Starting phenix.real_space_refine on Fri Nov 17 20:12:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/11_2023/7w0d_32239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/11_2023/7w0d_32239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/11_2023/7w0d_32239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/11_2023/7w0d_32239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/11_2023/7w0d_32239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/11_2023/7w0d_32239_updated.pdb" } resolution = 4.18 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= 0.005 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 107 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 12567 2.51 5 N 3476 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 353": "OD1" <-> "OD2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 20322 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1103 Classifications: {'RNA': 52} Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna3p': 51} Chain: "G" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 117 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "A" Number of atoms: 12490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 12490 Classifications: {'peptide': 1544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 63, 'TRANS': 1480} Chain breaks: 2 Chain: "F" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5312 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 22, 'TRANS': 637} Chain: "C" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1100 Classifications: {'RNA': 52} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 25} Link IDs: {'rna2p': 1, 'rna3p': 50} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.12, per 1000 atoms: 0.55 Number of scatterers: 20322 At special positions: 0 Unit cell: (127.735, 100.672, 204.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 107 15.00 Mg 2 11.99 O 4068 8.00 N 3476 7.00 C 12567 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: 9.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 15 sheets defined 47.2% alpha, 7.7% beta 43 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 10.85 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 4.297A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.625A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.502A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 205 through 214 removed outlier: 4.133A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.540A pdb=" N LEU A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 291 Processing helix chain 'A' and resid 294 through 313 removed outlier: 3.885A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 342 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.661A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.768A pdb=" N ARG A 511 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU A 512 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 527 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 528 " --> pdb=" O HIS A 525 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 532 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 4.296A pdb=" N PHE A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 568 through 581 removed outlier: 4.582A pdb=" N LEU A 572 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 638 through 656 Processing helix chain 'A' and resid 668 through 679 removed outlier: 4.445A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 removed outlier: 3.731A pdb=" N TYR A 686 " --> pdb=" O HIS A 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 686' Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.709A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 863 through 868 removed outlier: 4.316A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.505A pdb=" N MET A 922 " --> pdb=" O TYR A 918 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 964 No H-bonds generated for 'chain 'A' and resid 961 through 964' Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 983 through 1015 removed outlier: 3.568A pdb=" N ILE A 990 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Proline residue: A 993 - end of helix removed outlier: 3.680A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1175 through 1181 Processing helix chain 'A' and resid 1183 through 1185 No H-bonds generated for 'chain 'A' and resid 1183 through 1185' Processing helix chain 'A' and resid 1191 through 1198 Processing helix chain 'A' and resid 1210 through 1231 removed outlier: 4.020A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1247 Processing helix chain 'A' and resid 1250 through 1258 Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1273 through 1276 No H-bonds generated for 'chain 'A' and resid 1273 through 1276' Processing helix chain 'A' and resid 1286 through 1293 Processing helix chain 'A' and resid 1296 through 1301 removed outlier: 3.853A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE A1301 " --> pdb=" O GLU A1297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1296 through 1301' Processing helix chain 'A' and resid 1304 through 1309 Processing helix chain 'A' and resid 1314 through 1318 Processing helix chain 'A' and resid 1325 through 1340 removed outlier: 3.642A pdb=" N ASN A1338 " --> pdb=" O GLY A1334 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1352 removed outlier: 3.651A pdb=" N VAL A1352 " --> pdb=" O SER A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1380 removed outlier: 3.802A pdb=" N GLU A1371 " --> pdb=" O ALA A1367 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A1377 " --> pdb=" O LEU A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1392 removed outlier: 4.210A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1405 No H-bonds generated for 'chain 'A' and resid 1403 through 1405' Processing helix chain 'A' and resid 1409 through 1411 No H-bonds generated for 'chain 'A' and resid 1409 through 1411' Processing helix chain 'A' and resid 1417 through 1419 No H-bonds generated for 'chain 'A' and resid 1417 through 1419' Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1433 through 1440 Processing helix chain 'A' and resid 1448 through 1453 Processing helix chain 'A' and resid 1469 through 1490 removed outlier: 4.640A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1507 removed outlier: 4.212A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1518 Processing helix chain 'A' and resid 1521 through 1524 Processing helix chain 'A' and resid 1531 through 1546 Processing helix chain 'A' and resid 1610 through 1627 removed outlier: 3.602A pdb=" N ILE A1620 " --> pdb=" O LEU A1616 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1650 Proline residue: A1643 - end of helix removed outlier: 3.724A pdb=" N ARG A1650 " --> pdb=" O GLN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1661 No H-bonds generated for 'chain 'A' and resid 1658 through 1661' Processing helix chain 'A' and resid 1702 through 1721 Processing helix chain 'F' and resid 10 through 21 removed outlier: 4.242A pdb=" N ARG F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 48 removed outlier: 5.046A pdb=" N GLN F 47 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 67 through 80 Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 100 through 108 removed outlier: 4.607A pdb=" N GLU F 105 " --> pdb=" O MET F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.949A pdb=" N LEU F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE F 157 " --> pdb=" O PHE F 153 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR F 158 " --> pdb=" O MET F 154 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 194 removed outlier: 3.626A pdb=" N GLU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 removed outlier: 4.569A pdb=" N TYR F 214 " --> pdb=" O ASN F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 251 removed outlier: 4.306A pdb=" N ASP F 250 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 removed outlier: 7.439A pdb=" N ILE F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N TYR F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA F 295 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 304 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL F 305 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 344 removed outlier: 3.550A pdb=" N MET F 322 " --> pdb=" O SER F 318 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 362 Processing helix chain 'F' and resid 365 through 378 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 395 through 410 removed outlier: 4.004A pdb=" N LYS F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 446 through 451 Processing helix chain 'F' and resid 485 through 494 Processing helix chain 'F' and resid 511 through 534 Processing helix chain 'F' and resid 544 through 551 Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.638A pdb=" N THR F 581 " --> pdb=" O ARG F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 605 Processing helix chain 'F' and resid 608 through 610 No H-bonds generated for 'chain 'F' and resid 608 through 610' Processing helix chain 'F' and resid 638 through 656 removed outlier: 3.937A pdb=" N ILE F 643 " --> pdb=" O LYS F 639 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 656 " --> pdb=" O VAL F 652 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.238A pdb=" N ASN A 198 " --> pdb=" O ILE A 25 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 85 through 88 removed outlier: 6.495A pdb=" N VAL A 111 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR A 88 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL A 113 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU A 61 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 136 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET A 63 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE A 138 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG A 167 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE A 138 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 169 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 219 through 225 Processing sheet with id= D, first strand: chain 'A' and resid 594 through 596 Processing sheet with id= E, first strand: chain 'A' and resid 703 through 706 removed outlier: 4.014A pdb=" N ARG A 703 " --> pdb=" O ILE A1361 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 786 through 789 removed outlier: 3.678A pdb=" N LEU A 830 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 729 through 733 removed outlier: 3.549A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 834 through 836 Processing sheet with id= I, first strand: chain 'A' and resid 881 through 883 removed outlier: 3.858A pdb=" N THR A 883 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 969 through 972 removed outlier: 4.723A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1674 through 1676 removed outlier: 3.743A pdb=" N ILE A1674 " --> pdb=" O MET A1681 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A1681 " --> pdb=" O ILE A1674 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1684 through 1688 removed outlier: 3.655A pdb=" N CYS A1684 " --> pdb=" O VAL A1695 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 198 through 200 removed outlier: 3.638A pdb=" N GLY F 24 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR F 172 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG F 167 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG F 59 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL F 136 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 61 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE F 138 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET F 63 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY F 114 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 88 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 219 through 224 removed outlier: 3.767A pdb=" N THR F 506 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 593 through 597 removed outlier: 4.437A pdb=" N VAL F 615 " --> pdb=" O LEU F 597 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 11.06 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3891 1.33 - 1.45: 5494 1.45 - 1.57: 11196 1.57 - 1.70: 211 1.70 - 1.82: 160 Bond restraints: 20952 Sorted by residual: bond pdb=" CA SER F 462 " pdb=" C SER F 462 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.11e+00 bond pdb=" CD GLN F 520 " pdb=" OE1 GLN F 520 " ideal model delta sigma weight residual 1.231 1.206 0.025 1.90e-02 2.77e+03 1.72e+00 bond pdb=" CD GLU A 209 " pdb=" OE1 GLU A 209 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.21e+00 bond pdb=" CA GLU F 140 " pdb=" CB GLU F 140 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.17e+00 bond pdb=" N GLU A 499 " pdb=" CA GLU A 499 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 ... (remaining 20947 not shown) Histogram of bond angle deviations from ideal: 97.64 - 105.42: 818 105.42 - 113.19: 11683 113.19 - 120.97: 10471 120.97 - 128.74: 5671 128.74 - 136.51: 196 Bond angle restraints: 28839 Sorted by residual: angle pdb=" C LYS F 164 " pdb=" N LEU F 165 " pdb=" CA LEU F 165 " ideal model delta sigma weight residual 120.94 133.24 -12.30 1.90e+00 2.77e-01 4.19e+01 angle pdb=" N GLN F 520 " pdb=" CA GLN F 520 " pdb=" CB GLN F 520 " ideal model delta sigma weight residual 110.28 116.73 -6.45 1.55e+00 4.16e-01 1.73e+01 angle pdb=" C LYS A 164 " pdb=" N LEU A 165 " pdb=" CA LEU A 165 " ideal model delta sigma weight residual 120.69 131.59 -10.90 2.95e+00 1.15e-01 1.37e+01 angle pdb=" C TYR F 519 " pdb=" N GLN F 520 " pdb=" CA GLN F 520 " ideal model delta sigma weight residual 120.31 115.31 5.00 1.52e+00 4.33e-01 1.08e+01 angle pdb=" N ASP F 636 " pdb=" CA ASP F 636 " pdb=" C ASP F 636 " ideal model delta sigma weight residual 111.03 114.68 -3.65 1.11e+00 8.12e-01 1.08e+01 ... (remaining 28834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.75: 11318 18.75 - 37.51: 980 37.51 - 56.26: 111 56.26 - 75.02: 42 75.02 - 93.77: 13 Dihedral angle restraints: 12464 sinusoidal: 5887 harmonic: 6577 Sorted by residual: dihedral pdb=" CA ILE A1654 " pdb=" C ILE A1654 " pdb=" N ASN A1655 " pdb=" CA ASN A1655 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C5' ADP A1802 " pdb=" O5' ADP A1802 " pdb=" PA ADP A1802 " pdb=" O2A ADP A1802 " ideal model delta sinusoidal sigma weight residual -60.00 -153.77 93.77 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" CA MET A 101 " pdb=" C MET A 101 " pdb=" N TRP A 102 " pdb=" CA TRP A 102 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 12461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2253 0.032 - 0.064: 732 0.064 - 0.096: 231 0.096 - 0.128: 103 0.128 - 0.160: 15 Chirality restraints: 3334 Sorted by residual: chirality pdb=" CG LEU F 249 " pdb=" CB LEU F 249 " pdb=" CD1 LEU F 249 " pdb=" CD2 LEU F 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA MET A 208 " pdb=" N MET A 208 " pdb=" C MET A 208 " pdb=" CB MET A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE F 138 " pdb=" N ILE F 138 " pdb=" C ILE F 138 " pdb=" CB ILE F 138 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 3331 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1402 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A1403 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1403 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1403 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1634 " 0.015 2.00e-02 2.50e+03 1.02e-02 2.59e+00 pdb=" CG TRP A1634 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A1634 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1634 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1634 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1634 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1634 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1634 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1634 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1634 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 904 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.022 5.00e-02 4.00e+02 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 452 2.63 - 3.20: 20010 3.20 - 3.77: 35525 3.77 - 4.33: 46995 4.33 - 4.90: 70282 Nonbonded interactions: 173264 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O3B ADP A1802 " model vdw 2.067 2.170 nonbonded pdb="MG MG F1801 " pdb=" O1B ADP F1802 " model vdw 2.077 2.170 nonbonded pdb=" O2' C D 27 " pdb=" OE2 GLU A 393 " model vdw 2.124 2.440 nonbonded pdb=" OG1 THR A1272 " pdb=" OG1 THR A1276 " model vdw 2.140 2.440 nonbonded pdb=" OG1 THR A 484 " pdb=" OD1 ASN A 486 " model vdw 2.160 2.440 ... (remaining 173259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N9 or name C8 or \ name N7 or name C5 or name C6 or name O6 or name N1 or name C2 or name N2 or nam \ e N3 or name C4 )) or resid 2 through 52)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 4.460 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 64.090 Find NCS groups from input model: 0.530 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.002 0.032 20952 Z= 0.151 Angle : 0.584 12.300 28839 Z= 0.305 Chirality : 0.039 0.160 3334 Planarity : 0.004 0.043 3299 Dihedral : 13.755 93.774 8196 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % 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: -0.30 (0.18), residues: 2221 helix: 0.60 (0.16), residues: 1046 sheet: -0.89 (0.32), residues: 250 loop : -0.83 (0.21), residues: 925 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.3215 time to fit residues: 81.6405 Evaluate side-chains 132 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2242 time to fit residues: 3.3417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.0040 chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN A 520 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20952 Z= 0.356 Angle : 0.672 10.936 28839 Z= 0.341 Chirality : 0.041 0.154 3334 Planarity : 0.005 0.044 3299 Dihedral : 7.555 89.925 3691 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.10 % Allowed : 6.91 % Favored : 92.99 % 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: -0.63 (0.18), residues: 2221 helix: 0.32 (0.16), residues: 1045 sheet: -1.06 (0.32), residues: 257 loop : -0.97 (0.21), residues: 919 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.3300 time to fit residues: 79.4249 Evaluate side-chains 123 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1889 time to fit residues: 3.3679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20952 Z= 0.182 Angle : 0.563 9.728 28839 Z= 0.283 Chirality : 0.039 0.154 3334 Planarity : 0.004 0.046 3299 Dihedral : 7.265 80.173 3691 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % 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: -0.43 (0.18), residues: 2221 helix: 0.55 (0.16), residues: 1037 sheet: -1.15 (0.31), residues: 261 loop : -0.88 (0.21), residues: 923 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.3281 time to fit residues: 79.0888 Evaluate side-chains 129 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20952 Z= 0.329 Angle : 0.643 11.195 28839 Z= 0.326 Chirality : 0.041 0.145 3334 Planarity : 0.004 0.039 3299 Dihedral : 7.388 75.264 3691 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.18 % 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: -0.73 (0.18), residues: 2221 helix: 0.28 (0.16), residues: 1047 sheet: -1.21 (0.32), residues: 257 loop : -1.06 (0.21), residues: 917 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 149 average time/residue: 0.3335 time to fit residues: 79.0055 Evaluate side-chains 124 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2377 time to fit residues: 3.5705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1639 ASN ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20952 Z= 0.412 Angle : 0.719 12.648 28839 Z= 0.366 Chirality : 0.043 0.161 3334 Planarity : 0.005 0.051 3299 Dihedral : 7.727 76.959 3691 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.26 % Rotamer: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % 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: -1.14 (0.18), residues: 2221 helix: -0.10 (0.16), residues: 1045 sheet: -1.34 (0.33), residues: 247 loop : -1.24 (0.21), residues: 929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 147 average time/residue: 0.3220 time to fit residues: 76.5543 Evaluate side-chains 121 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2413 time to fit residues: 3.5328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN A 210 ASN A 266 GLN A 354 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20952 Z= 0.174 Angle : 0.578 10.309 28839 Z= 0.292 Chirality : 0.040 0.143 3334 Planarity : 0.004 0.039 3299 Dihedral : 7.443 76.879 3691 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % 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: -0.62 (0.18), residues: 2221 helix: 0.41 (0.16), residues: 1035 sheet: -1.26 (0.33), residues: 241 loop : -1.01 (0.21), residues: 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.3274 time to fit residues: 77.9571 Evaluate side-chains 126 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.210 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2452 time to fit residues: 3.3741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.0470 chunk 25 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 266 GLN A 354 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20952 Z= 0.193 Angle : 0.580 10.329 28839 Z= 0.293 Chirality : 0.040 0.176 3334 Planarity : 0.004 0.094 3299 Dihedral : 7.315 75.429 3691 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.05 % Allowed : 1.64 % Favored : 98.31 % 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: -0.52 (0.18), residues: 2221 helix: 0.47 (0.16), residues: 1035 sheet: -1.15 (0.33), residues: 241 loop : -0.95 (0.21), residues: 945 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.3436 time to fit residues: 81.9753 Evaluate side-chains 125 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 20 optimal weight: 0.0000 chunk 175 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN A 266 GLN A 354 ASN A 570 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20952 Z= 0.148 Angle : 0.559 8.814 28839 Z= 0.281 Chirality : 0.039 0.142 3334 Planarity : 0.004 0.068 3299 Dihedral : 7.088 73.093 3691 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2221 helix: 0.60 (0.16), residues: 1038 sheet: -1.02 (0.33), residues: 242 loop : -0.88 (0.21), residues: 941 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.3323 time to fit residues: 81.4158 Evaluate side-chains 131 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2313 time to fit residues: 3.3318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20952 Z= 0.154 Angle : 0.575 10.495 28839 Z= 0.287 Chirality : 0.039 0.177 3334 Planarity : 0.004 0.046 3299 Dihedral : 6.978 72.694 3691 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2221 helix: 0.62 (0.17), residues: 1038 sheet: -0.95 (0.33), residues: 241 loop : -0.77 (0.22), residues: 942 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3341 time to fit residues: 83.7084 Evaluate side-chains 131 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 231 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 454 ASN A 520 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20952 Z= 0.149 Angle : 0.563 9.517 28839 Z= 0.279 Chirality : 0.039 0.147 3334 Planarity : 0.004 0.044 3299 Dihedral : 6.891 72.336 3691 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.25 (0.18), residues: 2221 helix: 0.68 (0.17), residues: 1034 sheet: -1.06 (0.32), residues: 267 loop : -0.75 (0.22), residues: 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3424 time to fit residues: 82.7223 Evaluate side-chains 131 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 169 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 33 optimal weight: 0.0970 chunk 161 optimal weight: 4.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 520 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.065687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047771 restraints weight = 138105.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049220 restraints weight = 80936.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050178 restraints weight = 56923.576| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20952 Z= 0.139 Angle : 0.554 8.670 28839 Z= 0.275 Chirality : 0.038 0.146 3334 Planarity : 0.004 0.041 3299 Dihedral : 6.750 71.762 3691 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 (0.19), residues: 2221 helix: 0.76 (0.17), residues: 1030 sheet: -0.97 (0.32), residues: 256 loop : -0.69 (0.22), residues: 935 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.87 seconds wall clock time: 62 minutes 22.31 seconds (3742.31 seconds total)