Starting phenix.real_space_refine on Fri Mar 15 18:57:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe4_33154/03_2024/7xe4_33154_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe4_33154/03_2024/7xe4_33154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe4_33154/03_2024/7xe4_33154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe4_33154/03_2024/7xe4_33154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe4_33154/03_2024/7xe4_33154_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe4_33154/03_2024/7xe4_33154_updated.pdb" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 8258 2.51 5 N 2051 2.21 5 O 2145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 279": "OD1" <-> "OD2" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 691": "OD1" <-> "OD2" Residue "F PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 741": "OE1" <-> "OE2" Residue "F TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 832": "OE1" <-> "OE2" Residue "F GLU 859": "OE1" <-> "OE2" Residue "F GLU 934": "OE1" <-> "OE2" Residue "F TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 974": "OE1" <-> "OE2" Residue "F PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 984": "OE1" <-> "OE2" Residue "F GLU 989": "OE1" <-> "OE2" Residue "F GLU 991": "OE1" <-> "OE2" Residue "F GLU 1110": "OE1" <-> "OE2" Residue "F GLU 1141": "OE1" <-> "OE2" Residue "F PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1222": "OD1" <-> "OD2" Residue "F GLU 1240": "OE1" <-> "OE2" Residue "F TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1353": "OD1" <-> "OD2" Residue "F PHE 1370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1380": "OE1" <-> "OE2" Residue "F PHE 1475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1858": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12529 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 12246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 12246 Classifications: {'peptide': 1503} Link IDs: {'PTRANS': 65, 'TRANS': 1437} Chain breaks: 10 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 255 Unusual residues: {'C14': 1, 'D10': 6, 'D12': 3, 'DD9': 7, 'HP6': 7, 'XKP': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 7.28, per 1000 atoms: 0.58 Number of scatterers: 12529 At special positions: 0 Unit cell: (113.16, 119.6, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 1 15.00 O 2145 8.00 N 2051 7.00 C 8258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 658 " - pdb=" SG CYS F 669 " distance=2.22 Simple disulfide: pdb=" SG CYS F1328 " - pdb=" SG CYS F1345 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F1849 " Time building additional restraints: 5.01 Conformation dependent library (CDL) restraints added in 2.2 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 3 sheets defined 54.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'F' and resid 161 through 175 Processing helix chain 'F' and resid 179 through 198 removed outlier: 3.719A pdb=" N ARG F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 213 removed outlier: 3.947A pdb=" N LEU F 206 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 Processing helix chain 'F' and resid 233 through 242 Processing helix chain 'F' and resid 283 through 293 removed outlier: 3.536A pdb=" N MET F 293 " --> pdb=" O TRP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 314 removed outlier: 4.066A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 336 Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 390 through 398 removed outlier: 3.594A pdb=" N GLN F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU F 396 " --> pdb=" O ASP F 392 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP F 398 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 405 removed outlier: 4.061A pdb=" N LYS F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 420 through 422 No H-bonds generated for 'chain 'F' and resid 420 through 422' Processing helix chain 'F' and resid 424 through 427 removed outlier: 4.246A pdb=" N GLY F 427 " --> pdb=" O LEU F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 424 through 427' Processing helix chain 'F' and resid 444 through 450 removed outlier: 4.213A pdb=" N LEU F 448 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL F 449 " --> pdb=" O TRP F 445 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 444 through 450' Processing helix chain 'F' and resid 453 through 469 removed outlier: 3.790A pdb=" N VAL F 457 " --> pdb=" O ASN F 453 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 458 " --> pdb=" O ARG F 454 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE F 462 " --> pdb=" O MET F 458 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 467 " --> pdb=" O PHE F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 516 removed outlier: 4.141A pdb=" N GLY F 500 " --> pdb=" O CYS F 496 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR F 501 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL F 502 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA F 503 " --> pdb=" O GLY F 499 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER F 504 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER F 516 " --> pdb=" O LEU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 542 Processing helix chain 'F' and resid 545 through 550 Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 563 through 581 Processing helix chain 'F' and resid 617 through 637 removed outlier: 4.021A pdb=" N PHE F 629 " --> pdb=" O TRP F 625 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR F 633 " --> pdb=" O PHE F 629 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER F 634 " --> pdb=" O ALA F 630 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR F 637 " --> pdb=" O TYR F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 650 removed outlier: 3.843A pdb=" N ARG F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 671 No H-bonds generated for 'chain 'F' and resid 669 through 671' Processing helix chain 'F' and resid 673 through 685 Processing helix chain 'F' and resid 687 through 710 removed outlier: 4.388A pdb=" N THR F 692 " --> pdb=" O PHE F 688 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 698 " --> pdb=" O LEU F 694 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 700 " --> pdb=" O TYR F 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 727 through 733 removed outlier: 3.753A pdb=" N SER F 732 " --> pdb=" O LYS F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 764 removed outlier: 3.520A pdb=" N VAL F 753 " --> pdb=" O LEU F 749 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 756 " --> pdb=" O GLN F 752 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 758 " --> pdb=" O TRP F 754 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 761 " --> pdb=" O ILE F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 773 removed outlier: 4.149A pdb=" N GLN F 773 " --> pdb=" O ILE F 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 769 through 773' Processing helix chain 'F' and resid 794 through 796 No H-bonds generated for 'chain 'F' and resid 794 through 796' Processing helix chain 'F' and resid 810 through 812 No H-bonds generated for 'chain 'F' and resid 810 through 812' Processing helix chain 'F' and resid 814 through 826 removed outlier: 4.004A pdb=" N LEU F 826 " --> pdb=" O PHE F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 860 No H-bonds generated for 'chain 'F' and resid 858 through 860' Processing helix chain 'F' and resid 872 through 879 Processing helix chain 'F' and resid 883 through 895 Processing helix chain 'F' and resid 933 through 945 Processing helix chain 'F' and resid 951 through 971 removed outlier: 4.715A pdb=" N ASN F 959 " --> pdb=" O SER F 955 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR F 960 " --> pdb=" O GLY F 956 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER F 961 " --> pdb=" O PHE F 957 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG F 962 " --> pdb=" O MET F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 974 through 977 No H-bonds generated for 'chain 'F' and resid 974 through 977' Processing helix chain 'F' and resid 983 through 994 Processing helix chain 'F' and resid 1007 through 1009 No H-bonds generated for 'chain 'F' and resid 1007 through 1009' Processing helix chain 'F' and resid 1012 through 1024 removed outlier: 3.921A pdb=" N GLU F1016 " --> pdb=" O PRO F1012 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN F1017 " --> pdb=" O HIS F1013 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F1018 " --> pdb=" O GLU F1014 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F1022 " --> pdb=" O ALA F1018 " (cutoff:3.500A) Processing helix chain 'F' and resid 1084 through 1089 removed outlier: 3.632A pdb=" N HIS F1088 " --> pdb=" O ASP F1084 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA F1089 " --> pdb=" O ASN F1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1084 through 1089' Processing helix chain 'F' and resid 1115 through 1120 removed outlier: 4.179A pdb=" N ALA F1120 " --> pdb=" O ARG F1116 " (cutoff:3.500A) Processing helix chain 'F' and resid 1169 through 1186 removed outlier: 3.633A pdb=" N GLN F1186 " --> pdb=" O ARG F1182 " (cutoff:3.500A) Processing helix chain 'F' and resid 1201 through 1206 removed outlier: 3.815A pdb=" N THR F1206 " --> pdb=" O THR F1202 " (cutoff:3.500A) Processing helix chain 'F' and resid 1224 through 1232 removed outlier: 3.545A pdb=" N ARG F1232 " --> pdb=" O ASN F1228 " (cutoff:3.500A) Processing helix chain 'F' and resid 1274 through 1278 Processing helix chain 'F' and resid 1284 through 1291 removed outlier: 3.812A pdb=" N THR F1289 " --> pdb=" O ASP F1285 " (cutoff:3.500A) Processing helix chain 'F' and resid 1295 through 1324 removed outlier: 3.693A pdb=" N ASN F1300 " --> pdb=" O GLY F1296 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F1302 " --> pdb=" O HIS F1298 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE F1303 " --> pdb=" O LEU F1299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F1305 " --> pdb=" O ASN F1301 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN F1309 " --> pdb=" O GLN F1305 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F1314 " --> pdb=" O MET F1310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN F1317 " --> pdb=" O LEU F1313 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU F1324 " --> pdb=" O SER F1320 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1378 removed outlier: 4.290A pdb=" N VAL F1355 " --> pdb=" O ALA F1351 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG F1356 " --> pdb=" O VAL F1352 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F1357 " --> pdb=" O ASP F1353 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F1360 " --> pdb=" O ARG F1356 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER F1361 " --> pdb=" O ARG F1357 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F1364 " --> pdb=" O LEU F1360 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL F1365 " --> pdb=" O SER F1361 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE F1370 " --> pdb=" O PHE F1366 " (cutoff:3.500A) Proline residue: F1372 - end of helix removed outlier: 4.023A pdb=" N VAL F1375 " --> pdb=" O VAL F1371 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F1376 " --> pdb=" O PRO F1372 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F1377 " --> pdb=" O ILE F1373 " (cutoff:3.500A) Processing helix chain 'F' and resid 1383 through 1391 removed outlier: 3.893A pdb=" N GLN F1388 " --> pdb=" O TRP F1384 " (cutoff:3.500A) Processing helix chain 'F' and resid 1399 through 1405 Processing helix chain 'F' and resid 1409 through 1417 Processing helix chain 'F' and resid 1438 through 1444 removed outlier: 3.734A pdb=" N ARG F1444 " --> pdb=" O ILE F1440 " (cutoff:3.500A) Processing helix chain 'F' and resid 1451 through 1466 Processing helix chain 'F' and resid 1470 through 1483 removed outlier: 4.227A pdb=" N LEU F1473 " --> pdb=" O ALA F1470 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP F1474 " --> pdb=" O PRO F1471 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA F1477 " --> pdb=" O TRP F1474 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F1479 " --> pdb=" O TRP F1476 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER F1480 " --> pdb=" O ALA F1477 " (cutoff:3.500A) Processing helix chain 'F' and resid 1497 through 1511 removed outlier: 3.548A pdb=" N ASP F1505 " --> pdb=" O LEU F1501 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F1507 " --> pdb=" O TYR F1503 " (cutoff:3.500A) Processing helix chain 'F' and resid 1560 through 1563 No H-bonds generated for 'chain 'F' and resid 1560 through 1563' Processing helix chain 'F' and resid 1566 through 1583 removed outlier: 5.779A pdb=" N TYR F1571 " --> pdb=" O PRO F1567 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F1572 " --> pdb=" O CYS F1568 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS F1575 " --> pdb=" O TYR F1571 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA F1578 " --> pdb=" O GLY F1574 " (cutoff:3.500A) Processing helix chain 'F' and resid 1599 through 1606 removed outlier: 3.549A pdb=" N ILE F1603 " --> pdb=" O VAL F1599 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS F1605 " --> pdb=" O ARG F1601 " (cutoff:3.500A) Processing helix chain 'F' and resid 1608 through 1625 removed outlier: 3.594A pdb=" N SER F1624 " --> pdb=" O CYS F1620 " (cutoff:3.500A) Processing helix chain 'F' and resid 1639 through 1664 removed outlier: 3.911A pdb=" N ILE F1652 " --> pdb=" O GLY F1648 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS F1654 " --> pdb=" O ALA F1650 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP F1662 " --> pdb=" O PHE F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1670 through 1696 removed outlier: 4.348A pdb=" N ILE F1674 " --> pdb=" O VAL F1670 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY F1675 " --> pdb=" O ARG F1671 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F1692 " --> pdb=" O HIS F1688 " (cutoff:3.500A) Processing helix chain 'F' and resid 1725 through 1752 removed outlier: 3.667A pdb=" N LEU F1730 " --> pdb=" O PRO F1726 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F1733 " --> pdb=" O GLU F1729 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F1742 " --> pdb=" O SER F1738 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F1750 " --> pdb=" O LEU F1746 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F1751 " --> pdb=" O GLY F1747 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE F1752 " --> pdb=" O HIS F1748 " (cutoff:3.500A) Processing helix chain 'F' and resid 1755 through 1758 No H-bonds generated for 'chain 'F' and resid 1755 through 1758' Processing helix chain 'F' and resid 1764 through 1774 removed outlier: 3.527A pdb=" N LEU F1774 " --> pdb=" O MET F1770 " (cutoff:3.500A) Processing helix chain 'F' and resid 1787 through 1823 removed outlier: 3.522A pdb=" N LYS F1799 " --> pdb=" O ARG F1795 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F1800 " --> pdb=" O MET F1796 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F1802 " --> pdb=" O LYS F1798 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F1803 " --> pdb=" O LYS F1799 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE F1805 " --> pdb=" O CYS F1801 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F1815 " --> pdb=" O PHE F1811 " (cutoff:3.500A) Proline residue: F1818 - end of helix removed outlier: 5.152A pdb=" N ALA F1823 " --> pdb=" O ALA F1819 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 779 through 781 Processing sheet with id= B, first strand: chain 'F' and resid 1198 through 1200 removed outlier: 6.519A pdb=" N GLN F1029 " --> pdb=" O VAL F1002 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET F1004 " --> pdb=" O GLN F1029 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA F1031 " --> pdb=" O MET F1004 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F1051 " --> pdb=" O PHE F1068 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE F1068 " --> pdb=" O LEU F1051 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 1150 through 1152 removed outlier: 3.566A pdb=" N GLY F1152 " --> pdb=" O LYS F1237 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1374 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: 3.76 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2098 1.32 - 1.45: 3484 1.45 - 1.57: 7130 1.57 - 1.69: 2 1.69 - 1.82: 118 Bond restraints: 12832 Sorted by residual: bond pdb=" C17 XKP F1925 " pdb=" C22 XKP F1925 " ideal model delta sigma weight residual 1.524 1.306 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C SER F1398 " pdb=" N PRO F1399 " ideal model delta sigma weight residual 1.335 1.390 -0.054 1.36e-02 5.41e+03 1.60e+01 bond pdb=" C GLN F1842 " pdb=" N PRO F1843 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.66e+00 bond pdb=" C8 XKP F1925 " pdb=" O2 XKP F1925 " ideal model delta sigma weight residual 1.409 1.452 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" N ILE F 455 " pdb=" CA ILE F 455 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.32e-02 5.74e+03 4.42e+00 ... (remaining 12827 not shown) Histogram of bond angle deviations from ideal: 96.17 - 103.77: 175 103.77 - 111.37: 5388 111.37 - 118.97: 4787 118.97 - 126.57: 6730 126.57 - 134.17: 224 Bond angle restraints: 17304 Sorted by residual: angle pdb=" N VAL F 882 " pdb=" CA VAL F 882 " pdb=" C VAL F 882 " ideal model delta sigma weight residual 113.71 107.39 6.32 9.50e-01 1.11e+00 4.43e+01 angle pdb=" N ILE F1844 " pdb=" CA ILE F1844 " pdb=" C ILE F1844 " ideal model delta sigma weight residual 113.71 107.97 5.74 9.50e-01 1.11e+00 3.65e+01 angle pdb=" C ASN F 280 " pdb=" CA ASN F 280 " pdb=" CB ASN F 280 " ideal model delta sigma weight residual 116.54 110.67 5.87 1.15e+00 7.56e-01 2.61e+01 angle pdb=" C ASP F 231 " pdb=" CA ASP F 231 " pdb=" CB ASP F 231 " ideal model delta sigma weight residual 117.23 110.35 6.88 1.36e+00 5.41e-01 2.56e+01 angle pdb=" N LEU F1757 " pdb=" CA LEU F1757 " pdb=" C LEU F1757 " ideal model delta sigma weight residual 114.75 108.67 6.08 1.26e+00 6.30e-01 2.33e+01 ... (remaining 17299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.78: 7323 28.78 - 57.57: 280 57.57 - 86.35: 24 86.35 - 115.14: 2 115.14 - 143.92: 7 Dihedral angle restraints: 7636 sinusoidal: 3217 harmonic: 4419 Sorted by residual: dihedral pdb=" CB CYS F1328 " pdb=" SG CYS F1328 " pdb=" SG CYS F1345 " pdb=" CB CYS F1345 " ideal model delta sinusoidal sigma weight residual 93.00 146.31 -53.31 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA LEU F1840 " pdb=" C LEU F1840 " pdb=" N PHE F1841 " pdb=" CA PHE F1841 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" C6 XKP F1925 " pdb=" C7 XKP F1925 " pdb=" C8 XKP F1925 " pdb=" O2 XKP F1925 " ideal model delta sinusoidal sigma weight residual -67.90 76.02 -143.92 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 7633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1669 0.067 - 0.133: 212 0.133 - 0.200: 10 0.200 - 0.267: 1 0.267 - 0.333: 1 Chirality restraints: 1893 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-02 2.50e+03 2.78e+02 chirality pdb=" C7 XKP F1925 " pdb=" C6 XKP F1925 " pdb=" C8 XKP F1925 " pdb=" O6 XKP F1925 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA THR F 438 " pdb=" N THR F 438 " pdb=" C THR F 438 " pdb=" CB THR F 438 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1890 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F1849 " 0.102 2.00e-02 2.50e+03 9.87e-02 1.22e+02 pdb=" CG ASN F1849 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN F1849 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN F1849 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.064 2.00e-02 2.50e+03 5.28e-02 3.48e+01 pdb=" C7 NAG A 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 699 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C VAL F 699 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL F 699 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN F 700 " 0.017 2.00e-02 2.50e+03 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1273 2.74 - 3.28: 12860 3.28 - 3.82: 18668 3.82 - 4.36: 21394 4.36 - 4.90: 36769 Nonbonded interactions: 90964 Sorted by model distance: nonbonded pdb=" NE2 HIS F 771 " pdb=" O GLU F 807 " model vdw 2.199 2.520 nonbonded pdb=" O ARG F 852 " pdb=" OG1 THR F 949 " model vdw 2.200 2.440 nonbonded pdb=" O SER F 751 " pdb=" ND2 ASN F 755 " model vdw 2.204 2.520 nonbonded pdb=" OD1 ASN F1849 " pdb=" O5 NAG A 1 " model vdw 2.211 3.040 nonbonded pdb=" O ARG F1728 " pdb=" OG1 THR F1731 " model vdw 2.225 2.440 ... (remaining 90959 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: 0.640 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: 3.040 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.060 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.006 0.218 12832 Z= 0.369 Angle : 0.861 11.295 17304 Z= 0.504 Chirality : 0.045 0.333 1893 Planarity : 0.005 0.070 2142 Dihedral : 15.211 143.921 4772 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.99 % Favored : 89.60 % Rotamer: Outliers : 0.45 % Allowed : 0.53 % Favored : 99.02 % 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: -2.45 (0.22), residues: 1481 helix: -0.35 (0.19), residues: 777 sheet: -2.30 (0.69), residues: 54 loop : -3.26 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F1474 HIS 0.004 0.001 HIS F 188 PHE 0.026 0.002 PHE F1658 TYR 0.039 0.002 TYR F 148 ARG 0.010 0.001 ARG F 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 709 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.5914 (t80) REVERT: F 774 LYS cc_start: 0.8980 (pttt) cc_final: 0.8681 (ttpt) REVERT: F 878 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8836 (tm-30) REVERT: F 1400 MET cc_start: 0.2644 (tmm) cc_final: 0.1041 (ptp) outliers start: 6 outliers final: 2 residues processed: 177 average time/residue: 0.2573 time to fit residues: 65.8876 Evaluate side-chains 142 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 669 CYS Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 709 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 40.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1220 ASN F1854 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12832 Z= 0.239 Angle : 0.669 9.594 17304 Z= 0.346 Chirality : 0.043 0.241 1893 Planarity : 0.005 0.066 2142 Dihedral : 9.711 134.944 1886 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.87 % Favored : 88.93 % Rotamer: Outliers : 0.83 % Allowed : 8.48 % Favored : 90.68 % 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: -1.87 (0.22), residues: 1481 helix: 0.15 (0.19), residues: 803 sheet: -1.63 (0.75), residues: 52 loop : -3.18 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F1474 HIS 0.006 0.001 HIS F 765 PHE 0.021 0.001 PHE F1658 TYR 0.023 0.002 TYR F 148 ARG 0.004 0.000 ARG F 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: F 317 GLN cc_start: 0.8570 (tm130) cc_final: 0.8321 (tm-30) REVERT: F 774 LYS cc_start: 0.8928 (pttt) cc_final: 0.8630 (ttpt) REVERT: F 878 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8788 (tm-30) REVERT: F 884 TRP cc_start: 0.9144 (t-100) cc_final: 0.8749 (t-100) REVERT: F 1220 ASN cc_start: 0.7246 (t160) cc_final: 0.6932 (m-40) REVERT: F 1499 PHE cc_start: 0.8715 (t80) cc_final: 0.8493 (t80) REVERT: F 1736 GLU cc_start: 0.9054 (tp30) cc_final: 0.8734 (tp30) REVERT: F 1796 MET cc_start: 0.8289 (tpt) cc_final: 0.7620 (tpt) outliers start: 11 outliers final: 5 residues processed: 162 average time/residue: 0.2411 time to fit residues: 56.9307 Evaluate side-chains 149 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 617 ASP Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 40.0000 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 40.0000 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12832 Z= 0.183 Angle : 0.604 10.616 17304 Z= 0.309 Chirality : 0.041 0.233 1893 Planarity : 0.004 0.072 2142 Dihedral : 8.840 154.845 1879 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.25 % Favored : 90.55 % Rotamer: Outliers : 1.67 % Allowed : 12.20 % Favored : 86.14 % 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: -1.48 (0.22), residues: 1481 helix: 0.49 (0.19), residues: 797 sheet: -1.41 (0.77), residues: 54 loop : -3.03 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F1474 HIS 0.005 0.001 HIS F1647 PHE 0.014 0.001 PHE F1499 TYR 0.018 0.001 TYR F 148 ARG 0.005 0.000 ARG F 817 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.475 Fit side-chains REVERT: F 317 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: F 386 LYS cc_start: 0.8844 (mttm) cc_final: 0.8608 (mttm) REVERT: F 774 LYS cc_start: 0.8932 (pttt) cc_final: 0.8604 (ttpt) REVERT: F 878 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8773 (tm-30) REVERT: F 884 TRP cc_start: 0.9130 (t-100) cc_final: 0.8742 (t-100) REVERT: F 1053 ASP cc_start: 0.8429 (t0) cc_final: 0.8175 (t0) REVERT: F 1220 ASN cc_start: 0.7350 (t160) cc_final: 0.6975 (m-40) REVERT: F 1400 MET cc_start: 0.2668 (tmm) cc_final: 0.1047 (ptp) REVERT: F 1499 PHE cc_start: 0.8535 (t80) cc_final: 0.8292 (t80) REVERT: F 1503 TYR cc_start: 0.9407 (t80) cc_final: 0.9176 (t80) REVERT: F 1736 GLU cc_start: 0.8959 (tp30) cc_final: 0.8624 (tp30) outliers start: 22 outliers final: 9 residues processed: 178 average time/residue: 0.2510 time to fit residues: 64.6372 Evaluate side-chains 159 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1271 LEU Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1617 LEU Chi-restraints excluded: chain F residue 1844 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12832 Z= 0.348 Angle : 0.668 9.297 17304 Z= 0.339 Chirality : 0.043 0.206 1893 Planarity : 0.005 0.066 2142 Dihedral : 8.695 149.244 1879 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.80 % Favored : 88.99 % Rotamer: Outliers : 2.20 % Allowed : 15.83 % Favored : 81.97 % 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: -1.37 (0.23), residues: 1481 helix: 0.60 (0.19), residues: 796 sheet: -1.41 (0.76), residues: 54 loop : -2.99 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F1474 HIS 0.008 0.001 HIS F 188 PHE 0.016 0.001 PHE F1499 TYR 0.022 0.001 TYR F 148 ARG 0.005 0.000 ARG F 817 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.389 Fit side-chains REVERT: F 774 LYS cc_start: 0.8963 (pttt) cc_final: 0.8588 (ttmt) REVERT: F 878 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8782 (tm-30) REVERT: F 884 TRP cc_start: 0.9149 (t-100) cc_final: 0.8778 (t-100) REVERT: F 1053 ASP cc_start: 0.8456 (t0) cc_final: 0.8229 (t0) REVERT: F 1220 ASN cc_start: 0.7564 (t160) cc_final: 0.7198 (m-40) REVERT: F 1327 MET cc_start: 0.8921 (mpp) cc_final: 0.8653 (mpp) REVERT: F 1400 MET cc_start: 0.2655 (tmm) cc_final: 0.1087 (ptp) REVERT: F 1499 PHE cc_start: 0.8614 (t80) cc_final: 0.8305 (t80) REVERT: F 1565 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7896 (mm) REVERT: F 1736 GLU cc_start: 0.8971 (tp30) cc_final: 0.8632 (tp30) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2474 time to fit residues: 60.1110 Evaluate side-chains 164 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 617 ASP Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 967 LEU Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1238 HIS Chi-restraints excluded: chain F residue 1271 LEU Chi-restraints excluded: chain F residue 1308 LEU Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1479 LEU Chi-restraints excluded: chain F residue 1565 ILE Chi-restraints excluded: chain F residue 1617 LEU Chi-restraints excluded: chain F residue 1797 VAL Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 0.0670 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 40.0000 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12832 Z= 0.329 Angle : 0.648 10.244 17304 Z= 0.331 Chirality : 0.043 0.207 1893 Planarity : 0.004 0.072 2142 Dihedral : 8.349 126.183 1879 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.33 % Favored : 89.47 % Rotamer: Outliers : 2.50 % Allowed : 17.12 % Favored : 80.38 % 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: -1.30 (0.23), residues: 1481 helix: 0.70 (0.19), residues: 789 sheet: -1.28 (0.77), residues: 54 loop : -2.98 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F1474 HIS 0.006 0.001 HIS F 188 PHE 0.020 0.001 PHE F 821 TYR 0.025 0.001 TYR F 148 ARG 0.006 0.000 ARG F 817 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 878 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8780 (tm-30) REVERT: F 884 TRP cc_start: 0.9135 (t-100) cc_final: 0.8794 (t-100) REVERT: F 1220 ASN cc_start: 0.7602 (t160) cc_final: 0.7090 (t0) REVERT: F 1400 MET cc_start: 0.2654 (tmm) cc_final: 0.0980 (ptp) REVERT: F 1499 PHE cc_start: 0.8613 (t80) cc_final: 0.8296 (t80) REVERT: F 1565 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7903 (mm) REVERT: F 1736 GLU cc_start: 0.8951 (tp30) cc_final: 0.8610 (tp30) outliers start: 33 outliers final: 22 residues processed: 170 average time/residue: 0.2431 time to fit residues: 60.2604 Evaluate side-chains 164 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 617 ASP Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 967 LEU Chi-restraints excluded: chain F residue 1108 TYR Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1238 HIS Chi-restraints excluded: chain F residue 1271 LEU Chi-restraints excluded: chain F residue 1308 LEU Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1479 LEU Chi-restraints excluded: chain F residue 1565 ILE Chi-restraints excluded: chain F residue 1617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.385 > 50: distance: 55 - 67: 5.290 distance: 63 - 67: 3.249 distance: 67 - 68: 3.689 distance: 68 - 69: 5.321 distance: 68 - 71: 3.001 distance: 69 - 70: 12.976 distance: 69 - 73: 8.039 distance: 71 - 72: 3.222 distance: 73 - 74: 6.986 distance: 74 - 75: 14.700 distance: 74 - 77: 6.504 distance: 75 - 76: 7.547 distance: 75 - 81: 10.326 distance: 77 - 78: 3.115 distance: 78 - 79: 5.570 distance: 82 - 83: 7.063 distance: 82 - 85: 9.776 distance: 83 - 84: 17.239 distance: 83 - 89: 12.295 distance: 85 - 86: 10.712 distance: 85 - 87: 15.579 distance: 86 - 88: 5.213 distance: 89 - 90: 10.205 distance: 90 - 91: 15.444 distance: 90 - 93: 5.773 distance: 91 - 92: 18.311 distance: 91 - 100: 12.042 distance: 93 - 94: 6.047 distance: 94 - 95: 14.195 distance: 94 - 96: 9.551 distance: 95 - 97: 11.571 distance: 96 - 98: 7.921 distance: 97 - 99: 14.533 distance: 98 - 99: 11.546 distance: 100 - 101: 12.409 distance: 101 - 102: 24.669 distance: 101 - 104: 24.935 distance: 102 - 103: 15.676 distance: 102 - 105: 12.338 distance: 105 - 106: 24.286 distance: 105 - 111: 16.304 distance: 106 - 107: 10.742 distance: 106 - 109: 4.754 distance: 107 - 108: 23.336 distance: 107 - 112: 11.031 distance: 109 - 110: 17.542 distance: 110 - 111: 42.779 distance: 112 - 113: 8.835 distance: 113 - 116: 4.181 distance: 114 - 115: 5.595 distance: 114 - 123: 5.021 distance: 116 - 117: 10.356 distance: 117 - 118: 7.306 distance: 117 - 119: 15.180 distance: 118 - 120: 24.517 distance: 119 - 121: 15.532 distance: 120 - 122: 20.501 distance: 121 - 122: 18.400 distance: 123 - 124: 10.081 distance: 124 - 125: 15.743 distance: 124 - 127: 6.590 distance: 125 - 126: 13.649 distance: 125 - 130: 12.896 distance: 127 - 128: 13.089 distance: 127 - 129: 13.041 distance: 130 - 131: 5.524 distance: 131 - 132: 45.239 distance: 131 - 134: 11.734 distance: 132 - 133: 39.076 distance: 132 - 141: 37.382 distance: 134 - 135: 8.842 distance: 135 - 136: 36.916 distance: 135 - 137: 19.497 distance: 136 - 138: 10.239 distance: 137 - 139: 29.425 distance: 138 - 140: 11.983 distance: 139 - 140: 18.851 distance: 141 - 142: 24.561 distance: 142 - 143: 14.522 distance: 142 - 145: 29.547 distance: 143 - 144: 17.660 distance: 143 - 149: 28.492 distance: 145 - 146: 19.477 distance: 146 - 147: 29.696 distance: 146 - 148: 20.293