Starting phenix.real_space_refine on Sun Dec 10 06:36:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/12_2023/7zgk_14708_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/12_2023/7zgk_14708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/12_2023/7zgk_14708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/12_2023/7zgk_14708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/12_2023/7zgk_14708_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/12_2023/7zgk_14708_neut.pdb" } resolution = 3.59 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= -0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 8656 2.51 5 N 2300 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 61": "OD1" <-> "OD2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "B PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1153": "OE1" <-> "OE2" Residue "B TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13639 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4907 Classifications: {'peptide': 630} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7197 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 861} Chain breaks: 2 Chain: "C" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1535 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Time building chain proxies: 7.44, per 1000 atoms: 0.55 Number of scatterers: 13639 At special positions: 0 Unit cell: (83.628, 132.48, 185.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2627 8.00 N 2300 7.00 C 8656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 873 " - pdb=" SG CYS B1513 " distance=2.03 Simple disulfide: pdb=" SG CYS B1101 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1358 " - pdb=" SG CYS B1489 " distance=2.03 Simple disulfide: pdb=" SG CYS B1389 " - pdb=" SG CYS B1458 " distance=2.03 Simple disulfide: pdb=" SG CYS B1506 " - pdb=" SG CYS B1511 " distance=2.03 Simple disulfide: pdb=" SG CYS B1518 " - pdb=" SG CYS B1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1537 " - pdb=" SG CYS B1661 " distance=2.03 Simple disulfide: pdb=" SG CYS B1637 " - pdb=" SG CYS B1646 " 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 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 25 sheets defined 29.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.683A pdb=" N VAL A 320 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.779A pdb=" N ASN A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 452 " --> pdb=" O VAL A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.536A pdb=" N GLU A 484 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 removed outlier: 3.867A pdb=" N LEU A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'B' and resid 997 through 1004 removed outlier: 3.586A pdb=" N LEU B1000 " --> pdb=" O ALA B 997 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B1001 " --> pdb=" O GLU B 998 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS B1002 " --> pdb=" O ARG B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1033 through 1038 Processing helix chain 'B' and resid 1040 through 1059 removed outlier: 3.737A pdb=" N GLY B1044 " --> pdb=" O GLU B1040 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B1059 " --> pdb=" O GLN B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1089 removed outlier: 3.594A pdb=" N LEU B1088 " --> pdb=" O LYS B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1112 removed outlier: 3.551A pdb=" N LEU B1100 " --> pdb=" O ASP B1096 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1138 through 1156 removed outlier: 3.654A pdb=" N ALA B1142 " --> pdb=" O GLU B1138 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP B1156 " --> pdb=" O GLN B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1179 removed outlier: 3.926A pdb=" N ASN B1179 " --> pdb=" O PHE B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1183 Processing helix chain 'B' and resid 1185 through 1198 removed outlier: 3.686A pdb=" N GLN B1198 " --> pdb=" O TYR B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1204 through 1213 Processing helix chain 'B' and resid 1214 through 1218 removed outlier: 3.623A pdb=" N LYS B1217 " --> pdb=" O ALA B1214 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B1218 " --> pdb=" O LYS B1215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1214 through 1218' Processing helix chain 'B' and resid 1225 through 1244 removed outlier: 3.566A pdb=" N ASN B1229 " --> pdb=" O LYS B1225 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1259 removed outlier: 4.158A pdb=" N VAL B1252 " --> pdb=" O PHE B1248 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1285 Processing helix chain 'B' and resid 1414 through 1423 removed outlier: 3.963A pdb=" N ASN B1423 " --> pdb=" O LYS B1419 " (cutoff:3.500A) Processing helix chain 'B' and resid 1430 through 1435 Processing helix chain 'B' and resid 1528 through 1536 Processing helix chain 'B' and resid 1588 through 1594 removed outlier: 4.294A pdb=" N GLU B1592 " --> pdb=" O ILE B1588 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B1593 " --> pdb=" O LYS B1589 " (cutoff:3.500A) Processing helix chain 'B' and resid 1639 through 1659 removed outlier: 4.511A pdb=" N LYS B1644 " --> pdb=" O GLU B1640 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN B1645 " --> pdb=" O GLU B1641 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.521A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.928A pdb=" N GLY C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.649A pdb=" N ALA C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 119 removed outlier: 3.572A pdb=" N GLU C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.569A pdb=" N ALA C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.566A pdb=" N GLU C 206 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C 209 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 226 removed outlier: 4.372A pdb=" N ALA C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 300 removed outlier: 3.722A pdb=" N THR C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.662A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 8.789A pdb=" N THR A 41 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.433A pdb=" N LEU A 34 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER A 70 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP A 61 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 68 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.205A pdb=" N VAL A 163 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A 179 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 165 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN A 177 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 167 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 238 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 283 removed outlier: 7.085A pdb=" N VAL A 326 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER A 344 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA A 328 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU A 342 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 330 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN A 340 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU A 332 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N MET A 338 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.625A pdb=" N ARG A 425 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 390 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 389 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 399 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 455 through 459 Processing sheet with id=AB2, first strand: chain 'A' and resid 500 through 507 removed outlier: 3.702A pdb=" N LYS A 502 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR A 489 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR A 536 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 529 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 564 through 567 Processing sheet with id=AB4, first strand: chain 'B' and resid 770 through 771 Processing sheet with id=AB5, first strand: chain 'B' and resid 775 through 777 Processing sheet with id=AB6, first strand: chain 'B' and resid 763 through 764 removed outlier: 5.778A pdb=" N VAL B 839 " --> pdb=" O VAL B 932 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 763 through 764 Processing sheet with id=AB8, first strand: chain 'B' and resid 829 through 834 removed outlier: 3.690A pdb=" N VAL B 850 " --> pdb=" O ASP B 832 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 829 through 834 removed outlier: 3.690A pdb=" N VAL B 850 " --> pdb=" O ASP B 832 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 936 through 947 removed outlier: 6.248A pdb=" N ARG B 937 " --> pdb=" O ALA B1350 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B1350 " --> pdb=" O ARG B 937 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN B 939 " --> pdb=" O TYR B1348 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR B1348 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR B 941 " --> pdb=" O THR B1346 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B1346 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 959 through 962 Processing sheet with id=AC3, first strand: chain 'B' and resid 1362 through 1368 Processing sheet with id=AC4, first strand: chain 'B' and resid 1427 through 1428 removed outlier: 3.543A pdb=" N TYR B1447 " --> pdb=" O TYR B1428 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA B1481 " --> pdb=" O GLU B1487 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU B1487 " --> pdb=" O ALA B1481 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1504 through 1507 Processing sheet with id=AC6, first strand: chain 'B' and resid 1568 through 1570 removed outlier: 5.604A pdb=" N THR B1568 " --> pdb=" O LYS B1546 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS B1546 " --> pdb=" O THR B1568 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B1544 " --> pdb=" O LYS B1570 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR B1543 " --> pdb=" O GLY B1606 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B1606 " --> pdb=" O TYR B1543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1551 through 1553 removed outlier: 4.256A pdb=" N LYS B1551 " --> pdb=" O ILE B1562 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1695 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: 6.31 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2516 1.33 - 1.45: 3315 1.45 - 1.57: 7983 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13904 Sorted by residual: bond pdb=" N ILE C 309 " pdb=" CA ILE C 309 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.82e+00 bond pdb=" N GLN C 301 " pdb=" CA GLN C 301 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.37e+00 bond pdb=" N LYS C 303 " pdb=" CA LYS C 303 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.91e+00 bond pdb=" N GLU B1614 " pdb=" CA GLU B1614 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.22e-02 6.72e+03 7.74e+00 bond pdb=" N VAL C 308 " pdb=" CA VAL C 308 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 ... (remaining 13899 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.24: 454 107.24 - 113.97: 7903 113.97 - 120.69: 5532 120.69 - 127.42: 4801 127.42 - 134.14: 142 Bond angle restraints: 18832 Sorted by residual: angle pdb=" N LYS C 298 " pdb=" CA LYS C 298 " pdb=" C LYS C 298 " ideal model delta sigma weight residual 111.40 105.89 5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N VAL C 299 " pdb=" CA VAL C 299 " pdb=" C VAL C 299 " ideal model delta sigma weight residual 112.04 106.45 5.59 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA VAL C 295 " pdb=" C VAL C 295 " pdb=" O VAL C 295 " ideal model delta sigma weight residual 120.64 116.49 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" CA LEU C 305 " pdb=" C LEU C 305 " pdb=" O LEU C 305 " ideal model delta sigma weight residual 120.92 116.69 4.23 1.12e+00 7.97e-01 1.43e+01 angle pdb=" N PRO C 304 " pdb=" CA PRO C 304 " pdb=" C PRO C 304 " ideal model delta sigma weight residual 111.57 117.24 -5.67 1.52e+00 4.33e-01 1.39e+01 ... (remaining 18827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 7633 17.53 - 35.06: 694 35.06 - 52.58: 132 52.58 - 70.11: 22 70.11 - 87.64: 14 Dihedral angle restraints: 8495 sinusoidal: 3470 harmonic: 5025 Sorted by residual: dihedral pdb=" CB CYS B1389 " pdb=" SG CYS B1389 " pdb=" SG CYS B1458 " pdb=" CB CYS B1458 " ideal model delta sinusoidal sigma weight residual -86.00 -27.81 -58.19 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS B 873 " pdb=" SG CYS B 873 " pdb=" SG CYS B1513 " pdb=" CB CYS B1513 " ideal model delta sinusoidal sigma weight residual 93.00 57.80 35.20 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA CYS B1101 " pdb=" CB CYS B1101 " pdb=" SG CYS B1101 " pdb=" SG CYS B1158 " ideal model delta sinusoidal sigma weight residual -73.00 -0.84 -72.16 1 2.00e+01 2.50e-03 1.66e+01 ... (remaining 8492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1436 0.032 - 0.064: 417 0.064 - 0.096: 106 0.096 - 0.128: 156 0.128 - 0.160: 12 Chirality restraints: 2127 Sorted by residual: chirality pdb=" CA VAL C 299 " pdb=" N VAL C 299 " pdb=" C VAL C 299 " pdb=" CB VAL C 299 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA LEU B1618 " pdb=" N LEU B1618 " pdb=" C LEU B1618 " pdb=" CB LEU B1618 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ILE C 309 " pdb=" N ILE C 309 " pdb=" C ILE C 309 " pdb=" CB ILE C 309 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 2124 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 303 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" C LYS C 303 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS C 303 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO C 304 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 223 " 0.016 2.00e-02 2.50e+03 1.49e-02 5.53e+00 pdb=" CG TRP C 223 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 223 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 223 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 223 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 223 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 223 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B1173 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C GLY B1173 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY B1173 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B1174 " 0.009 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 0.45 - 1.34: 8 1.34 - 2.23: 27 2.23 - 3.12: 10289 3.12 - 4.01: 32721 4.01 - 4.90: 60021 Warning: very small nonbonded interaction distances. Nonbonded interactions: 103066 Sorted by model distance: nonbonded pdb=" CG GLN B1112 " pdb=" NH1 ARG C 77 " model vdw 0.454 3.520 nonbonded pdb=" OG1 THR B1170 " pdb=" OH TYR C 70 " model vdw 0.883 2.440 nonbonded pdb=" NZ LYS B1171 " pdb=" CD2 TYR C 70 " model vdw 0.985 3.420 nonbonded pdb=" CE LYS B1171 " pdb=" CD2 TYR C 70 " model vdw 1.025 3.740 nonbonded pdb=" OE1 GLN B1112 " pdb=" CD ARG C 77 " model vdw 1.071 3.440 ... (remaining 103061 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 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.380 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.750 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 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 0.050 13904 Z= 0.146 Angle : 0.450 5.669 18832 Z= 0.255 Chirality : 0.043 0.160 2127 Planarity : 0.003 0.038 2429 Dihedral : 13.815 87.641 5222 Min Nonbonded Distance : 0.454 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.23 % Favored : 97.60 % Rotamer: Outliers : 0.46 % Allowed : 0.27 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 1.65 (0.21), residues: 1705 helix: 2.99 (0.27), residues: 404 sheet: 1.44 (0.23), residues: 514 loop : -0.16 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 223 HIS 0.003 0.000 HIS A 47 PHE 0.008 0.001 PHE A 112 TYR 0.013 0.001 TYR A 261 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 109 average time/residue: 0.3128 time to fit residues: 48.4320 Evaluate side-chains 61 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 54.8839 > 50: distance: 26 - 107: 8.451 distance: 29 - 104: 16.259 distance: 42 - 91: 22.433 distance: 45 - 88: 15.045 distance: 54 - 72: 6.650 distance: 69 - 70: 3.158 distance: 70 - 71: 3.389 distance: 70 - 73: 5.897 distance: 71 - 72: 4.418 distance: 71 - 77: 3.492 distance: 73 - 74: 5.069 distance: 74 - 75: 5.929 distance: 74 - 76: 4.904 distance: 77 - 78: 5.284 distance: 77 - 210: 8.392 distance: 78 - 79: 6.338 distance: 78 - 81: 4.724 distance: 79 - 80: 6.437 distance: 79 - 88: 5.907 distance: 80 - 207: 8.203 distance: 81 - 82: 4.568 distance: 82 - 83: 7.770 distance: 82 - 84: 8.956 distance: 83 - 85: 7.764 distance: 84 - 86: 3.933 distance: 85 - 87: 7.370 distance: 88 - 89: 4.846 distance: 89 - 90: 7.946 distance: 89 - 92: 12.415 distance: 90 - 91: 12.737 distance: 92 - 93: 8.160 distance: 93 - 94: 4.928 distance: 93 - 95: 5.322 distance: 96 - 97: 22.073 distance: 97 - 98: 16.135 distance: 97 - 100: 15.287 distance: 98 - 99: 18.391 distance: 98 - 104: 3.988 distance: 100 - 101: 18.827 distance: 101 - 102: 15.193 distance: 101 - 103: 24.794 distance: 104 - 105: 14.389 distance: 105 - 106: 5.221 distance: 105 - 108: 6.911 distance: 106 - 107: 8.197 distance: 106 - 115: 9.739 distance: 108 - 109: 18.903 distance: 109 - 110: 41.926 distance: 110 - 111: 17.374 distance: 111 - 112: 5.442 distance: 112 - 113: 6.930 distance: 112 - 114: 6.847 distance: 115 - 116: 3.295 distance: 116 - 117: 5.643 distance: 116 - 119: 12.141 distance: 117 - 118: 23.851 distance: 117 - 123: 6.826 distance: 119 - 120: 37.559 distance: 120 - 121: 34.088 distance: 121 - 122: 37.888 distance: 123 - 124: 5.929 distance: 124 - 125: 9.042 distance: 125 - 126: 7.030 distance: 125 - 131: 6.021 distance: 126 - 147: 30.986 distance: 127 - 128: 16.091 distance: 128 - 129: 7.559 distance: 131 - 132: 13.517 distance: 132 - 133: 12.367 distance: 132 - 135: 23.310 distance: 133 - 134: 16.943 distance: 133 - 142: 11.143 distance: 135 - 136: 18.030 distance: 136 - 137: 24.898 distance: 137 - 138: 20.420 distance: 138 - 139: 5.659 distance: 139 - 140: 17.132 distance: 139 - 141: 11.646 distance: 142 - 143: 13.277 distance: 143 - 144: 13.845 distance: 143 - 146: 6.521 distance: 144 - 145: 13.491 distance: 144 - 147: 15.055 distance: 147 - 148: 8.788 distance: 148 - 149: 14.421 distance: 148 - 151: 12.694 distance: 149 - 150: 6.183 distance: 149 - 157: 7.579 distance: 152 - 153: 14.541 distance: 152 - 154: 13.794 distance: 153 - 155: 14.771 distance: 154 - 156: 11.786 distance: 155 - 156: 6.096