mtp180) cc_final: 0.7632 (mtp85) REVERT: A 1034 GLU cc_start: 0.7652 (pt0) cc_final: 0.7208 (mm-30) REVERT: A 1143 ASN cc_start: 0.7436 (m-40) cc_final: 0.6554 (p0) REVERT: A 1172 LYS cc_start: 0.7046 (pttm) cc_final: 0.6424 (mmtm) REVERT: A 1183 LYS cc_start: 0.5627 (mttt) cc_final: 0.5407 (mtpt) REVERT: A 1184 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7130 (tm-30) REVERT: A 1213 GLU cc_start: 0.7353 (tt0) cc_final: 0.7021 (tm-30) REVERT: A 1269 ILE cc_start: 0.8067 (tt) cc_final: 0.7589 (pt) REVERT: A 1389 MET cc_start: 0.7684 (mmp) cc_final: 0.7357 (mmp) REVERT: A 1494 MET cc_start: 0.8457 (mtp) cc_final: 0.7767 (mtp) REVERT: A 1531 LYS cc_start: 0.7072 (mtpt) cc_final: 0.6327 (mttp) REVERT: A 1651 LYS cc_start: 0.5652 (mttt) cc_final: 0.5142 (ttpt) REVERT: B 107 ARG cc_start: 0.6935 (tpp-160) cc_final: 0.6619 (ttm-80) REVERT: B 157 MET cc_start: 0.6406 (tpp) cc_final: 0.5716 (tpp) REVERT: B 190 MET cc_start: 0.4378 (mtp) cc_final: 0.4075 (mmm) REVERT: B 248 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6115 (pp20) REVERT: B 266 LYS cc_start: 0.5738 (ttmt) cc_final: 0.5154 (tptt) outliers start: 54 outliers final: 43 residues processed: 229 average time/residue: 0.2596 time to fit residues: 87.3044 Evaluate side-chains 230 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 ASN A1541 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13918 Z= 0.273 Angle : 0.558 11.123 18813 Z= 0.284 Chirality : 0.040 0.155 2118 Planarity : 0.004 0.040 2388 Dihedral : 4.605 57.899 1825 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.69 % Allowed : 17.68 % Favored : 78.63 % 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 (0.21), residues: 1640 helix: 1.32 (0.18), residues: 817 sheet: -0.23 (0.40), residues: 176 loop : -0.84 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1292 HIS 0.006 0.001 HIS A1456 PHE 0.021 0.002 PHE B 306 TYR 0.032 0.002 TYR A1000 ARG 0.005 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 181 time to evaluate : 1.520 Fit side-chains REVERT: A 101 MET cc_start: 0.6192 (mtm) cc_final: 0.5922 (ttp) REVERT: A 174 VAL cc_start: 0.7959 (t) cc_final: 0.7695 (m) REVERT: A 190 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 217 LYS cc_start: 0.7309 (mtmm) cc_final: 0.6696 (mmtp) REVERT: A 357 GLU cc_start: 0.5454 (mt-10) cc_final: 0.4902 (mp0) REVERT: A 361 ASN cc_start: 0.6268 (t0) cc_final: 0.5903 (t0) REVERT: A 393 GLU cc_start: 0.7875 (tp30) cc_final: 0.7063 (tt0) REVERT: A 444 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7289 (mtmt) REVERT: A 464 LEU cc_start: 0.4350 (OUTLIER) cc_final: 0.3929 (mm) REVERT: A 483 LYS cc_start: 0.8028 (mttt) cc_final: 0.6549 (tptt) REVERT: A 527 ASP cc_start: 0.6576 (m-30) cc_final: 0.6260 (m-30) REVERT: A 589 PHE cc_start: 0.7854 (m-80) cc_final: 0.7610 (m-80) REVERT: A 635 MET cc_start: 0.6250 (mmm) cc_final: 0.5982 (mmm) REVERT: A 654 TYR cc_start: 0.7421 (t80) cc_final: 0.7064 (t80) REVERT: A 658 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7413 (mp0) REVERT: A 670 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6541 (tm-30) REVERT: A 768 MET cc_start: 0.8336 (ptp) cc_final: 0.7946 (ptp) REVERT: A 792 ASN cc_start: 0.6794 (m-40) cc_final: 0.6376 (t0) REVERT: A 999 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.8008 (mtp) REVERT: A 1029 MET cc_start: 0.8229 (tpp) cc_final: 0.7823 (tpp) REVERT: A 1031 ARG cc_start: 0.8560 (mtp180) cc_final: 0.7647 (mtp85) REVERT: A 1034 GLU cc_start: 0.7986 (pt0) cc_final: 0.7299 (mm-30) REVERT: A 1143 ASN cc_start: 0.7216 (m-40) cc_final: 0.6649 (p0) REVERT: A 1172 LYS cc_start: 0.7122 (pttm) cc_final: 0.6462 (mmtm) REVERT: A 1183 LYS cc_start: 0.5698 (mttt) cc_final: 0.5472 (mtpt) REVERT: A 1184 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7187 (tm-30) REVERT: A 1213 GLU cc_start: 0.7493 (tt0) cc_final: 0.7153 (tm-30) REVERT: A 1269 ILE cc_start: 0.8137 (tt) cc_final: 0.7669 (pt) REVERT: A 1389 MET cc_start: 0.7881 (mmp) cc_final: 0.7550 (mmp) REVERT: A 1494 MET cc_start: 0.8485 (mtp) cc_final: 0.7752 (mtp) REVERT: A 1531 LYS cc_start: 0.7029 (mtpt) cc_final: 0.6253 (mtmt) REVERT: A 1651 LYS cc_start: 0.5883 (mttt) cc_final: 0.5289 (ttmt) REVERT: B 107 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6723 (ttm-80) REVERT: B 157 MET cc_start: 0.6473 (tpp) cc_final: 0.5684 (tpp) REVERT: B 190 MET cc_start: 0.4367 (mtp) cc_final: 0.4072 (mmt) REVERT: B 248 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6107 (pp20) REVERT: B 266 LYS cc_start: 0.6072 (ttmt) cc_final: 0.5460 (tptm) outliers start: 56 outliers final: 48 residues processed: 219 average time/residue: 0.2484 time to fit residues: 80.5661 Evaluate side-chains 229 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1495 ASN Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 166 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13918 Z= 0.149 Angle : 0.490 13.882 18813 Z= 0.249 Chirality : 0.038 0.154 2118 Planarity : 0.003 0.041 2388 Dihedral : 4.413 59.122 1825 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.43 % Allowed : 18.01 % Favored : 78.56 % 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: 0.72 (0.21), residues: 1640 helix: 1.59 (0.18), residues: 820 sheet: -0.10 (0.40), residues: 177 loop : -0.77 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1292 HIS 0.005 0.001 HIS A1019 PHE 0.020 0.001 PHE B 306 TYR 0.023 0.001 TYR A1000 ARG 0.005 0.000 ARG B 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 1.379 Fit side-chains REVERT: A 174 VAL cc_start: 0.7870 (t) cc_final: 0.7609 (m) REVERT: A 190 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 217 LYS cc_start: 0.7313 (mtmm) cc_final: 0.6699 (mmtp) REVERT: A 239 SER cc_start: 0.6620 (m) cc_final: 0.6286 (t) REVERT: A 282 ASN cc_start: 0.7212 (m-40) cc_final: 0.6302 (m-40) REVERT: A 357 GLU cc_start: 0.5439 (mt-10) cc_final: 0.4895 (mp0) REVERT: A 361 ASN cc_start: 0.6270 (t0) cc_final: 0.5904 (t0) REVERT: A 393 GLU cc_start: 0.7849 (tp30) cc_final: 0.7143 (tt0) REVERT: A 444 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7303 (mtpt) REVERT: A 464 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.3719 (tp) REVERT: A 483 LYS cc_start: 0.8115 (mttt) cc_final: 0.6634 (tptt) REVERT: A 589 PHE cc_start: 0.7828 (m-80) cc_final: 0.7574 (m-80) REVERT: A 654 TYR cc_start: 0.7293 (t80) cc_final: 0.6951 (t80) REVERT: A 670 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6460 (tm-30) REVERT: A 768 MET cc_start: 0.8279 (ptp) cc_final: 0.7890 (ptp) REVERT: A 787 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7818 (mt-10) REVERT: A 792 ASN cc_start: 0.6761 (m-40) cc_final: 0.6361 (t0) REVERT: A 1029 MET cc_start: 0.8203 (tpp) cc_final: 0.7810 (tpp) REVERT: A 1031 ARG cc_start: 0.8557 (mtp180) cc_final: 0.7667 (mtp85) REVERT: A 1034 GLU cc_start: 0.7806 (pt0) cc_final: 0.7291 (mm-30) REVERT: A 1143 ASN cc_start: 0.7200 (m-40) cc_final: 0.6675 (p0) REVERT: A 1172 LYS cc_start: 0.7067 (pttm) cc_final: 0.6447 (mmtm) REVERT: A 1183 LYS cc_start: 0.5656 (mttt) cc_final: 0.5428 (mtpt) REVERT: A 1184 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7183 (tm-30) REVERT: A 1213 GLU cc_start: 0.7366 (tt0) cc_final: 0.7031 (tm-30) REVERT: A 1269 ILE cc_start: 0.8093 (tt) cc_final: 0.7628 (pt) REVERT: A 1494 MET cc_start: 0.8467 (mtp) cc_final: 0.7778 (mtp) REVERT: A 1531 LYS cc_start: 0.7081 (mtpt) cc_final: 0.6331 (mttp) REVERT: A 1651 LYS cc_start: 0.5638 (mttt) cc_final: 0.5131 (ttpt) REVERT: B 107 ARG cc_start: 0.7053 (tpp-160) cc_final: 0.6734 (ttm-80) REVERT: B 157 MET cc_start: 0.6354 (tpp) cc_final: 0.5613 (tpp) REVERT: B 190 MET cc_start: 0.4454 (mtp) cc_final: 0.4079 (mmt) REVERT: B 248 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6048 (pp20) REVERT: B 266 LYS cc_start: 0.5759 (ttmt) cc_final: 0.5135 (tptm) outliers start: 52 outliers final: 43 residues processed: 222 average time/residue: 0.2639 time to fit residues: 88.2020 Evaluate side-chains 228 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1492 THR Chi-restraints excluded: chain A residue 1562 ASP Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A1338 ASN ** 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 = 0.4037 r_free = 0.4037 target = 0.188268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151743 restraints weight = 15834.253| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.13 r_work: 0.3292 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13918 Z= 0.147 Angle : 0.487 14.053 18813 Z= 0.247 Chirality : 0.038 0.150 2118 Planarity : 0.003 0.040 2388 Dihedral : 4.334 59.420 1825 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.17 % Allowed : 18.07 % Favored : 78.76 % 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: 0.82 (0.21), residues: 1640 helix: 1.65 (0.18), residues: 820 sheet: -0.05 (0.41), residues: 175 loop : -0.69 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1292 HIS 0.004 0.001 HIS A1019 PHE 0.023 0.001 PHE A1542 TYR 0.024 0.001 TYR A1000 ARG 0.005 0.000 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3110.37 seconds wall clock time: 57 minutes 3.55 seconds (3423.55 seconds total)