Starting phenix.real_space_refine on Sat Aug 8 13:28:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9plr_71721/08_2026/9plr_71721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9plr_71721/08_2026/9plr_71721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9plr_71721/08_2026/9plr_71721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9plr_71721/08_2026/9plr_71721.map" model { file = "/net/cci-nas-00/data/ceres_data/9plr_71721/08_2026/9plr_71721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9plr_71721/08_2026/9plr_71721.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 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 171 5.16 5 C 17436 2.51 5 N 4681 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2445, 19304 Classifications: {'peptide': 2445} Link IDs: {'PTRANS': 104, 'TRANS': 2340} Chain breaks: 30 Chain: "C" Number of atoms: 8044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 8044 Classifications: {'peptide': 977} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 933} Chain breaks: 6 Time building chain proxies: 5.30, per 1000 atoms: 0.19 Number of scatterers: 27348 At special positions: 0 Unit cell: (136.697, 162.282, 192.984, 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 171 16.00 O 5060 8.00 N 4681 7.00 C 17436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6538 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 26 sheets defined 61.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.587A pdb=" N GLY A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 104 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 127 through 145 removed outlier: 3.951A pdb=" N VAL A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.767A pdb=" N MET A 188 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.150A pdb=" N LEU A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 290 Processing helix chain 'A' and resid 303 through 315 removed outlier: 4.729A pdb=" N GLU A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.510A pdb=" N HIS A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 379 through 395 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 407 through 419 removed outlier: 4.231A pdb=" N ALA A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 441 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 451 through 471 removed outlier: 3.859A pdb=" N GLU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.630A pdb=" N SER A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 569 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 597 through 613 Proline residue: A 605 - end of helix Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.881A pdb=" N CYS A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 removed outlier: 3.733A pdb=" N ARG A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Proline residue: A 637 - end of helix Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 653 through 670 Processing helix chain 'A' and resid 673 through 694 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.728A pdb=" N ILE A 805 " --> pdb=" O PRO A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 818 through 836 Processing helix chain 'A' and resid 838 through 853 Processing helix chain 'A' and resid 855 through 860 removed outlier: 3.907A pdb=" N HIS A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 876 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.521A pdb=" N LEU A 885 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 911 Processing helix chain 'A' and resid 914 through 926 Processing helix chain 'A' and resid 927 through 956 Processing helix chain 'A' and resid 967 through 975 removed outlier: 3.654A pdb=" N LYS A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1076 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1097 through 1115 Processing helix chain 'A' and resid 1124 through 1143 Proline residue: A1140 - end of helix Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1181 through 1186 removed outlier: 4.136A pdb=" N LEU A1186 " --> pdb=" O VAL A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1211 removed outlier: 3.808A pdb=" N ASN A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1237 through 1255 removed outlier: 3.854A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1294 Proline residue: A1285 - end of helix Processing helix chain 'A' and resid 1417 through 1427 Processing helix chain 'A' and resid 1432 through 1454 removed outlier: 5.091A pdb=" N LEU A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) Proline residue: A1445 - end of helix Processing helix chain 'A' and resid 1457 through 1472 Processing helix chain 'A' and resid 1473 through 1499 Processing helix chain 'A' and resid 1509 through 1520 removed outlier: 3.652A pdb=" N MET A1517 " --> pdb=" O TRP A1513 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA A1518 " --> pdb=" O ILE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1540 removed outlier: 4.395A pdb=" N LEU A1531 " --> pdb=" O ALA A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 removed outlier: 3.506A pdb=" N CYS A1544 " --> pdb=" O LEU A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1575 removed outlier: 3.750A pdb=" N VAL A1556 " --> pdb=" O GLY A1552 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Proline residue: A1566 - end of helix Processing helix chain 'A' and resid 1582 through 1609 Processing helix chain 'A' and resid 1631 through 1644 Processing helix chain 'A' and resid 1751 through 1768 Processing helix chain 'A' and resid 1771 through 1786 Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1799 through 1807 removed outlier: 3.819A pdb=" N MET A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1812 removed outlier: 3.639A pdb=" N GLY A1812 " --> pdb=" O GLN A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1829 Processing helix chain 'A' and resid 1830 through 1848 Processing helix chain 'A' and resid 1862 through 1865 Processing helix chain 'A' and resid 1866 through 1874 Processing helix chain 'A' and resid 1874 through 1881 Processing helix chain 'A' and resid 1881 through 1892 Processing helix chain 'A' and resid 1907 through 1917 Processing helix chain 'A' and resid 1939 through 1954 removed outlier: 3.827A pdb=" N ALA A1954 " --> pdb=" O LEU A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2082 Processing helix chain 'A' and resid 2082 through 2092 removed outlier: 4.055A pdb=" N ALA A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A2087 " --> pdb=" O VAL A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2127 through 2142 removed outlier: 3.592A pdb=" N LEU A2131 " --> pdb=" O ASP A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2146 through 2166 removed outlier: 3.904A pdb=" N ALA A2151 " --> pdb=" O ASP A2147 " (cutoff:3.500A) Processing helix chain 'A' and resid 2169 through 2188 Processing helix chain 'A' and resid 2211 through 2219 Processing helix chain 'A' and resid 2220 through 2227 Processing helix chain 'A' and resid 2228 through 2232 Processing helix chain 'A' and resid 2238 through 2259 Proline residue: A2249 - end of helix removed outlier: 3.517A pdb=" N THR A2252 " --> pdb=" O LYS A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2646 through 2659 Processing helix chain 'A' and resid 2662 through 2696 removed outlier: 3.730A pdb=" N HIS A2677 " --> pdb=" O SER A2673 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3195 Processing helix chain 'A' and resid 3201 through 3213 Processing helix chain 'A' and resid 3215 through 3234 Processing helix chain 'A' and resid 3328 through 3346 Processing helix chain 'A' and resid 3388 through 3398 removed outlier: 3.620A pdb=" N MET A3398 " --> pdb=" O LYS A3394 " (cutoff:3.500A) Processing helix chain 'A' and resid 3430 through 3438 removed outlier: 3.603A pdb=" N LEU A3438 " --> pdb=" O LEU A3434 " (cutoff:3.500A) Processing helix chain 'A' and resid 3440 through 3446 removed outlier: 3.658A pdb=" N SER A3446 " --> pdb=" O VAL A3442 " (cutoff:3.500A) Processing helix chain 'A' and resid 3446 through 3461 Processing helix chain 'A' and resid 3576 through 3588 removed outlier: 3.856A pdb=" N GLU A3586 " --> pdb=" O GLN A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3595 through 3612 Processing helix chain 'A' and resid 3612 through 3650 Processing helix chain 'A' and resid 3723 through 3725 No H-bonds generated for 'chain 'A' and resid 3723 through 3725' Processing helix chain 'A' and resid 3726 through 3731 Processing helix chain 'A' and resid 3734 through 3751 removed outlier: 3.955A pdb=" N ASP A3751 " --> pdb=" O ILE A3747 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3869 Processing helix chain 'A' and resid 3873 through 3878 Processing helix chain 'A' and resid 3879 through 3890 Processing helix chain 'A' and resid 3954 through 3962 Processing helix chain 'A' and resid 3962 through 3973 Processing helix chain 'A' and resid 3980 through 3987 removed outlier: 3.866A pdb=" N VAL A3984 " --> pdb=" O PRO A3981 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A3985 " --> pdb=" O PHE A3982 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A3987 " --> pdb=" O VAL A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 3988 through 3992 removed outlier: 3.782A pdb=" N VAL A3991 " --> pdb=" O TYR A3988 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4002 Processing helix chain 'A' and resid 4025 through 4035 Processing helix chain 'A' and resid 4038 through 4043 Processing helix chain 'A' and resid 4057 through 4073 Processing helix chain 'A' and resid 4096 through 4100 removed outlier: 3.820A pdb=" N CYS A4099 " --> pdb=" O SER A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4102 through 4121 Processing helix chain 'A' and resid 4129 through 4138 Processing helix chain 'A' and resid 4142 through 4144 No H-bonds generated for 'chain 'A' and resid 4142 through 4144' Processing helix chain 'A' and resid 4145 through 4150 Processing helix chain 'A' and resid 4150 through 4161 Processing helix chain 'A' and resid 4164 through 4168 Processing helix chain 'A' and resid 4202 through 4217 Processing helix chain 'A' and resid 4219 through 4234 removed outlier: 4.017A pdb=" N ILE A4233 " --> pdb=" O GLY A4229 " (cutoff:3.500A) Processing helix chain 'A' and resid 4235 through 4240 Processing helix chain 'A' and resid 4243 through 4253 Processing helix chain 'A' and resid 4258 through 4265 Processing helix chain 'A' and resid 4275 through 4288 Processing helix chain 'A' and resid 4289 through 4302 Processing helix chain 'A' and resid 4310 through 4313 Processing helix chain 'A' and resid 4352 through 4364 Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 222 through 235 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 255 through 270 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.581A pdb=" N PHE C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 359 through 368 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.984A pdb=" N LYS C 378 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 495 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 601 through 614 Processing helix chain 'C' and resid 647 through 653 Processing helix chain 'C' and resid 712 through 725 Proline residue: C 718 - end of helix Processing helix chain 'C' and resid 752 through 757 Processing helix chain 'C' and resid 782 through 792 Processing helix chain 'C' and resid 818 through 831 Processing helix chain 'C' and resid 833 through 835 No H-bonds generated for 'chain 'C' and resid 833 through 835' Processing helix chain 'C' and resid 860 through 866 Processing helix chain 'C' and resid 884 through 890 Processing helix chain 'C' and resid 917 through 929 Processing helix chain 'C' and resid 958 through 962 Processing helix chain 'C' and resid 976 through 981 removed outlier: 4.439A pdb=" N ASP C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1029 Processing helix chain 'C' and resid 1033 through 1038 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 200 Processing sheet with id=AA2, first strand: chain 'A' and resid 698 through 699 removed outlier: 5.823A pdb=" N ILE A 698 " --> pdb=" O ILE A 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1626 through 1629 Processing sheet with id=AA4, first strand: chain 'A' and resid 1893 through 1895 Processing sheet with id=AA5, first strand: chain 'A' and resid 3289 through 3291 removed outlier: 3.636A pdb=" N THR A3298 " --> pdb=" O MET A3290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3301 through 3302 Processing sheet with id=AA7, first strand: chain 'A' and resid 4016 through 4021 removed outlier: 6.121A pdb=" N MET A4017 " --> pdb=" O TYR A4047 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A4049 " --> pdb=" O MET A4017 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A4019 " --> pdb=" O VAL A4049 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 4081 through 4082 Processing sheet with id=AA9, first strand: chain 'A' and resid 4175 through 4180 Processing sheet with id=AB1, first strand: chain 'A' and resid 4266 through 4268 removed outlier: 6.962A pdb=" N GLU A4267 " --> pdb=" O ILE A4325 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ARG A4327 " --> pdb=" O GLU A4267 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 4315 through 4316 removed outlier: 3.714A pdb=" N GLY A4319 " --> pdb=" O GLY A4316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 85 through 86 removed outlier: 7.475A pdb=" N LYS C 113 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET C 171 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 115 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN C 169 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 347 removed outlier: 6.557A pdb=" N LYS C 327 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 352 removed outlier: 6.314A pdb=" N TYR C 514 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 513 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 455 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET C 515 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 453 " --> pdb=" O MET C 515 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 517 " --> pdb=" O HIS C 451 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 352 removed outlier: 6.314A pdb=" N TYR C 514 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 513 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 455 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET C 515 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 453 " --> pdb=" O MET C 515 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 517 " --> pdb=" O HIS C 451 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AC2, first strand: chain 'C' and resid 592 through 596 removed outlier: 5.235A pdb=" N THR C 659 " --> pdb=" O MET C 625 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 698 through 708 removed outlier: 5.705A pdb=" N LEU C 699 " --> pdb=" O ASP C 693 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP C 693 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR C 701 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N MET C 691 " --> pdb=" O TYR C 701 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 703 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N ASP C 764 " --> pdb=" O ASP C 684 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET C 686 " --> pdb=" O ASP C 764 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ILE C 766 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE C 688 " --> pdb=" O ILE C 766 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE C 768 " --> pdb=" O PHE C 688 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS C 690 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE C 765 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU C 742 " --> pdb=" O VAL C 738 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 809 through 814 removed outlier: 4.778A pdb=" N LYS C 874 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR C 877 " --> pdb=" O PHE C 840 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE C 839 " --> pdb=" O LEU C 853 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 894 through 899 Processing sheet with id=AC6, first strand: chain 'C' and resid 948 through 953 removed outlier: 5.114A pdb=" N ILE C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 945 " --> pdb=" O ILE C 949 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 941 " --> pdb=" O HIS C 953 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 948 through 953 removed outlier: 5.114A pdb=" N ILE C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 945 " --> pdb=" O ILE C 949 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 941 " --> pdb=" O HIS C 953 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1002 through 1011 removed outlier: 6.631A pdb=" N ILE C1005 " --> pdb=" O HIS C 994 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS C 994 " --> pdb=" O ILE C1005 " (cutoff:3.500A) 1614 hydrogen bonds defined for protein. 4632 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: 8.78 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8919 1.34 - 1.46: 4863 1.46 - 1.58: 13829 1.58 - 1.70: 0 1.70 - 1.82: 270 Bond restraints: 27881 Sorted by residual: bond pdb=" CA SER A 782 " pdb=" CB SER A 782 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.51e-02 4.39e+03 5.66e+00 bond pdb=" C LEU A1874 " pdb=" N GLY A1875 " ideal model delta sigma weight residual 1.339 1.324 0.015 7.50e-03 1.78e+04 4.01e+00 bond pdb=" CA VAL C 256 " pdb=" CB VAL C 256 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 3.81e+00 bond pdb=" CA GLY A1875 " pdb=" C GLY A1875 " ideal model delta sigma weight residual 1.512 1.523 -0.012 7.70e-03 1.69e+04 2.35e+00 bond pdb=" CA THR A1786 " pdb=" C THR A1786 " ideal model delta sigma weight residual 1.522 1.495 0.026 1.72e-02 3.38e+03 2.33e+00 ... (remaining 27876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 37514 3.44 - 6.87: 175 6.87 - 10.31: 11 10.31 - 13.74: 2 13.74 - 17.18: 1 Bond angle restraints: 37703 Sorted by residual: angle pdb=" CG1 ILE A2182 " pdb=" CB ILE A2182 " pdb=" CG2 ILE A2182 " ideal model delta sigma weight residual 110.70 93.52 17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C LEU A3992 " pdb=" N ASP A3993 " pdb=" CA ASP A3993 " ideal model delta sigma weight residual 120.94 129.55 -8.61 1.57e+00 4.06e-01 3.01e+01 angle pdb=" N GLY A1856 " pdb=" CA GLY A1856 " pdb=" C GLY A1856 " ideal model delta sigma weight residual 113.18 102.58 10.60 2.37e+00 1.78e-01 2.00e+01 angle pdb=" C ALA A1527 " pdb=" N THR A1528 " pdb=" CA THR A1528 " ideal model delta sigma weight residual 122.42 115.47 6.95 1.77e+00 3.19e-01 1.54e+01 angle pdb=" C LEU A 287 " pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta sigma weight residual 122.66 118.86 3.80 9.70e-01 1.06e+00 1.54e+01 ... (remaining 37698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15840 17.58 - 35.15: 891 35.15 - 52.73: 195 52.73 - 70.31: 33 70.31 - 87.88: 8 Dihedral angle restraints: 16967 sinusoidal: 6947 harmonic: 10020 Sorted by residual: dihedral pdb=" CA GLU A2124 " pdb=" C GLU A2124 " pdb=" N ASP A2125 " pdb=" CA ASP A2125 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TRP A 54 " pdb=" C TRP A 54 " pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta harmonic sigma weight residual 180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASP A1144 " pdb=" C ASP A1144 " pdb=" N GLU A1145 " pdb=" CA GLU A1145 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 16964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3963 0.076 - 0.152: 346 0.152 - 0.228: 9 0.228 - 0.304: 2 0.304 - 0.380: 1 Chirality restraints: 4321 Sorted by residual: chirality pdb=" CB ILE A1514 " pdb=" CA ILE A1514 " pdb=" CG1 ILE A1514 " pdb=" CG2 ILE A1514 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE A2182 " pdb=" CA ILE A2182 " pdb=" CG1 ILE A2182 " pdb=" CG2 ILE A2182 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU A3598 " pdb=" CB LEU A3598 " pdb=" CD1 LEU A3598 " pdb=" CD2 LEU A3598 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4318 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1944 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.88e+01 pdb=" C GLU A1944 " -0.093 2.00e-02 2.50e+03 pdb=" O GLU A1944 " 0.035 2.00e-02 2.50e+03 pdb=" N VAL A1945 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1044 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C ALA A1044 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA A1044 " -0.034 2.00e-02 2.50e+03 pdb=" N ARG A1045 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A2672 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C VAL A2672 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL A2672 " 0.032 2.00e-02 2.50e+03 pdb=" N SER A2673 " 0.028 2.00e-02 2.50e+03 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 13610 2.98 - 3.46: 28807 3.46 - 3.94: 45087 3.94 - 4.42: 53190 4.42 - 4.90: 82841 Nonbonded interactions: 223535 Sorted by model distance: nonbonded pdb=" O SER A 962 " pdb=" OG SER A 962 " model vdw 2.505 3.040 nonbonded pdb=" O GLN A1661 " pdb=" N MET A1665 " model vdw 2.540 3.120 nonbonded pdb=" OE2 GLU A1829 " pdb=" OH TYR A2082 " model vdw 2.545 3.040 nonbonded pdb=" C THR A2146 " pdb=" OG1 THR A2146 " model vdw 2.550 2.616 nonbonded pdb=" O SER A 648 " pdb=" OG SER A 648 " model vdw 2.551 3.040 ... (remaining 223530 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 28.630 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.003 0.045 27881 Z= 0.170 Angle : 0.711 17.181 37703 Z= 0.418 Chirality : 0.043 0.380 4321 Planarity : 0.008 0.109 4800 Dihedral : 11.862 87.883 10429 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 2.16 % Allowed : 5.23 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3346 helix: -0.94 (0.11), residues: 1896 sheet: 0.80 (0.27), residues: 356 loop : -0.20 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 273 TYR 0.028 0.002 TYR A4154 PHE 0.026 0.001 PHE A 776 TRP 0.024 0.002 TRP A4065 HIS 0.010 0.001 HIS A2664 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (27881) covalent geometry : angle 0.71105 / 0.42 (37703) hydrogen bonds : bond 0.11607 / 7.71 ( 1598) hydrogen bonds : angle 6.08263 / 4.28 ( 4632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7733 (tpt) cc_final: 0.7327 (tpt) REVERT: A 905 MET cc_start: 0.9208 (tmm) cc_final: 0.8905 (tmm) REVERT: A 1072 LYS cc_start: 0.9502 (mttt) cc_final: 0.9181 (pttt) REVERT: A 1145 GLU cc_start: 0.7646 (pm20) cc_final: 0.7437 (pm20) REVERT: A 1265 TYR cc_start: 0.7651 (m-80) cc_final: 0.7309 (m-80) REVERT: A 1466 MET cc_start: 0.9117 (mmm) cc_final: 0.8904 (mmm) REVERT: A 1538 GLU cc_start: 0.8728 (tt0) cc_final: 0.8464 (tp30) REVERT: A 2185 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9310 (p) REVERT: A 3603 ASN cc_start: 0.8723 (t0) cc_final: 0.8483 (m-40) REVERT: C 102 MET cc_start: 0.2870 (ptp) cc_final: 0.2554 (mpt) REVERT: C 245 MET cc_start: 0.5957 (mtm) cc_final: 0.4506 (mtm) REVERT: C 279 LEU cc_start: 0.9390 (tp) cc_final: 0.9096 (tp) REVERT: C 328 MET cc_start: 0.8839 (ptt) cc_final: 0.8277 (ppp) REVERT: C 501 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6606 (p-80) REVERT: C 613 MET cc_start: 0.9101 (mmm) cc_final: 0.8775 (ptt) REVERT: C 805 ASN cc_start: 0.8903 (m-40) cc_final: 0.8686 (m110) REVERT: C 966 THR cc_start: 0.7754 (p) cc_final: 0.7532 (p) REVERT: C 996 HIS cc_start: 0.8087 (p-80) cc_final: 0.7866 (p90) REVERT: C 1070 MET cc_start: 0.8726 (tpp) cc_final: 0.8526 (mmm) outliers start: 66 outliers final: 5 residues processed: 330 average time/residue: 0.7851 time to fit residues: 298.8941 Evaluate side-chains 161 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2185 THR Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain C residue 501 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 HIS A 568 GLN A1155 GLN A1522 GLN A1826 HIS A1868 ASN A1890 ASN ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN A3736 GLN A4044 ASN A4202 ASN A4212 GLN C 156 HIS C 294 HIS C 351 GLN C 414 GLN C 417 GLN C 418 ASN C 470 ASN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN C 581 ASN C 792 HIS ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 HIS C1016 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.117714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.073706 restraints weight = 108035.880| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.00 r_work: 0.3156 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27881 Z= 0.245 Angle : 0.665 10.080 37703 Z= 0.337 Chirality : 0.043 0.207 4321 Planarity : 0.005 0.067 4800 Dihedral : 4.749 58.237 3679 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.42 % Allowed : 8.79 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3346 helix: 1.12 (0.12), residues: 1932 sheet: 0.65 (0.27), residues: 357 loop : 0.42 (0.21), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 77 TYR 0.019 0.001 TYR A4000 PHE 0.024 0.002 PHE A4001 TRP 0.019 0.002 TRP A4065 HIS 0.009 0.001 HIS A2664 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 (27881) covalent geometry : angle 0.66544 / 0.34 (37703) hydrogen bonds : bond 0.04583 / 2.99 ( 1598) hydrogen bonds : angle 4.61565 / 3.27 ( 4632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.8676 (ttt-90) cc_final: 0.8458 (ttm-80) REVERT: A 375 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: A 905 MET cc_start: 0.9090 (tmm) cc_final: 0.8872 (tmm) REVERT: A 1072 LYS cc_start: 0.9486 (mttt) cc_final: 0.9141 (pptt) REVERT: A 1538 GLU cc_start: 0.9240 (tt0) cc_final: 0.8897 (tp30) REVERT: A 2689 ARG cc_start: 0.9506 (OUTLIER) cc_final: 0.9143 (ttm170) REVERT: A 3603 ASN cc_start: 0.9024 (t0) cc_final: 0.8733 (m-40) REVERT: A 4317 MET cc_start: 0.8141 (mtt) cc_final: 0.7831 (mmt) REVERT: C 328 MET cc_start: 0.9005 (ptt) cc_final: 0.8498 (ppp) REVERT: C 613 MET cc_start: 0.9158 (mmm) cc_final: 0.8831 (ptt) REVERT: C 625 MET cc_start: 0.8964 (tpp) cc_final: 0.8676 (tpp) REVERT: C 637 MET cc_start: 0.6216 (tpt) cc_final: 0.5697 (tpt) REVERT: C 743 THR cc_start: 0.3333 (OUTLIER) cc_final: 0.2979 (p) REVERT: C 761 MET cc_start: 0.6890 (mtt) cc_final: 0.6513 (ptp) REVERT: C 805 ASN cc_start: 0.9213 (m-40) cc_final: 0.9007 (m110) REVERT: C 960 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: C 988 MET cc_start: 0.8644 (mmm) cc_final: 0.8183 (mmp) REVERT: C 1044 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7826 (tmm) outliers start: 74 outliers final: 29 residues processed: 212 average time/residue: 0.7581 time to fit residues: 187.1276 Evaluate side-chains 164 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1581 LYS Chi-restraints excluded: chain A residue 1675 ARG Chi-restraints excluded: chain A residue 1912 GLU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 2108 VAL Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 SER Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2185 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 4301 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 338 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 299 optimal weight: 0.0980 chunk 49 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3637 GLN A3736 GLN C 451 HIS ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 HIS C1016 HIS C1052 ASN C1072 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.117720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.073457 restraints weight = 107688.581| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 4.12 r_work: 0.3158 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27881 Z= 0.179 Angle : 0.593 9.349 37703 Z= 0.297 Chirality : 0.041 0.322 4321 Planarity : 0.004 0.054 4800 Dihedral : 4.358 56.004 3672 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.32 % Allowed : 9.47 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.15), residues: 3346 helix: 1.76 (0.12), residues: 1923 sheet: 0.59 (0.27), residues: 359 loop : 0.47 (0.21), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1018 TYR 0.016 0.001 TYR A1265 PHE 0.037 0.001 PHE C 364 TRP 0.021 0.001 TRP A4065 HIS 0.010 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (27881) covalent geometry : angle 0.59297 / 0.30 (37703) hydrogen bonds : bond 0.04050 / 2.65 ( 1598) hydrogen bonds : angle 4.31829 / 3.05 ( 4632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 137 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 905 MET cc_start: 0.9029 (tmm) cc_final: 0.8780 (tmm) REVERT: A 1538 GLU cc_start: 0.9218 (tt0) cc_final: 0.8820 (tp30) REVERT: A 2250 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9336 (tp) REVERT: A 2689 ARG cc_start: 0.9507 (OUTLIER) cc_final: 0.9128 (ttm170) REVERT: A 3451 GLU cc_start: 0.9351 (tt0) cc_final: 0.8943 (tp30) REVERT: A 3582 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8688 (tm-30) REVERT: A 3603 ASN cc_start: 0.9108 (t0) cc_final: 0.8844 (m-40) REVERT: A 4317 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8499 (mmt) REVERT: C 100 MET cc_start: 0.5262 (mtp) cc_final: 0.4677 (mpp) REVERT: C 328 MET cc_start: 0.9038 (ptt) cc_final: 0.8551 (ppp) REVERT: C 407 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7437 (mpt) REVERT: C 613 MET cc_start: 0.9140 (mmm) cc_final: 0.8833 (ptt) REVERT: C 625 MET cc_start: 0.9050 (tpp) cc_final: 0.8674 (tpp) REVERT: C 637 MET cc_start: 0.6285 (tpt) cc_final: 0.5750 (tpt) REVERT: C 686 MET cc_start: 0.4908 (tmm) cc_final: 0.4350 (tmm) REVERT: C 761 MET cc_start: 0.6912 (mtt) cc_final: 0.6559 (ptp) REVERT: C 805 ASN cc_start: 0.9204 (m-40) cc_final: 0.9000 (m110) REVERT: C 864 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8937 (mm) REVERT: C 895 LYS cc_start: 0.9243 (mtmt) cc_final: 0.9002 (pptt) REVERT: C 960 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: C 988 MET cc_start: 0.8792 (mmm) cc_final: 0.8354 (mmp) outliers start: 71 outliers final: 25 residues processed: 195 average time/residue: 0.6817 time to fit residues: 157.4653 Evaluate side-chains 157 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1675 ARG Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1870 ILE Chi-restraints excluded: chain A residue 1912 GLU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 SER Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2662 SER Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4317 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 192 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 252 optimal weight: 9.9990 chunk 269 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 238 optimal weight: 50.0000 chunk 147 optimal weight: 0.0050 chunk 283 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 309 optimal weight: 30.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 175 ASN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 GLN A3976 HIS ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.118263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.075235 restraints weight = 107504.142| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.84 r_work: 0.3195 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27881 Z= 0.123 Angle : 0.552 9.772 37703 Z= 0.274 Chirality : 0.039 0.291 4321 Planarity : 0.004 0.063 4800 Dihedral : 4.171 55.567 3671 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.89 % Allowed : 10.48 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.15), residues: 3346 helix: 2.04 (0.12), residues: 1924 sheet: 0.60 (0.26), residues: 361 loop : 0.51 (0.21), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1018 TYR 0.019 0.001 TYR A4000 PHE 0.019 0.001 PHE A 776 TRP 0.016 0.001 TRP A4065 HIS 0.006 0.001 HIS A3962 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27881) covalent geometry : angle 0.55194 / 0.27 (37703) hydrogen bonds : bond 0.03635 / 2.37 ( 1598) hydrogen bonds : angle 4.10225 / 2.90 ( 4632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 904 MET cc_start: 0.8747 (mmm) cc_final: 0.8528 (mmm) REVERT: A 905 MET cc_start: 0.8977 (tmm) cc_final: 0.8770 (tmm) REVERT: A 1538 GLU cc_start: 0.9215 (tt0) cc_final: 0.8755 (tp30) REVERT: A 2250 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9341 (tp) REVERT: A 2689 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.9068 (ttm-80) REVERT: A 3451 GLU cc_start: 0.9371 (tt0) cc_final: 0.8964 (tp30) REVERT: A 3582 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8688 (tm-30) REVERT: A 3603 ASN cc_start: 0.9167 (t0) cc_final: 0.8899 (m-40) REVERT: A 4317 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8251 (mmt) REVERT: C 328 MET cc_start: 0.9055 (ptt) cc_final: 0.8556 (ppp) REVERT: C 407 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7734 (mpt) REVERT: C 613 MET cc_start: 0.9163 (mmm) cc_final: 0.8842 (ptt) REVERT: C 625 MET cc_start: 0.8963 (tpp) cc_final: 0.8715 (tpp) REVERT: C 761 MET cc_start: 0.6977 (mtt) cc_final: 0.6603 (ptp) REVERT: C 805 ASN cc_start: 0.9166 (m-40) cc_final: 0.8951 (m110) REVERT: C 864 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8932 (mm) REVERT: C 895 LYS cc_start: 0.9243 (mtmt) cc_final: 0.9024 (pptt) REVERT: C 960 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: C 988 MET cc_start: 0.8875 (mmm) cc_final: 0.8437 (mmp) REVERT: C 1044 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7702 (tmm) REVERT: C 1045 MET cc_start: 0.7848 (mmm) cc_final: 0.7439 (mmm) outliers start: 58 outliers final: 26 residues processed: 178 average time/residue: 0.6550 time to fit residues: 137.5871 Evaluate side-chains 161 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1675 ARG Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1912 GLU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 SER Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2187 MET Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2662 SER Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4317 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 286 optimal weight: 30.0000 chunk 118 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 316 optimal weight: 10.0000 chunk 112 optimal weight: 0.0060 chunk 306 optimal weight: 1.9990 chunk 235 optimal weight: 50.0000 chunk 214 optimal weight: 20.0000 chunk 231 optimal weight: 40.0000 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4339 HIS ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 986 ASN ** 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 = 0.4463 r_free = 0.4463 target = 0.117680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.074019 restraints weight = 107277.203| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.93 r_work: 0.3159 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27881 Z= 0.143 Angle : 0.554 9.808 37703 Z= 0.274 Chirality : 0.039 0.249 4321 Planarity : 0.004 0.046 4800 Dihedral : 4.076 55.607 3671 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.06 % Allowed : 11.30 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.15), residues: 3346 helix: 2.21 (0.12), residues: 1923 sheet: 0.52 (0.27), residues: 347 loop : 0.56 (0.21), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 860 TYR 0.016 0.001 TYR A1265 PHE 0.018 0.001 PHE A 776 TRP 0.015 0.001 TRP A4065 HIS 0.006 0.001 HIS A2664 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (27881) covalent geometry : angle 0.55371 / 0.27 (37703) hydrogen bonds : bond 0.03643 / 2.38 ( 1598) hydrogen bonds : angle 4.05066 / 2.87 ( 4632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 905 MET cc_start: 0.9106 (tmm) cc_final: 0.8877 (tmm) REVERT: A 1538 GLU cc_start: 0.9304 (tt0) cc_final: 0.8880 (tp30) REVERT: A 2689 ARG cc_start: 0.9557 (OUTLIER) cc_final: 0.9132 (ttm-80) REVERT: A 3451 GLU cc_start: 0.9291 (tt0) cc_final: 0.8885 (tp30) REVERT: A 3582 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 3603 ASN cc_start: 0.9225 (t0) cc_final: 0.8960 (m-40) REVERT: A 4317 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8106 (mmt) REVERT: C 100 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4909 (mpp) REVERT: C 102 MET cc_start: 0.1533 (ptp) cc_final: -0.0185 (ptt) REVERT: C 328 MET cc_start: 0.9059 (ptt) cc_final: 0.8543 (ppp) REVERT: C 407 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7939 (mpt) REVERT: C 501 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.5887 (p-80) REVERT: C 613 MET cc_start: 0.9159 (mmm) cc_final: 0.8845 (ptt) REVERT: C 625 MET cc_start: 0.9031 (tpp) cc_final: 0.8705 (tpp) REVERT: C 686 MET cc_start: 0.4321 (tmm) cc_final: 0.3453 (tmm) REVERT: C 761 MET cc_start: 0.6963 (mtt) cc_final: 0.6633 (ptp) REVERT: C 805 ASN cc_start: 0.9204 (m-40) cc_final: 0.8999 (m110) REVERT: C 817 MET cc_start: 0.7208 (mtt) cc_final: 0.6737 (mpp) REVERT: C 864 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8885 (mm) REVERT: C 895 LYS cc_start: 0.9247 (mtmt) cc_final: 0.9001 (pptt) REVERT: C 960 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: C 988 MET cc_start: 0.8981 (mmm) cc_final: 0.8556 (mmp) REVERT: C 1044 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7713 (tmm) REVERT: C 1045 MET cc_start: 0.7633 (mmm) cc_final: 0.7352 (mmm) outliers start: 63 outliers final: 28 residues processed: 181 average time/residue: 0.6327 time to fit residues: 135.9937 Evaluate side-chains 163 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1870 ILE Chi-restraints excluded: chain A residue 1912 GLU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 SER Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2187 MET Chi-restraints excluded: chain A residue 2662 SER Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4317 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 303 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 313 optimal weight: 30.0000 chunk 173 optimal weight: 0.9990 chunk 237 optimal weight: 40.0000 chunk 305 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 HIS ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.116355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.071394 restraints weight = 108059.767| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.18 r_work: 0.3091 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27881 Z= 0.235 Angle : 0.624 10.338 37703 Z= 0.308 Chirality : 0.041 0.255 4321 Planarity : 0.004 0.071 4800 Dihedral : 4.186 57.638 3671 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.22 % Allowed : 11.95 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.15), residues: 3346 helix: 2.20 (0.12), residues: 1926 sheet: 0.28 (0.27), residues: 349 loop : 0.54 (0.21), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3957 TYR 0.016 0.001 TYR A1265 PHE 0.023 0.001 PHE A1592 TRP 0.013 0.001 TRP A4065 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (27881) covalent geometry : angle 0.62358 / 0.31 (37703) hydrogen bonds : bond 0.04092 / 2.69 ( 1598) hydrogen bonds : angle 4.21547 / 3.00 ( 4632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1538 GLU cc_start: 0.9310 (tt0) cc_final: 0.8883 (tp30) REVERT: A 2180 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.8767 (mpp) REVERT: A 2689 ARG cc_start: 0.9550 (OUTLIER) cc_final: 0.9218 (ttm170) REVERT: A 3451 GLU cc_start: 0.9319 (tt0) cc_final: 0.8943 (tp30) REVERT: A 3582 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 3603 ASN cc_start: 0.9316 (t0) cc_final: 0.9006 (m-40) REVERT: A 4073 MET cc_start: -0.4185 (OUTLIER) cc_final: -0.4391 (tpt) REVERT: C 328 MET cc_start: 0.9131 (ptt) cc_final: 0.8662 (ppp) REVERT: C 407 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7819 (mpt) REVERT: C 613 MET cc_start: 0.9145 (mmm) cc_final: 0.8853 (ptt) REVERT: C 686 MET cc_start: 0.4670 (tmm) cc_final: 0.4043 (tmm) REVERT: C 761 MET cc_start: 0.7013 (mtt) cc_final: 0.6733 (ptp) REVERT: C 817 MET cc_start: 0.7458 (mtt) cc_final: 0.7024 (mpp) REVERT: C 864 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8956 (mm) REVERT: C 895 LYS cc_start: 0.9232 (mtmt) cc_final: 0.8993 (pptt) REVERT: C 960 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: C 988 MET cc_start: 0.9024 (mmm) cc_final: 0.8597 (mmp) REVERT: C 1044 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7784 (tmm) outliers start: 68 outliers final: 28 residues processed: 183 average time/residue: 0.6606 time to fit residues: 143.2690 Evaluate side-chains 163 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1870 ILE Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 SER Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2180 MET Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2187 MET Chi-restraints excluded: chain A residue 2662 SER Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4073 MET Chi-restraints excluded: chain A residue 4172 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 854 ARG Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 239 optimal weight: 40.0000 chunk 120 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 290 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN A3215 HIS ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.117833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.074444 restraints weight = 107127.121| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.09 r_work: 0.3175 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27881 Z= 0.106 Angle : 0.549 11.419 37703 Z= 0.270 Chirality : 0.039 0.344 4321 Planarity : 0.003 0.045 4800 Dihedral : 4.056 54.196 3670 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.50 % Allowed : 12.87 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.15), residues: 3346 helix: 2.33 (0.12), residues: 1929 sheet: 0.35 (0.27), residues: 342 loop : 0.56 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2522 TYR 0.021 0.001 TYR A4000 PHE 0.019 0.001 PHE A1137 TRP 0.013 0.001 TRP A4065 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (27881) covalent geometry : angle 0.54932 / 0.27 (37703) hydrogen bonds : bond 0.03474 / 2.28 ( 1598) hydrogen bonds : angle 3.99279 / 2.84 ( 4632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1176 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8459 (mmm) REVERT: A 1538 GLU cc_start: 0.9235 (tt0) cc_final: 0.8786 (tp30) REVERT: A 2689 ARG cc_start: 0.9550 (OUTLIER) cc_final: 0.9208 (ttm170) REVERT: A 3451 GLU cc_start: 0.9321 (tt0) cc_final: 0.8925 (tp30) REVERT: A 3582 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 3603 ASN cc_start: 0.9317 (t0) cc_final: 0.8999 (m-40) REVERT: A 4317 MET cc_start: 0.8709 (mmt) cc_final: 0.8426 (mmm) REVERT: C 102 MET cc_start: 0.0903 (ptp) cc_final: -0.0368 (ptt) REVERT: C 171 MET cc_start: 0.6430 (mpt) cc_final: 0.6083 (mmt) REVERT: C 328 MET cc_start: 0.9150 (ptt) cc_final: 0.8702 (ppp) REVERT: C 407 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7998 (mpt) REVERT: C 501 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.6505 (p-80) REVERT: C 613 MET cc_start: 0.9157 (mmm) cc_final: 0.8856 (ptt) REVERT: C 686 MET cc_start: 0.4763 (tmm) cc_final: 0.4201 (tmm) REVERT: C 761 MET cc_start: 0.7016 (mtt) cc_final: 0.6727 (ptp) REVERT: C 817 MET cc_start: 0.7732 (mtt) cc_final: 0.7293 (mpp) REVERT: C 864 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8976 (mm) REVERT: C 960 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: C 988 MET cc_start: 0.9069 (mmm) cc_final: 0.8620 (mmp) REVERT: C 1044 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7769 (tmm) REVERT: C 1070 MET cc_start: 0.8279 (mmm) cc_final: 0.6968 (tmm) outliers start: 46 outliers final: 27 residues processed: 168 average time/residue: 0.6470 time to fit residues: 128.5027 Evaluate side-chains 163 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1675 ARG Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1768 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1937 VAL Chi-restraints excluded: chain A residue 2144 SER Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2187 MET Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2238 ASN Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3887 PHE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4172 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 262 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 336 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 312 optimal weight: 30.0000 chunk 263 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.115728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.070645 restraints weight = 107845.026| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.99 r_work: 0.3070 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27881 Z= 0.280 Angle : 0.673 11.698 37703 Z= 0.329 Chirality : 0.043 0.311 4321 Planarity : 0.004 0.053 4800 Dihedral : 4.204 57.942 3670 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 12.87 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.15), residues: 3346 helix: 2.23 (0.12), residues: 1925 sheet: 0.15 (0.27), residues: 346 loop : 0.54 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3957 TYR 0.017 0.001 TYR A1265 PHE 0.031 0.002 PHE C 364 TRP 0.012 0.001 TRP A4065 HIS 0.008 0.001 HIS A2664 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.28 (27881) covalent geometry : angle 0.67349 / 0.33 (37703) hydrogen bonds : bond 0.04264 / 2.81 ( 1598) hydrogen bonds : angle 4.29080 / 3.06 ( 4632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7945 (mtm) cc_final: 0.7521 (ptm) REVERT: A 532 MET cc_start: 0.8920 (tpp) cc_final: 0.8598 (tpp) REVERT: A 1538 GLU cc_start: 0.9266 (tt0) cc_final: 0.8855 (tp30) REVERT: A 2218 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9159 (mmpt) REVERT: A 2689 ARG cc_start: 0.9576 (OUTLIER) cc_final: 0.9266 (ttm170) REVERT: A 3451 GLU cc_start: 0.9309 (tt0) cc_final: 0.8968 (tp30) REVERT: A 3582 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 3603 ASN cc_start: 0.9405 (t0) cc_final: 0.9118 (m-40) REVERT: A 4317 MET cc_start: 0.8551 (mmt) cc_final: 0.8211 (mmm) REVERT: C 102 MET cc_start: 0.0838 (ptp) cc_final: -0.0061 (ptt) REVERT: C 171 MET cc_start: 0.6396 (mpt) cc_final: 0.5986 (mmt) REVERT: C 328 MET cc_start: 0.9164 (ptt) cc_final: 0.8679 (ppp) REVERT: C 613 MET cc_start: 0.9168 (mmm) cc_final: 0.8866 (ptt) REVERT: C 648 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7400 (ppp) REVERT: C 686 MET cc_start: 0.4898 (tmm) cc_final: 0.4393 (tmm) REVERT: C 761 MET cc_start: 0.7079 (mtt) cc_final: 0.6766 (ptp) REVERT: C 817 MET cc_start: 0.7720 (mtt) cc_final: 0.7279 (mpp) REVERT: C 864 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 960 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: C 988 MET cc_start: 0.9106 (mmm) cc_final: 0.8372 (mpm) REVERT: C 1044 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7641 (tmm) REVERT: C 1070 MET cc_start: 0.8402 (mmm) cc_final: 0.7158 (tmm) outliers start: 58 outliers final: 24 residues processed: 175 average time/residue: 0.6335 time to fit residues: 131.6269 Evaluate side-chains 156 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1937 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2218 LYS Chi-restraints excluded: chain A residue 2238 ASN Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3398 MET Chi-restraints excluded: chain A residue 3887 PHE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4172 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 854 ARG Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 93 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 327 optimal weight: 0.8980 chunk 296 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4035 HIS A4202 ASN ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN ** C 986 ASN ** 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 = 0.4448 r_free = 0.4448 target = 0.116904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.072723 restraints weight = 107999.039| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.95 r_work: 0.3140 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27881 Z= 0.143 Angle : 0.600 12.488 37703 Z= 0.291 Chirality : 0.040 0.360 4321 Planarity : 0.004 0.049 4800 Dihedral : 4.152 55.473 3670 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.40 % Allowed : 13.46 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.15), residues: 3346 helix: 2.32 (0.12), residues: 1925 sheet: 0.19 (0.27), residues: 342 loop : 0.60 (0.21), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3957 TYR 0.023 0.001 TYR A4000 PHE 0.024 0.001 PHE C 364 TRP 0.013 0.001 TRP A4065 HIS 0.006 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (27881) covalent geometry : angle 0.60050 / 0.29 (37703) hydrogen bonds : bond 0.03676 / 2.41 ( 1598) hydrogen bonds : angle 4.11840 / 2.93 ( 4632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8102 (mtm) cc_final: 0.7669 (ptm) REVERT: A 532 MET cc_start: 0.8880 (tpp) cc_final: 0.8542 (mmm) REVERT: A 1538 GLU cc_start: 0.9290 (tt0) cc_final: 0.8856 (tp30) REVERT: A 2689 ARG cc_start: 0.9580 (OUTLIER) cc_final: 0.9279 (ttm170) REVERT: A 3451 GLU cc_start: 0.9238 (tt0) cc_final: 0.8896 (tp30) REVERT: A 3582 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 3603 ASN cc_start: 0.9399 (t0) cc_final: 0.9115 (m-40) REVERT: A 4317 MET cc_start: 0.8448 (mmt) cc_final: 0.8071 (mmm) REVERT: C 171 MET cc_start: 0.6362 (mpt) cc_final: 0.5916 (mmt) REVERT: C 328 MET cc_start: 0.9167 (ptt) cc_final: 0.8691 (ppp) REVERT: C 501 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.6378 (p-80) REVERT: C 613 MET cc_start: 0.9172 (mmm) cc_final: 0.8876 (ptt) REVERT: C 648 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7328 (ppp) REVERT: C 686 MET cc_start: 0.5046 (tmm) cc_final: 0.4524 (tmm) REVERT: C 743 THR cc_start: 0.3700 (OUTLIER) cc_final: 0.3437 (p) REVERT: C 761 MET cc_start: 0.7080 (mtt) cc_final: 0.6754 (ptp) REVERT: C 817 MET cc_start: 0.7719 (mtt) cc_final: 0.7251 (mpp) REVERT: C 864 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 960 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8623 (pm20) REVERT: C 988 MET cc_start: 0.9159 (mmm) cc_final: 0.8753 (mmp) REVERT: C 1044 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7578 (tmm) REVERT: C 1070 MET cc_start: 0.8354 (mmm) cc_final: 0.7202 (tmm) outliers start: 43 outliers final: 24 residues processed: 164 average time/residue: 0.5982 time to fit residues: 116.2290 Evaluate side-chains 156 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1675 ARG Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1858 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1937 VAL Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2238 ASN Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4172 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 146 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4035 HIS ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 986 ASN ** 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 = 0.4454 r_free = 0.4454 target = 0.117313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.076448 restraints weight = 109664.956| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.95 r_work: 0.3146 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27881 Z= 0.119 Angle : 0.596 13.101 37703 Z= 0.286 Chirality : 0.040 0.377 4321 Planarity : 0.004 0.049 4800 Dihedral : 4.076 52.698 3670 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.18 % Allowed : 13.91 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.15), residues: 3346 helix: 2.30 (0.12), residues: 1936 sheet: 0.30 (0.27), residues: 338 loop : 0.62 (0.21), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3957 TYR 0.019 0.001 TYR C 224 PHE 0.022 0.001 PHE C 364 TRP 0.013 0.001 TRP A4065 HIS 0.016 0.001 HIS A4035 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (27881) covalent geometry : angle 0.59621 / 0.29 (37703) hydrogen bonds : bond 0.03495 / 2.29 ( 1598) hydrogen bonds : angle 4.03877 / 2.87 ( 4632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8012 (mtm) cc_final: 0.7594 (ptm) REVERT: A 532 MET cc_start: 0.8923 (tpp) cc_final: 0.8717 (mmm) REVERT: A 1538 GLU cc_start: 0.9336 (tt0) cc_final: 0.8862 (tp30) REVERT: A 2180 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8706 (mpp) REVERT: A 2689 ARG cc_start: 0.9594 (OUTLIER) cc_final: 0.9229 (ttm-80) REVERT: A 3451 GLU cc_start: 0.9258 (tt0) cc_final: 0.8898 (tp30) REVERT: A 3582 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8744 (tm-30) REVERT: A 3603 ASN cc_start: 0.9403 (t0) cc_final: 0.9113 (m-40) REVERT: A 4317 MET cc_start: 0.8798 (mmt) cc_final: 0.8540 (mmm) REVERT: C 171 MET cc_start: 0.6387 (mpt) cc_final: 0.5970 (mmt) REVERT: C 328 MET cc_start: 0.9210 (ptt) cc_final: 0.8747 (ppp) REVERT: C 501 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6459 (p-80) REVERT: C 565 MET cc_start: 0.6149 (tmm) cc_final: 0.5782 (tmm) REVERT: C 613 MET cc_start: 0.9158 (mmm) cc_final: 0.8886 (ptt) REVERT: C 648 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7422 (ppp) REVERT: C 686 MET cc_start: 0.4971 (tmm) cc_final: 0.4483 (tmm) REVERT: C 743 THR cc_start: 0.3929 (OUTLIER) cc_final: 0.3673 (p) REVERT: C 761 MET cc_start: 0.6990 (mtt) cc_final: 0.6720 (ptp) REVERT: C 817 MET cc_start: 0.7776 (mtt) cc_final: 0.7301 (mpp) REVERT: C 864 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8951 (mm) REVERT: C 960 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: C 988 MET cc_start: 0.9182 (mmm) cc_final: 0.8512 (mpm) REVERT: C 1044 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7496 (tmm) REVERT: C 1070 MET cc_start: 0.8384 (mmm) cc_final: 0.7170 (tmm) outliers start: 36 outliers final: 24 residues processed: 159 average time/residue: 0.6379 time to fit residues: 120.0929 Evaluate side-chains 159 residues out of total 3062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1937 VAL Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2180 MET Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2238 ASN Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 2689 ARG Chi-restraints excluded: chain A residue 3288 VAL Chi-restraints excluded: chain A residue 3303 ILE Chi-restraints excluded: chain A residue 3887 PHE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4026 VAL Chi-restraints excluded: chain A residue 4172 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1044 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 152 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 282 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 239 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4035 HIS ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 986 ASN ** 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 = 0.4449 r_free = 0.4449 target = 0.116981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.073097 restraints weight = 107621.753| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.03 r_work: 0.3139 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27881 Z= 0.142 Angle : 0.611 13.045 37703 Z= 0.293 Chirality : 0.040 0.374 4321 Planarity : 0.004 0.050 4800 Dihedral : 4.059 57.884 3670 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.34 % Allowed : 13.62 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.15), residues: 3346 helix: 2.33 (0.12), residues: 1937 sheet: 0.25 (0.27), residues: 338 loop : 0.62 (0.21), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3957 TYR 0.022 0.001 TYR C 224 PHE 0.020 0.001 PHE C 364 TRP 0.012 0.001 TRP A4065 HIS 0.016 0.001 HIS A4035 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (27881) covalent geometry : angle 0.61144 / 0.29 (37703) hydrogen bonds : bond 0.03573 / 2.34 ( 1598) hydrogen bonds : angle 4.09386 / 2.92 ( 4632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15624.26 seconds wall clock time: 265 minutes 29.33 seconds (15929.33 seconds total)