Starting phenix.real_space_refine on Thu Jul 31 17:37:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgk_14708/07_2025/7zgk_14708_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgk_14708/07_2025/7zgk_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/cci-nas-00/data/ceres_data/7zgk_14708/07_2025/7zgk_14708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgk_14708/07_2025/7zgk_14708.map" model { file = "/net/cci-nas-00/data/ceres_data/7zgk_14708/07_2025/7zgk_14708_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgk_14708/07_2025/7zgk_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-5711/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: 8.03, per 1000 atoms: 0.59 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.9 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: 1.92 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: 5.80 Time building geometry restraints manager: 4.10 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: 0.88 - 1.69: 5 1.69 - 2.49: 66 2.49 - 3.29: 14636 3.29 - 4.10: 31615 4.10 - 4.90: 56736 Warning: very small nonbonded interaction distances. Nonbonded interactions: 103058 Sorted by model distance: nonbonded pdb=" OG1 THR B1170 " pdb=" OH TYR C 70 " model vdw 0.883 3.040 nonbonded pdb=" OE1 GLN B1112 " pdb=" CD ARG C 77 " model vdw 1.071 3.440 nonbonded pdb=" OE1 GLN B1112 " pdb=" NE ARG C 77 " model vdw 1.247 3.120 nonbonded pdb=" CE LYS B1171 " pdb=" CE2 TYR C 70 " model vdw 1.250 2.992 nonbonded pdb=" CD GLN B1112 " pdb=" CZ ARG C 77 " model vdw 1.657 2.800 ... (remaining 103053 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.690 Find NCS groups from input model: 0.130 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: 40.360 ------------------------------------------------------------------------------- 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 : 0.009 0.976 13915 Z= 0.920 Angle : 0.450 5.669 18850 Z= 0.255 Chirality : 0.043 0.160 2127 Planarity : 0.003 0.038 2429 Dihedral : 13.815 87.641 5222 Min Nonbonded Distance : 0.883 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 Details of bonding type rmsd hydrogen bonds : bond 0.13682 ( 603) hydrogen bonds : angle 5.28998 ( 1695) SS BOND : bond 0.00127 ( 9) SS BOND : angle 0.49054 ( 18) covalent geometry : bond 0.00222 (13904) covalent geometry : angle 0.44962 (18832) Misc. bond : bond 0.75861 ( 2) *********************** 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 to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.487 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: 0.3293 time to fit residues: 51.4609 Evaluate side-chains 62 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 B1289 HIS B1617 ASN C 66 ASN C 301 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.044522 restraints weight = 102046.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045694 restraints weight = 52201.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046448 restraints weight = 35027.391| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13915 Z= 0.218 Angle : 0.627 7.239 18850 Z= 0.325 Chirality : 0.044 0.203 2127 Planarity : 0.004 0.035 2429 Dihedral : 3.877 56.400 1855 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 0.80 % Allowed : 6.23 % Favored : 92.97 % 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: 2.19 (0.26), residues: 425 sheet: 1.30 (0.23), residues: 529 loop : -0.22 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 552 HIS 0.008 0.001 HIS A 47 PHE 0.019 0.002 PHE A 112 TYR 0.017 0.002 TYR C 70 ARG 0.009 0.001 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 603) hydrogen bonds : angle 4.49792 ( 1695) SS BOND : bond 0.00259 ( 9) SS BOND : angle 2.21229 ( 18) covalent geometry : bond 0.00476 (13904) covalent geometry : angle 0.62306 (18832) Misc. bond : bond 0.00440 ( 2) *********************** 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 82 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1129 MET cc_start: 0.9014 (mmm) cc_final: 0.8577 (mmm) REVERT: B 1141 MET cc_start: 0.9076 (mmm) cc_final: 0.8690 (mmm) REVERT: B 1388 ILE cc_start: 0.9288 (mt) cc_final: 0.9077 (mm) REVERT: B 1400 MET cc_start: 0.8090 (mtt) cc_final: 0.7876 (mtt) REVERT: B 1407 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7588 (ptp) REVERT: B 1656 MET cc_start: -0.3144 (ptt) cc_final: -0.3563 (ptt) REVERT: C 47 HIS cc_start: 0.8229 (m-70) cc_final: 0.8022 (m-70) outliers start: 12 outliers final: 4 residues processed: 77 average time/residue: 0.2545 time to fit residues: 31.0392 Evaluate side-chains 63 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 1407 MET Chi-restraints excluded: chain C residue 66 ASN 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 127 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.063054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.043646 restraints weight = 103429.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.044829 restraints weight = 50987.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.045625 restraints weight = 33825.250| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13915 Z= 0.219 Angle : 0.582 7.714 18850 Z= 0.302 Chirality : 0.043 0.163 2127 Planarity : 0.004 0.047 2429 Dihedral : 3.784 18.438 1851 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 0.93 % Allowed : 8.22 % Favored : 90.85 % 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: 1.16 (0.21), residues: 1705 helix: 2.26 (0.26), residues: 429 sheet: 1.26 (0.23), residues: 525 loop : -0.48 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1255 HIS 0.008 0.001 HIS A 47 PHE 0.019 0.002 PHE C 67 TYR 0.020 0.002 TYR C 70 ARG 0.008 0.000 ARG A 481 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 603) hydrogen bonds : angle 4.51446 ( 1695) SS BOND : bond 0.00231 ( 9) SS BOND : angle 2.28620 ( 18) covalent geometry : bond 0.00472 (13904) covalent geometry : angle 0.57750 (18832) Misc. bond : bond 0.00215 ( 2) *********************** 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 77 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 MET cc_start: 0.8652 (ttp) cc_final: 0.8143 (tmm) REVERT: B 1015 MET cc_start: 0.8907 (mmp) cc_final: 0.8687 (mmp) REVERT: B 1129 MET cc_start: 0.9177 (mmm) cc_final: 0.8639 (mmm) REVERT: B 1141 MET cc_start: 0.9406 (mmm) cc_final: 0.9045 (mmm) REVERT: B 1202 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8800 (tt) REVERT: B 1388 ILE cc_start: 0.9526 (mt) cc_final: 0.9311 (mm) REVERT: B 1400 MET cc_start: 0.8110 (mtt) cc_final: 0.7902 (mtt) REVERT: B 1407 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7569 (ptm) REVERT: B 1656 MET cc_start: -0.3063 (ptt) cc_final: -0.3841 (ptt) REVERT: C 47 HIS cc_start: 0.8178 (m-70) cc_final: 0.7945 (m-70) REVERT: C 66 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8613 (p0) outliers start: 14 outliers final: 4 residues processed: 74 average time/residue: 0.2670 time to fit residues: 31.0565 Evaluate side-chains 67 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1407 MET Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain C residue 66 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 153 optimal weight: 50.0000 chunk 89 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 B1355 GLN C 66 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.062548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.043027 restraints weight = 104175.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.044209 restraints weight = 51716.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044975 restraints weight = 34492.916| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13915 Z= 0.203 Angle : 0.581 8.658 18850 Z= 0.297 Chirality : 0.043 0.139 2127 Planarity : 0.004 0.049 2429 Dihedral : 3.863 17.802 1851 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 1.39 % Allowed : 8.89 % Favored : 89.72 % 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: 1.07 (0.21), residues: 1705 helix: 2.28 (0.26), residues: 428 sheet: 1.13 (0.23), residues: 524 loop : -0.53 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1255 HIS 0.007 0.001 HIS A 47 PHE 0.017 0.001 PHE A 112 TYR 0.031 0.001 TYR C 70 ARG 0.006 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 603) hydrogen bonds : angle 4.51195 ( 1695) SS BOND : bond 0.00195 ( 9) SS BOND : angle 2.34609 ( 18) covalent geometry : bond 0.00438 (13904) covalent geometry : angle 0.57632 (18832) Misc. bond : bond 0.00137 ( 2) *********************** 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 85 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.8673 (mmp) cc_final: 0.8471 (mmp) REVERT: B 1015 MET cc_start: 0.9040 (mmp) cc_final: 0.8824 (mmp) REVERT: B 1129 MET cc_start: 0.9191 (mmm) cc_final: 0.8849 (mmm) REVERT: B 1141 MET cc_start: 0.9445 (mmm) cc_final: 0.8982 (mmm) REVERT: B 1388 ILE cc_start: 0.9553 (mt) cc_final: 0.9303 (mm) REVERT: B 1407 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7921 (ptp) REVERT: B 1656 MET cc_start: -0.2652 (ptt) cc_final: -0.3448 (ptt) REVERT: C 45 MET cc_start: 0.8521 (mmm) cc_final: 0.8188 (mmm) REVERT: C 47 HIS cc_start: 0.8239 (m-70) cc_final: 0.7974 (m-70) outliers start: 21 outliers final: 12 residues processed: 81 average time/residue: 0.2404 time to fit residues: 30.7940 Evaluate side-chains 74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 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 1202 LEU Chi-restraints excluded: chain B residue 1407 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1349 HIS C 66 ASN C 120 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.061795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.042223 restraints weight = 104702.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043385 restraints weight = 52241.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.044175 restraints weight = 34965.423| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13915 Z= 0.234 Angle : 0.601 8.999 18850 Z= 0.308 Chirality : 0.043 0.156 2127 Planarity : 0.004 0.057 2429 Dihedral : 4.067 19.004 1851 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 1.46 % Allowed : 10.68 % Favored : 87.86 % 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: 1.02 (0.21), residues: 1705 helix: 2.32 (0.26), residues: 421 sheet: 1.07 (0.23), residues: 522 loop : -0.56 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 223 HIS 0.005 0.001 HIS A 333 PHE 0.017 0.002 PHE A 112 TYR 0.036 0.002 TYR C 70 ARG 0.006 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 603) hydrogen bonds : angle 4.60957 ( 1695) SS BOND : bond 0.00209 ( 9) SS BOND : angle 2.64413 ( 18) covalent geometry : bond 0.00503 (13904) covalent geometry : angle 0.59538 (18832) Misc. bond : bond 0.00227 ( 2) *********************** 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 86 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1015 MET cc_start: 0.9039 (mmp) cc_final: 0.8732 (mmp) REVERT: B 1018 MET cc_start: 0.8727 (ptm) cc_final: 0.8416 (ptm) REVERT: B 1129 MET cc_start: 0.9207 (mmm) cc_final: 0.8854 (mmm) REVERT: B 1141 MET cc_start: 0.9493 (mmm) cc_final: 0.9084 (mmm) REVERT: B 1202 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8867 (tt) REVERT: B 1407 MET cc_start: 0.8578 (mtm) cc_final: 0.7735 (ptm) REVERT: B 1656 MET cc_start: -0.2242 (ptt) cc_final: -0.3029 (ptt) REVERT: C 47 HIS cc_start: 0.8230 (m-70) cc_final: 0.7953 (m-70) REVERT: C 217 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8269 (mm-40) REVERT: C 265 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8891 (m) outliers start: 22 outliers final: 16 residues processed: 83 average time/residue: 0.2494 time to fit residues: 32.6656 Evaluate side-chains 78 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 430 GLU Chi-restraints excluded: chain A residue 460 VAL 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 944 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1202 LEU 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 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 115 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 30.0000 chunk 134 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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** ** B1567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3679 r_free = 0.3679 target = 0.061866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.042260 restraints weight = 104860.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043443 restraints weight = 51508.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.044205 restraints weight = 34090.436| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13915 Z= 0.184 Angle : 0.575 9.535 18850 Z= 0.292 Chirality : 0.043 0.147 2127 Planarity : 0.004 0.045 2429 Dihedral : 3.966 18.027 1851 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 1.26 % Allowed : 11.41 % Favored : 87.33 % 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: 2.27 (0.26), residues: 421 sheet: 1.05 (0.23), residues: 520 loop : -0.59 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.013 0.001 PHE A 112 TYR 0.059 0.001 TYR C 70 ARG 0.008 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 603) hydrogen bonds : angle 4.51524 ( 1695) SS BOND : bond 0.00204 ( 9) SS BOND : angle 2.46297 ( 18) covalent geometry : bond 0.00397 (13904) covalent geometry : angle 0.57058 (18832) Misc. bond : bond 0.00275 ( 2) *********************** 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 81 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 990 MET cc_start: 0.6061 (mpp) cc_final: 0.4526 (mpp) REVERT: B 1015 MET cc_start: 0.9084 (mmp) cc_final: 0.8751 (mmp) REVERT: B 1018 MET cc_start: 0.8735 (ptm) cc_final: 0.8426 (ptm) REVERT: B 1129 MET cc_start: 0.9173 (mmm) cc_final: 0.8816 (mmm) REVERT: B 1141 MET cc_start: 0.9486 (mmm) cc_final: 0.9095 (mmm) REVERT: B 1407 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8023 (ptp) REVERT: B 1656 MET cc_start: -0.2550 (ptt) cc_final: -0.3336 (ptt) REVERT: C 45 MET cc_start: 0.8122 (mmm) cc_final: 0.7896 (mmm) REVERT: C 47 HIS cc_start: 0.8341 (m-70) cc_final: 0.8065 (m-70) outliers start: 19 outliers final: 14 residues processed: 77 average time/residue: 0.2380 time to fit residues: 30.0569 Evaluate side-chains 73 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 350 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 570 SER 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 1202 LEU Chi-restraints excluded: chain B residue 1407 MET Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS 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 115 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 142 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042503 restraints weight = 104580.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043610 restraints weight = 51816.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044362 restraints weight = 34694.105| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13915 Z= 0.168 Angle : 0.575 12.533 18850 Z= 0.289 Chirality : 0.043 0.141 2127 Planarity : 0.003 0.044 2429 Dihedral : 3.919 18.575 1851 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 1.53 % Allowed : 11.54 % Favored : 86.94 % 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: 0.95 (0.21), residues: 1705 helix: 2.24 (0.26), residues: 420 sheet: 1.04 (0.23), residues: 519 loop : -0.58 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 223 HIS 0.004 0.001 HIS C 135 PHE 0.012 0.001 PHE A 112 TYR 0.049 0.001 TYR C 70 ARG 0.007 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 603) hydrogen bonds : angle 4.46898 ( 1695) SS BOND : bond 0.00211 ( 9) SS BOND : angle 2.38376 ( 18) covalent geometry : bond 0.00363 (13904) covalent geometry : angle 0.57009 (18832) Misc. bond : bond 0.00218 ( 2) *********************** 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 82 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1015 MET cc_start: 0.9113 (mmp) cc_final: 0.8756 (mmp) REVERT: B 1018 MET cc_start: 0.8760 (ptm) cc_final: 0.8429 (ptm) REVERT: B 1129 MET cc_start: 0.9161 (mmm) cc_final: 0.8785 (mmm) REVERT: B 1141 MET cc_start: 0.9497 (mmm) cc_final: 0.9133 (mmm) REVERT: B 1407 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8037 (ptp) REVERT: B 1656 MET cc_start: -0.2794 (ptt) cc_final: -0.3422 (ptt) REVERT: C 45 MET cc_start: 0.8211 (mmm) cc_final: 0.7935 (mmm) REVERT: C 47 HIS cc_start: 0.8339 (m-70) cc_final: 0.8053 (m-70) outliers start: 23 outliers final: 17 residues processed: 78 average time/residue: 0.2453 time to fit residues: 31.0494 Evaluate side-chains 75 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 1133 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1216 ASP Chi-restraints excluded: chain B residue 1407 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3673 r_free = 0.3673 target = 0.061646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.042135 restraints weight = 105168.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043284 restraints weight = 52156.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.044081 restraints weight = 35000.210| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13915 Z= 0.180 Angle : 0.591 13.376 18850 Z= 0.295 Chirality : 0.043 0.164 2127 Planarity : 0.004 0.048 2429 Dihedral : 3.968 21.504 1851 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 1.46 % Allowed : 11.94 % Favored : 86.60 % 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: 0.88 (0.21), residues: 1705 helix: 2.25 (0.26), residues: 419 sheet: 0.91 (0.23), residues: 523 loop : -0.59 (0.23), residues: 763 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 0.011 0.001 PHE A 112 TYR 0.054 0.001 TYR C 70 ARG 0.008 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 603) hydrogen bonds : angle 4.50348 ( 1695) SS BOND : bond 0.00187 ( 9) SS BOND : angle 2.40330 ( 18) covalent geometry : bond 0.00389 (13904) covalent geometry : angle 0.58626 (18832) Misc. bond : bond 0.00197 ( 2) *********************** 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 to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1015 MET cc_start: 0.9135 (mmp) cc_final: 0.8768 (mmp) REVERT: B 1018 MET cc_start: 0.8782 (ptm) cc_final: 0.8459 (ptm) REVERT: B 1129 MET cc_start: 0.9124 (mmm) cc_final: 0.8743 (mmm) REVERT: B 1141 MET cc_start: 0.9505 (mmm) cc_final: 0.9151 (mmm) REVERT: B 1407 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8016 (ptp) REVERT: B 1656 MET cc_start: -0.2575 (ptt) cc_final: -0.3165 (ptt) REVERT: C 45 MET cc_start: 0.8291 (mmm) cc_final: 0.8030 (mmm) REVERT: C 47 HIS cc_start: 0.8358 (m-70) cc_final: 0.8085 (m-70) outliers start: 22 outliers final: 17 residues processed: 76 average time/residue: 0.2270 time to fit residues: 28.0375 Evaluate side-chains 75 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 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 1133 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1216 ASP Chi-restraints excluded: chain B residue 1407 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.061989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042482 restraints weight = 103682.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043668 restraints weight = 51529.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.044421 restraints weight = 34367.352| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13915 Z= 0.134 Angle : 0.566 11.661 18850 Z= 0.281 Chirality : 0.043 0.172 2127 Planarity : 0.003 0.040 2429 Dihedral : 3.825 21.749 1851 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.26 % Allowed : 12.40 % Favored : 86.34 % 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: 0.91 (0.21), residues: 1705 helix: 2.15 (0.26), residues: 429 sheet: 1.05 (0.23), residues: 516 loop : -0.62 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.009 0.001 PHE A 529 TYR 0.048 0.001 TYR C 70 ARG 0.008 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 603) hydrogen bonds : angle 4.40621 ( 1695) SS BOND : bond 0.00190 ( 9) SS BOND : angle 2.18466 ( 18) covalent geometry : bond 0.00292 (13904) covalent geometry : angle 0.56220 (18832) Misc. bond : bond 0.00193 ( 2) *********************** 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 78 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1015 MET cc_start: 0.9145 (mmp) cc_final: 0.8763 (mmp) REVERT: B 1018 MET cc_start: 0.8781 (ptm) cc_final: 0.8445 (ptm) REVERT: B 1129 MET cc_start: 0.9155 (mmm) cc_final: 0.8767 (mmm) REVERT: B 1141 MET cc_start: 0.9501 (mmm) cc_final: 0.9115 (mmm) REVERT: B 1407 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8032 (ptp) REVERT: B 1656 MET cc_start: -0.2530 (ptt) cc_final: -0.3098 (ptt) REVERT: C 45 MET cc_start: 0.8337 (mmm) cc_final: 0.8050 (mmm) REVERT: C 47 HIS cc_start: 0.8350 (m-70) cc_final: 0.8079 (m-70) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.2339 time to fit residues: 28.4454 Evaluate side-chains 73 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 1078 LEU Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1216 ASP Chi-restraints excluded: chain B residue 1407 MET Chi-restraints excluded: chain B residue 1408 MET 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 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 167 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.062301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042806 restraints weight = 103257.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043997 restraints weight = 51113.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.044838 restraints weight = 34057.587| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13915 Z= 0.111 Angle : 0.568 14.685 18850 Z= 0.278 Chirality : 0.043 0.169 2127 Planarity : 0.003 0.040 2429 Dihedral : 3.707 21.543 1851 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 0.86 % Allowed : 12.67 % Favored : 86.47 % 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: 0.93 (0.21), residues: 1705 helix: 2.16 (0.26), residues: 428 sheet: 1.04 (0.23), residues: 523 loop : -0.60 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 223 HIS 0.005 0.001 HIS C 135 PHE 0.009 0.001 PHE A 529 TYR 0.047 0.001 TYR C 70 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 603) hydrogen bonds : angle 4.30840 ( 1695) SS BOND : bond 0.00177 ( 9) SS BOND : angle 1.99911 ( 18) covalent geometry : bond 0.00251 (13904) covalent geometry : angle 0.56531 (18832) Misc. bond : bond 0.00181 ( 2) ********************** 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 74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1015 MET cc_start: 0.9189 (mmp) cc_final: 0.8805 (mmp) REVERT: B 1018 MET cc_start: 0.8757 (ptm) cc_final: 0.8384 (ptm) REVERT: B 1129 MET cc_start: 0.9111 (mmm) cc_final: 0.8729 (mmm) REVERT: B 1141 MET cc_start: 0.9499 (mmm) cc_final: 0.9113 (mmm) REVERT: B 1202 LEU cc_start: 0.8977 (pp) cc_final: 0.8398 (mt) REVERT: B 1407 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8057 (ptp) REVERT: B 1656 MET cc_start: -0.2555 (ptt) cc_final: -0.3136 (ptt) REVERT: C 45 MET cc_start: 0.8367 (mmm) cc_final: 0.8072 (mmm) REVERT: C 47 HIS cc_start: 0.8361 (m-70) cc_final: 0.8084 (m-70) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.2276 time to fit residues: 26.5543 Evaluate side-chains 70 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 862 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1177 GLU Chi-restraints excluded: chain B residue 1407 MET Chi-restraints excluded: chain B residue 1408 MET Chi-restraints excluded: chain B residue 1511 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.061402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041942 restraints weight = 105471.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043111 restraints weight = 52338.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043825 restraints weight = 34865.824| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13915 Z= 0.177 Angle : 0.602 13.852 18850 Z= 0.296 Chirality : 0.043 0.165 2127 Planarity : 0.004 0.041 2429 Dihedral : 3.906 21.961 1851 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 0.80 % Allowed : 12.80 % Favored : 86.41 % 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: 2.13 (0.26), residues: 428 sheet: 1.02 (0.23), residues: 526 loop : -0.59 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 223 HIS 0.006 0.001 HIS C 135 PHE 0.020 0.001 PHE A 357 TYR 0.046 0.001 TYR C 70 ARG 0.009 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 603) hydrogen bonds : angle 4.43013 ( 1695) SS BOND : bond 0.00191 ( 9) SS BOND : angle 2.32479 ( 18) covalent geometry : bond 0.00386 (13904) covalent geometry : angle 0.59823 (18832) Misc. bond : bond 0.00174 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5087.57 seconds wall clock time: 88 minutes 39.85 seconds (5319.85 seconds total)