Starting phenix.real_space_refine on Thu Sep 26 17:30:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/09_2024/7zgk_14708_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/09_2024/7zgk_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_14708/09_2024/7zgk_14708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/09_2024/7zgk_14708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/09_2024/7zgk_14708_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgk_14708/09_2024/7zgk_14708_neut.cif" } 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. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.21, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 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: 1.74 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: 5.60 Time building geometry restraints manager: 3.68 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: 0.00 - 1.13: 18362 1.13 - 2.27: 318 2.27 - 3.40: 107 3.40 - 4.54: 36 4.54 - 5.67: 9 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 3.040 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 Time spend for trying shortcut: 0.00 ========== 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: 3.860 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.010 Find NCS groups from input model: 0.120 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- 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 : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1615 LYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4313 (mmmt) REVERT: B 1656 MET cc_start: -0.3946 (ptt) cc_final: -0.4661 (ptt) outliers start: 7 outliers final: 0 residues processed: 109 average time/residue: 0.3182 time to fit residues: 49.4597 Evaluate side-chains 62 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1615 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 512 GLN A 589 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 HIS B1617 ASN C 66 ASN C 301 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 13904 Z= 0.324 Angle : 0.631 7.449 18832 Z= 0.326 Chirality : 0.044 0.168 2127 Planarity : 0.005 0.109 2429 Dihedral : 3.917 58.571 1855 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 0.86 % Allowed : 6.10 % Favored : 93.04 % 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: 1.30 (0.21), residues: 1705 helix: 2.22 (0.26), residues: 425 sheet: 1.28 (0.23), residues: 529 loop : -0.22 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 552 HIS 0.009 0.002 HIS A 457 PHE 0.020 0.002 PHE A 112 TYR 0.015 0.002 TYR B1194 ARG 0.009 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 2 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 84 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1656 MET cc_start: -0.3455 (ptt) cc_final: -0.3676 (ptt) outliers start: 13 outliers final: 5 residues processed: 78 average time/residue: 0.2520 time to fit residues: 30.2950 Evaluate side-chains 63 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN C 66 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13904 Z= 0.191 Angle : 0.527 9.066 18832 Z= 0.271 Chirality : 0.043 0.163 2127 Planarity : 0.003 0.059 2429 Dihedral : 3.436 17.272 1851 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Rotamer: Outliers : 0.66 % Allowed : 8.36 % Favored : 90.98 % 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: 1.28 (0.21), residues: 1705 helix: 2.39 (0.26), residues: 429 sheet: 1.25 (0.23), residues: 516 loop : -0.34 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 223 HIS 0.007 0.001 HIS A 47 PHE 0.013 0.001 PHE A 112 TYR 0.032 0.001 TYR A 209 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 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 73 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0409 (tmm) cc_final: -0.0894 (tmm) REVERT: C 66 ASN cc_start: 0.4131 (OUTLIER) cc_final: 0.2926 (p0) outliers start: 10 outliers final: 3 residues processed: 72 average time/residue: 0.2707 time to fit residues: 29.9375 Evaluate side-chains 61 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 126 GLN B1270 GLN C 66 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13904 Z= 0.351 Angle : 0.622 9.032 18832 Z= 0.317 Chirality : 0.043 0.139 2127 Planarity : 0.004 0.066 2429 Dihedral : 4.000 19.048 1851 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 0.93 % Allowed : 9.42 % Favored : 89.66 % 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: 0.98 (0.21), residues: 1705 helix: 2.15 (0.26), residues: 427 sheet: 1.06 (0.23), residues: 528 loop : -0.52 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 223 HIS 0.009 0.002 HIS A 47 PHE 0.021 0.002 PHE A 112 TYR 0.019 0.002 TYR B1027 ARG 0.006 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 4 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 81 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0486 (tmm) cc_final: -0.0997 (tmm) REVERT: C 144 ASN cc_start: 0.4860 (p0) cc_final: 0.4526 (p0) REVERT: C 265 VAL cc_start: 0.4927 (OUTLIER) cc_final: 0.4125 (m) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.2444 time to fit residues: 29.5709 Evaluate side-chains 68 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 123 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 41 optimal weight: 0.0670 overall best weight: 2.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1355 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13904 Z= 0.289 Angle : 0.571 9.034 18832 Z= 0.294 Chirality : 0.043 0.145 2127 Planarity : 0.004 0.052 2429 Dihedral : 3.972 17.958 1851 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.53 % Allowed : 10.21 % Favored : 88.26 % 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: 0.94 (0.21), residues: 1705 helix: 2.14 (0.26), residues: 431 sheet: 1.06 (0.23), residues: 523 loop : -0.60 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.016 0.001 PHE A 112 TYR 0.017 0.001 TYR B1194 ARG 0.007 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 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 87 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0842 (tmm) cc_final: -0.1286 (tmm) REVERT: B 1656 MET cc_start: -0.4190 (ptt) cc_final: -0.4834 (ttp) REVERT: C 144 ASN cc_start: 0.5080 (p0) cc_final: 0.4712 (p0) REVERT: C 265 VAL cc_start: 0.4858 (OUTLIER) cc_final: 0.4488 (m) outliers start: 23 outliers final: 13 residues processed: 84 average time/residue: 0.2425 time to fit residues: 31.6825 Evaluate side-chains 74 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1349 HIS C 120 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13904 Z= 0.259 Angle : 0.579 11.626 18832 Z= 0.292 Chirality : 0.043 0.161 2127 Planarity : 0.004 0.050 2429 Dihedral : 3.939 17.817 1851 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 1.26 % Allowed : 10.81 % Favored : 87.93 % 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: 0.92 (0.21), residues: 1705 helix: 2.17 (0.26), residues: 429 sheet: 1.02 (0.23), residues: 523 loop : -0.61 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.013 0.001 PHE A 112 TYR 0.037 0.001 TYR C 70 ARG 0.007 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 6 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 84 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 990 MET cc_start: 0.4332 (mpp) cc_final: 0.3956 (mpp) REVERT: B 1563 MET cc_start: -0.0750 (tmm) cc_final: -0.1147 (tmm) REVERT: B 1656 MET cc_start: -0.4073 (ptt) cc_final: -0.4728 (ttp) REVERT: C 144 ASN cc_start: 0.5095 (p0) cc_final: 0.4756 (p0) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.2411 time to fit residues: 30.5702 Evaluate side-chains 75 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 76 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13904 Z= 0.160 Angle : 0.550 13.147 18832 Z= 0.275 Chirality : 0.043 0.145 2127 Planarity : 0.003 0.045 2429 Dihedral : 3.692 17.409 1851 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 1.13 % Allowed : 11.47 % Favored : 87.40 % 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: 0.97 (0.21), residues: 1705 helix: 2.17 (0.26), residues: 427 sheet: 1.08 (0.23), residues: 523 loop : -0.57 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.009 0.001 PHE A 529 TYR 0.032 0.001 TYR C 70 ARG 0.008 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 7 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 77 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0686 (tmm) cc_final: -0.1098 (tmm) REVERT: B 1656 MET cc_start: -0.3759 (ptt) cc_final: -0.4443 (ttp) REVERT: C 144 ASN cc_start: 0.5119 (p0) cc_final: 0.4748 (p0) outliers start: 17 outliers final: 9 residues processed: 75 average time/residue: 0.2460 time to fit residues: 29.0239 Evaluate side-chains 68 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 144 optimal weight: 40.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1663 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13904 Z= 0.344 Angle : 0.640 10.706 18832 Z= 0.323 Chirality : 0.043 0.145 2127 Planarity : 0.004 0.045 2429 Dihedral : 4.111 19.977 1851 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 1.33 % Allowed : 11.60 % Favored : 87.07 % 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: 0.83 (0.21), residues: 1705 helix: 2.14 (0.26), residues: 421 sheet: 0.89 (0.23), residues: 524 loop : -0.61 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 223 HIS 0.006 0.001 HIS C 135 PHE 0.024 0.002 PHE A 357 TYR 0.032 0.002 TYR C 70 ARG 0.008 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 8 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 81 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0506 (tmm) cc_final: -0.0970 (tmm) REVERT: C 144 ASN cc_start: 0.5255 (p0) cc_final: 0.4884 (p0) outliers start: 20 outliers final: 14 residues processed: 77 average time/residue: 0.2708 time to fit residues: 32.6817 Evaluate side-chains 74 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 829 PHE Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1216 ASP Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 0.0370 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13904 Z= 0.274 Angle : 0.615 11.287 18832 Z= 0.307 Chirality : 0.043 0.179 2127 Planarity : 0.004 0.045 2429 Dihedral : 4.055 19.596 1851 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 1.33 % Allowed : 11.87 % Favored : 86.80 % 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: 0.80 (0.21), residues: 1705 helix: 2.12 (0.26), residues: 420 sheet: 0.83 (0.23), residues: 527 loop : -0.59 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 223 HIS 0.006 0.001 HIS C 135 PHE 0.020 0.001 PHE A 357 TYR 0.031 0.001 TYR C 70 ARG 0.009 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 9 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 80 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0239 (tmm) cc_final: -0.0740 (tmm) REVERT: C 144 ASN cc_start: 0.5227 (p0) cc_final: 0.4847 (p0) outliers start: 20 outliers final: 13 residues processed: 77 average time/residue: 0.2620 time to fit residues: 31.2158 Evaluate side-chains 70 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 1216 ASP Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1639 ASP Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13904 Z= 0.160 Angle : 0.600 11.581 18832 Z= 0.295 Chirality : 0.043 0.174 2127 Planarity : 0.004 0.061 2429 Dihedral : 3.784 17.398 1851 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 0.66 % Allowed : 12.60 % Favored : 86.74 % 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: 0.79 (0.21), residues: 1705 helix: 1.99 (0.26), residues: 427 sheet: 0.97 (0.23), residues: 521 loop : -0.65 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 223 HIS 0.006 0.001 HIS C 135 PHE 0.012 0.001 PHE A 357 TYR 0.030 0.001 TYR C 70 ARG 0.009 0.000 ARG C 91 ********************** REFINEMENT MACRO_CYCLE 10 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 72 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: B 1563 MET cc_start: -0.0493 (tmm) cc_final: -0.0855 (tmm) REVERT: C 144 ASN cc_start: 0.5158 (p0) cc_final: 0.4812 (p0) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.2411 time to fit residues: 27.1045 Evaluate side-chains 66 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain C residue 288 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.061424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041994 restraints weight = 104201.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043136 restraints weight = 51707.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043895 restraints weight = 34677.369| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13904 Z= 0.261 Angle : 0.629 11.756 18832 Z= 0.312 Chirality : 0.043 0.168 2127 Planarity : 0.004 0.071 2429 Dihedral : 3.933 19.314 1851 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 0.86 % Allowed : 12.86 % Favored : 86.27 % 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: 0.75 (0.21), residues: 1705 helix: 1.93 (0.26), residues: 426 sheet: 0.93 (0.23), residues: 523 loop : -0.64 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 223 HIS 0.006 0.001 HIS C 135 PHE 0.023 0.001 PHE A 357 TYR 0.030 0.001 TYR C 70 ARG 0.015 0.001 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.59 seconds wall clock time: 43 minutes 46.68 seconds (2626.68 seconds total)