Starting phenix.real_space_refine on Mon Mar 25 06:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ato_15654/03_2024/8ato_15654_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ato_15654/03_2024/8ato_15654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ato_15654/03_2024/8ato_15654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ato_15654/03_2024/8ato_15654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ato_15654/03_2024/8ato_15654_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ato_15654/03_2024/8ato_15654_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.070 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 324 5.16 5 C 29881 2.51 5 N 7985 2.21 5 O 8719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 2321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46909 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2871, 22195 Classifications: {'peptide': 2871} Link IDs: {'PCIS': 3, 'PTRANS': 144, 'TRANS': 2723} Chain breaks: 35 Chain: "B" Number of atoms: 22348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 22348 Classifications: {'peptide': 2892} Link IDs: {'PCIS': 4, 'PTRANS': 144, 'TRANS': 2743} Chain breaks: 35 Chain: "C" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1183 Classifications: {'peptide': 150} Link IDs: {'TRANS': 149} Chain: "D" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1183 Classifications: {'peptide': 150} Link IDs: {'TRANS': 149} Time building chain proxies: 24.52, per 1000 atoms: 0.52 Number of scatterers: 46909 At special positions: 0 Unit cell: (159.168, 198.96, 214.711, 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 324 16.00 O 8719 8.00 N 7985 7.00 C 29881 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.44 Conformation dependent library (CDL) restraints added in 8.7 seconds 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11522 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 25 sheets defined 54.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.568A pdb=" N ILE A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 188 through 205 removed outlier: 4.110A pdb=" N HIS A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 217 Processing helix chain 'A' and resid 224 through 242 removed outlier: 4.062A pdb=" N ILE A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 262 removed outlier: 4.444A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.960A pdb=" N TYR A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.130A pdb=" N GLY A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.714A pdb=" N LYS A 359 " --> pdb=" O CYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 430 through 441 removed outlier: 4.611A pdb=" N VAL A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 868 through 874 Processing helix chain 'A' and resid 1018 through 1027 Processing helix chain 'A' and resid 1050 through 1058 removed outlier: 3.660A pdb=" N ARG A1057 " --> pdb=" O GLN A1053 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A1058 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1181 Processing helix chain 'A' and resid 1205 through 1211 Processing helix chain 'A' and resid 1313 through 1324 Processing helix chain 'A' and resid 1324 through 1337 removed outlier: 4.488A pdb=" N HIS A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1365 removed outlier: 3.606A pdb=" N ASN A1365 " --> pdb=" O GLY A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1382 removed outlier: 4.376A pdb=" N ASN A1374 " --> pdb=" O SER A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1395 Processing helix chain 'A' and resid 1397 through 1418 removed outlier: 3.700A pdb=" N CYS A1417 " --> pdb=" O SER A1413 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A1418 " --> pdb=" O ASN A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1435 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1444 through 1459 removed outlier: 3.833A pdb=" N VAL A1448 " --> pdb=" O THR A1444 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A1457 " --> pdb=" O VAL A1453 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A1459 " --> pdb=" O LEU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1483 removed outlier: 4.283A pdb=" N ASP A1483 " --> pdb=" O ARG A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1497 removed outlier: 3.678A pdb=" N ALA A1490 " --> pdb=" O THR A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1941 removed outlier: 4.265A pdb=" N MET A1916 " --> pdb=" O GLN A1912 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A1917 " --> pdb=" O HIS A1913 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A1919 " --> pdb=" O ALA A1915 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1958 Processing helix chain 'A' and resid 1960 through 1998 Processing helix chain 'A' and resid 2010 through 2018 removed outlier: 3.851A pdb=" N LEU A2014 " --> pdb=" O ASN A2010 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2041 Processing helix chain 'A' and resid 2048 through 2053 Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2093 through 2104 Processing helix chain 'A' and resid 2113 through 2127 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 4.199A pdb=" N GLU A2136 " --> pdb=" O SER A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2164 through 2183 Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 4.852A pdb=" N SER A2330 " --> pdb=" O GLU A2326 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A2331 " --> pdb=" O ARG A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.508A pdb=" N LEU A2351 " --> pdb=" O HIS A2347 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A2353 " --> pdb=" O ASP A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2375 Processing helix chain 'A' and resid 2376 through 2389 removed outlier: 3.993A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2401 through 2420 Processing helix chain 'A' and resid 2578 through 2600 removed outlier: 3.557A pdb=" N GLU A2590 " --> pdb=" O MET A2586 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A2593 " --> pdb=" O LEU A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2635 through 2648 Processing helix chain 'A' and resid 2649 through 2653 removed outlier: 3.539A pdb=" N VAL A2652 " --> pdb=" O MET A2649 " (cutoff:3.500A) Processing helix chain 'A' and resid 2656 through 2668 Processing helix chain 'A' and resid 2697 through 2711 Processing helix chain 'A' and resid 2715 through 2732 removed outlier: 3.654A pdb=" N ASN A2731 " --> pdb=" O THR A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2747 through 2755 Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.321A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS A2760 " --> pdb=" O PRO A2756 " (cutoff:3.500A) Processing helix chain 'A' and resid 2781 through 2802 removed outlier: 4.431A pdb=" N ALA A2785 " --> pdb=" O VAL A2781 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2821 removed outlier: 4.145A pdb=" N PHE A2808 " --> pdb=" O CYS A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 Processing helix chain 'A' and resid 2832 through 2844 Processing helix chain 'A' and resid 2852 through 2873 Processing helix chain 'A' and resid 2915 through 2931 removed outlier: 3.716A pdb=" N GLN A2931 " --> pdb=" O ASN A2927 " (cutoff:3.500A) Processing helix chain 'A' and resid 2979 through 2987 removed outlier: 3.975A pdb=" N LEU A2983 " --> pdb=" O TYR A2979 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3001 removed outlier: 3.666A pdb=" N MET A2991 " --> pdb=" O ASN A2987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A3001 " --> pdb=" O ALA A2997 " (cutoff:3.500A) Processing helix chain 'A' and resid 3031 through 3046 Processing helix chain 'A' and resid 3049 through 3062 Proline residue: A3056 - end of helix Processing helix chain 'A' and resid 3064 through 3068 removed outlier: 3.567A pdb=" N GLY A3067 " --> pdb=" O GLY A3064 " (cutoff:3.500A) Processing helix chain 'A' and resid 3078 through 3089 Processing helix chain 'A' and resid 3091 through 3101 Processing helix chain 'A' and resid 3102 through 3118 removed outlier: 3.729A pdb=" N LEU A3106 " --> pdb=" O GLY A3102 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3133 Processing helix chain 'A' and resid 3179 through 3184 Processing helix chain 'A' and resid 3231 through 3235 Processing helix chain 'A' and resid 3322 through 3326 Processing helix chain 'A' and resid 3327 through 3340 removed outlier: 3.854A pdb=" N LEU A3331 " --> pdb=" O SER A3327 " (cutoff:3.500A) Processing helix chain 'A' and resid 3341 through 3343 No H-bonds generated for 'chain 'A' and resid 3341 through 3343' Processing helix chain 'A' and resid 3344 through 3353 Processing helix chain 'A' and resid 3357 through 3368 Processing helix chain 'A' and resid 3374 through 3387 removed outlier: 3.685A pdb=" N ILE A3378 " --> pdb=" O HIS A3374 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A3380 " --> pdb=" O PRO A3376 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3402 Processing helix chain 'A' and resid 3428 through 3441 Processing helix chain 'A' and resid 3445 through 3466 Processing helix chain 'A' and resid 3490 through 3507 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.810A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3532 removed outlier: 3.590A pdb=" N PHE A3522 " --> pdb=" O ASP A3518 " (cutoff:3.500A) Processing helix chain 'A' and resid 3536 through 3553 Processing helix chain 'A' and resid 3553 through 3565 removed outlier: 4.226A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A3558 " --> pdb=" O PRO A3554 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A3559 " --> pdb=" O ASN A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3617 Processing helix chain 'A' and resid 3619 through 3629 removed outlier: 3.708A pdb=" N LYS A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A3625 " --> pdb=" O GLU A3621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A3627 " --> pdb=" O ILE A3623 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A3628 " --> pdb=" O LYS A3624 " (cutoff:3.500A) Processing helix chain 'A' and resid 3630 through 3644 Processing helix chain 'A' and resid 3682 through 3694 Processing helix chain 'A' and resid 3696 through 3704 Processing helix chain 'A' and resid 3708 through 3720 removed outlier: 3.984A pdb=" N TRP A3712 " --> pdb=" O VAL A3708 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A3713 " --> pdb=" O ASN A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 Processing helix chain 'A' and resid 3774 through 3792 Processing helix chain 'A' and resid 3806 through 3816 removed outlier: 3.649A pdb=" N ARG A3810 " --> pdb=" O GLY A3806 " (cutoff:3.500A) Processing helix chain 'A' and resid 3846 through 3850 Processing helix chain 'A' and resid 3865 through 3874 Processing helix chain 'A' and resid 3982 through 3993 Processing helix chain 'A' and resid 4069 through 4077 removed outlier: 3.699A pdb=" N MET A4077 " --> pdb=" O VAL A4073 " (cutoff:3.500A) Processing helix chain 'A' and resid 4078 through 4086 removed outlier: 4.149A pdb=" N LEU A4082 " --> pdb=" O GLY A4078 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A4083 " --> pdb=" O GLY A4079 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A4086 " --> pdb=" O LEU A4082 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4166 removed outlier: 3.654A pdb=" N LEU A4158 " --> pdb=" O PRO A4154 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A4166 " --> pdb=" O GLY A4162 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 removed outlier: 3.562A pdb=" N VAL A4173 " --> pdb=" O GLY A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4177 through 4188 removed outlier: 3.535A pdb=" N ALA A4181 " --> pdb=" O GLU A4177 " (cutoff:3.500A) Processing helix chain 'A' and resid 4199 through 4203 Processing helix chain 'A' and resid 4208 through 4210 No H-bonds generated for 'chain 'A' and resid 4208 through 4210' Processing helix chain 'A' and resid 4211 through 4224 Processing helix chain 'A' and resid 4228 through 4241 removed outlier: 3.694A pdb=" N VAL A4232 " --> pdb=" O THR A4228 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A4241 " --> pdb=" O MET A4237 " (cutoff:3.500A) Processing helix chain 'A' and resid 4242 through 4256 Processing helix chain 'A' and resid 4306 through 4332 Processing helix chain 'A' and resid 4357 through 4364 removed outlier: 3.819A pdb=" N GLU A4362 " --> pdb=" O SER A4358 " (cutoff:3.500A) Processing helix chain 'A' and resid 4368 through 4379 removed outlier: 3.756A pdb=" N ASN A4379 " --> pdb=" O SER A4375 " (cutoff:3.500A) Processing helix chain 'A' and resid 4383 through 4388 removed outlier: 4.221A pdb=" N ARG A4387 " --> pdb=" O LEU A4383 " (cutoff:3.500A) Processing helix chain 'A' and resid 4388 through 4405 Processing helix chain 'A' and resid 4408 through 4413 Processing helix chain 'A' and resid 4432 through 4448 Processing helix chain 'A' and resid 4479 through 4501 removed outlier: 3.518A pdb=" N GLU A4501 " --> pdb=" O GLN A4497 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.691A pdb=" N HIS B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.783A pdb=" N ALA B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 243 Processing helix chain 'B' and resid 247 through 262 removed outlier: 3.973A pdb=" N VAL B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.704A pdb=" N ARG B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.604A pdb=" N MET B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 367 through 374 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 863 through 868 removed outlier: 4.082A pdb=" N LEU B 867 " --> pdb=" O PRO B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1030 Processing helix chain 'B' and resid 1053 through 1057 removed outlier: 4.444A pdb=" N ARG B1057 " --> pdb=" O GLN B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1065 removed outlier: 3.955A pdb=" N GLN B1064 " --> pdb=" O GLN B1060 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1060 through 1065' Processing helix chain 'B' and resid 1068 through 1074 Processing helix chain 'B' and resid 1172 through 1177 Processing helix chain 'B' and resid 1189 through 1192 Processing helix chain 'B' and resid 1291 through 1294 removed outlier: 4.158A pdb=" N ASP B1294 " --> pdb=" O ARG B1291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1291 through 1294' Processing helix chain 'B' and resid 1313 through 1324 removed outlier: 3.513A pdb=" N PHE B1324 " --> pdb=" O ALA B1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1337 Processing helix chain 'B' and resid 1345 through 1363 Processing helix chain 'B' and resid 1370 through 1384 removed outlier: 3.601A pdb=" N ASN B1374 " --> pdb=" O SER B1370 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B1380 " --> pdb=" O ASN B1376 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1395 Processing helix chain 'B' and resid 1397 through 1418 Processing helix chain 'B' and resid 1424 through 1435 Processing helix chain 'B' and resid 1436 through 1442 Proline residue: B1440 - end of helix Processing helix chain 'B' and resid 1444 through 1458 removed outlier: 3.550A pdb=" N VAL B1448 " --> pdb=" O THR B1444 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B1457 " --> pdb=" O VAL B1453 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B1458 " --> pdb=" O LEU B1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 1459 through 1461 No H-bonds generated for 'chain 'B' and resid 1459 through 1461' Processing helix chain 'B' and resid 1462 through 1484 removed outlier: 3.694A pdb=" N ARG B1479 " --> pdb=" O THR B1475 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B1480 " --> pdb=" O ALA B1476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B1483 " --> pdb=" O ARG B1479 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B1484 " --> pdb=" O GLN B1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1497 Processing helix chain 'B' and resid 1823 through 1828 Processing helix chain 'B' and resid 1909 through 1940 Processing helix chain 'B' and resid 1949 through 1958 Processing helix chain 'B' and resid 1960 through 1998 Processing helix chain 'B' and resid 2010 through 2018 removed outlier: 3.911A pdb=" N GLN B2016 " --> pdb=" O GLU B2012 " (cutoff:3.500A) Processing helix chain 'B' and resid 2019 through 2040 Processing helix chain 'B' and resid 2047 through 2054 removed outlier: 3.834A pdb=" N GLN B2051 " --> pdb=" O PRO B2047 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B2052 " --> pdb=" O ALA B2048 " (cutoff:3.500A) Processing helix chain 'B' and resid 2055 through 2067 Processing helix chain 'B' and resid 2071 through 2087 Processing helix chain 'B' and resid 2093 through 2104 Processing helix chain 'B' and resid 2113 through 2128 Processing helix chain 'B' and resid 2129 through 2131 No H-bonds generated for 'chain 'B' and resid 2129 through 2131' Processing helix chain 'B' and resid 2132 through 2146 removed outlier: 3.860A pdb=" N GLU B2136 " --> pdb=" O SER B2132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2147 through 2150 Processing helix chain 'B' and resid 2164 through 2184 removed outlier: 3.825A pdb=" N THR B2184 " --> pdb=" O ASP B2180 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 3.682A pdb=" N SER B2330 " --> pdb=" O GLU B2326 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.828A pdb=" N PHE B2353 " --> pdb=" O ASP B2349 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B2365 " --> pdb=" O ILE B2361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2370 through 2375 removed outlier: 3.608A pdb=" N ILE B2374 " --> pdb=" O HIS B2370 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2389 removed outlier: 4.014A pdb=" N LEU B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 3.955A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2576 through 2599 removed outlier: 3.629A pdb=" N SER B2587 " --> pdb=" O LEU B2583 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B2590 " --> pdb=" O MET B2586 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B2593 " --> pdb=" O LEU B2589 " (cutoff:3.500A) Processing helix chain 'B' and resid 2635 through 2649 Processing helix chain 'B' and resid 2656 through 2669 Processing helix chain 'B' and resid 2697 through 2711 removed outlier: 3.583A pdb=" N TRP B2710 " --> pdb=" O THR B2706 " (cutoff:3.500A) Processing helix chain 'B' and resid 2715 through 2732 removed outlier: 3.620A pdb=" N ASN B2731 " --> pdb=" O THR B2727 " (cutoff:3.500A) Processing helix chain 'B' and resid 2747 through 2755 Processing helix chain 'B' and resid 2755 through 2768 removed outlier: 4.362A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B2760 " --> pdb=" O PRO B2756 " (cutoff:3.500A) Processing helix chain 'B' and resid 2781 through 2802 removed outlier: 4.473A pdb=" N ALA B2785 " --> pdb=" O VAL B2781 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B2786 " --> pdb=" O GLY B2782 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2820 removed outlier: 4.136A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 removed outlier: 3.524A pdb=" N THR B2828 " --> pdb=" O GLY B2824 " (cutoff:3.500A) Processing helix chain 'B' and resid 2832 through 2845 removed outlier: 4.141A pdb=" N GLU B2845 " --> pdb=" O GLU B2841 " (cutoff:3.500A) Processing helix chain 'B' and resid 2852 through 2873 removed outlier: 3.898A pdb=" N ILE B2856 " --> pdb=" O SER B2852 " (cutoff:3.500A) Processing helix chain 'B' and resid 2915 through 2931 removed outlier: 3.520A pdb=" N GLN B2931 " --> pdb=" O ASN B2927 " (cutoff:3.500A) Processing helix chain 'B' and resid 2980 through 2987 Processing helix chain 'B' and resid 2987 through 3000 Processing helix chain 'B' and resid 3031 through 3047 Processing helix chain 'B' and resid 3049 through 3063 Proline residue: B3056 - end of helix Processing helix chain 'B' and resid 3078 through 3089 Processing helix chain 'B' and resid 3091 through 3101 Processing helix chain 'B' and resid 3102 through 3118 Processing helix chain 'B' and resid 3125 through 3130 Processing helix chain 'B' and resid 3179 through 3184 removed outlier: 3.666A pdb=" N GLN B3184 " --> pdb=" O VAL B3181 " (cutoff:3.500A) Processing helix chain 'B' and resid 3231 through 3235 Processing helix chain 'B' and resid 3305 through 3309 removed outlier: 3.579A pdb=" N SER B3309 " --> pdb=" O THR B3306 " (cutoff:3.500A) Processing helix chain 'B' and resid 3322 through 3326 Processing helix chain 'B' and resid 3327 through 3340 removed outlier: 4.098A pdb=" N LEU B3331 " --> pdb=" O SER B3327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3353 Processing helix chain 'B' and resid 3357 through 3367 Processing helix chain 'B' and resid 3374 through 3387 removed outlier: 3.797A pdb=" N ILE B3378 " --> pdb=" O HIS B3374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3402 Processing helix chain 'B' and resid 3428 through 3441 Processing helix chain 'B' and resid 3445 through 3465 Processing helix chain 'B' and resid 3490 through 3507 Processing helix chain 'B' and resid 3512 through 3517 removed outlier: 3.654A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B3517 " --> pdb=" O LEU B3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3512 through 3517' Processing helix chain 'B' and resid 3518 through 3531 Processing helix chain 'B' and resid 3536 through 3553 removed outlier: 3.781A pdb=" N LYS B3540 " --> pdb=" O MET B3536 " (cutoff:3.500A) Processing helix chain 'B' and resid 3553 through 3565 removed outlier: 3.574A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) Processing helix chain 'B' and resid 3606 through 3617 Processing helix chain 'B' and resid 3619 through 3629 Processing helix chain 'B' and resid 3633 through 3642 removed outlier: 3.671A pdb=" N ARG B3637 " --> pdb=" O SER B3633 " (cutoff:3.500A) Processing helix chain 'B' and resid 3679 through 3694 removed outlier: 3.638A pdb=" N ALA B3684 " --> pdb=" O ALA B3680 " (cutoff:3.500A) Proline residue: B3685 - end of helix removed outlier: 3.710A pdb=" N GLY B3694 " --> pdb=" O LEU B3690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3697 through 3703 removed outlier: 3.613A pdb=" N ASP B3701 " --> pdb=" O HIS B3697 " (cutoff:3.500A) Processing helix chain 'B' and resid 3711 through 3721 Processing helix chain 'B' and resid 3752 through 3771 Processing helix chain 'B' and resid 3774 through 3790 Processing helix chain 'B' and resid 3806 through 3815 Processing helix chain 'B' and resid 3846 through 3850 Processing helix chain 'B' and resid 3865 through 3874 Processing helix chain 'B' and resid 3969 through 3973 removed outlier: 3.863A pdb=" N ALA B3973 " --> pdb=" O LYS B3970 " (cutoff:3.500A) Processing helix chain 'B' and resid 3982 through 3993 Processing helix chain 'B' and resid 4069 through 4077 removed outlier: 4.497A pdb=" N MET B4077 " --> pdb=" O VAL B4073 " (cutoff:3.500A) Processing helix chain 'B' and resid 4078 through 4087 Processing helix chain 'B' and resid 4154 through 4165 removed outlier: 3.754A pdb=" N PHE B4161 " --> pdb=" O SER B4157 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B4162 " --> pdb=" O LEU B4158 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B4163 " --> pdb=" O ALA B4159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B4165 " --> pdb=" O PHE B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4170 through 4175 removed outlier: 3.932A pdb=" N LEU B4174 " --> pdb=" O TYR B4170 " (cutoff:3.500A) Processing helix chain 'B' and resid 4178 through 4189 removed outlier: 3.537A pdb=" N LEU B4189 " --> pdb=" O LEU B4185 " (cutoff:3.500A) Processing helix chain 'B' and resid 4203 through 4207 removed outlier: 4.223A pdb=" N ASN B4207 " --> pdb=" O PRO B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4211 through 4224 removed outlier: 4.855A pdb=" N LEU B4217 " --> pdb=" O PRO B4213 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4241 Processing helix chain 'B' and resid 4242 through 4255 Processing helix chain 'B' and resid 4306 through 4332 Processing helix chain 'B' and resid 4358 through 4367 removed outlier: 3.621A pdb=" N GLU B4362 " --> pdb=" O SER B4358 " (cutoff:3.500A) Processing helix chain 'B' and resid 4368 through 4379 removed outlier: 3.818A pdb=" N ASN B4379 " --> pdb=" O SER B4375 " (cutoff:3.500A) Processing helix chain 'B' and resid 4381 through 4388 removed outlier: 3.604A pdb=" N ALA B4386 " --> pdb=" O VAL B4382 " (cutoff:3.500A) Processing helix chain 'B' and resid 4388 through 4405 Processing helix chain 'B' and resid 4408 through 4413 Processing helix chain 'B' and resid 4432 through 4451 removed outlier: 3.875A pdb=" N LEU B4436 " --> pdb=" O SER B4432 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B4449 " --> pdb=" O ASP B4445 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B4450 " --> pdb=" O THR B4446 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4502 removed outlier: 3.994A pdb=" N GLU B4501 " --> pdb=" O GLN B4497 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 53 removed outlier: 3.799A pdb=" N LEU C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 81 Processing helix chain 'C' and resid 82 through 108 removed outlier: 3.804A pdb=" N LEU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 87 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 150 Processing helix chain 'D' and resid 2 through 53 Processing helix chain 'D' and resid 58 through 108 Processing helix chain 'D' and resid 110 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.926A pdb=" N GLN A 118 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 127 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 128 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA3, first strand: chain 'A' and resid 903 through 906 removed outlier: 3.502A pdb=" N LEU A 915 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 905 " --> pdb=" O LYS A 913 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 913 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 924 " --> pdb=" O ILE A 914 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1031 through 1033 current: chain 'A' and resid 1077 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1077 through 1079 current: chain 'A' and resid 1198 through 1199 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1526 through 1529 removed outlier: 5.289A pdb=" N VAL A1527 " --> pdb=" O ASP A1794 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP A1794 " --> pdb=" O VAL A1527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1791 through 1806 current: chain 'A' and resid 1832 through 1835 Processing sheet with id=AA6, first strand: chain 'A' and resid 1777 through 1781 removed outlier: 3.771A pdb=" N ILE A1780 " --> pdb=" O ALA A1871 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1871 " --> pdb=" O ILE A1780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2877 through 2878 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2878 current: chain 'A' and resid 3257 through 3258 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 2891 through 2892 Processing sheet with id=AA9, first strand: chain 'A' and resid 3855 through 3861 removed outlier: 3.597A pdb=" N ARG A3856 " --> pdb=" O LEU A3826 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A3860 " --> pdb=" O VAL A3822 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N ILE A4002 " --> pdb=" O LYS A3821 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR A3823 " --> pdb=" O ILE A4002 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU A4004 " --> pdb=" O THR A3823 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A3825 " --> pdb=" O LEU A4004 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL A4006 " --> pdb=" O PHE A3825 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN A3827 " --> pdb=" O VAL A4006 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N LEU A4008 " --> pdb=" O GLN A3827 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.776A pdb=" N ILE B 94 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B 84 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 92 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 166 Processing sheet with id=AB3, first strand: chain 'B' and resid 314 through 316 removed outlier: 3.927A pdb=" N TYR B 315 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B 327 " --> pdb=" O TYR B 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 400 through 403 removed outlier: 3.686A pdb=" N CYS B 410 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 409 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS B 423 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE B 411 " --> pdb=" O HIS B 421 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 570 through 575 removed outlier: 3.670A pdb=" N GLY B 571 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 629 " --> pdb=" O GLY B 571 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 575 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG B 625 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 746 through 750 removed outlier: 3.625A pdb=" N GLY B 823 " --> pdb=" O ILE B 849 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 847 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 859 through 861 Processing sheet with id=AB8, first strand: chain 'B' and resid 940 through 946 removed outlier: 3.869A pdb=" N SER B 942 " --> pdb=" O CYS B 955 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 951 " --> pdb=" O CYS B 946 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1039 through 1041 removed outlier: 3.950A pdb=" N SER B1039 " --> pdb=" O VAL B1094 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B1041 " --> pdb=" O GLU B1092 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B1092 " --> pdb=" O THR B1041 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.361A pdb=" N THR B1076 " --> pdb=" O VAL B1049 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B1075 " --> pdb=" O VAL B1301 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN B1297 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B1298 " --> pdb=" O VAL B1109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B1109 " --> pdb=" O GLU B1298 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B1304 " --> pdb=" O HIS B1103 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS B1103 " --> pdb=" O ARG B1304 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B1203 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1186 through 1187 Processing sheet with id=AC3, first strand: chain 'B' and resid 1526 through 1528 removed outlier: 3.775A pdb=" N GLY B1526 " --> pdb=" O ASP B1794 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP B1794 " --> pdb=" O GLY B1526 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B1792 " --> pdb=" O GLN B1528 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1788 through 1805 current: chain 'B' and resid 1829 through 1834 Processing sheet with id=AC4, first strand: chain 'B' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2877 through 2879 current: chain 'B' and resid 3257 through 3258 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 2933 through 2934 removed outlier: 3.810A pdb=" N ALA B2978 " --> pdb=" O LEU B2934 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 3855 through 3861 removed outlier: 3.917A pdb=" N ARG B3856 " --> pdb=" O LEU B3826 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B3860 " --> pdb=" O VAL B3822 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B4002 " --> pdb=" O THR B3823 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B3827 " --> pdb=" O LEU B4004 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 3965 through 3966 2277 hydrogen bonds defined for protein. 6690 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: 22.70 Time building geometry restraints manager: 19.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12070 1.33 - 1.45: 7835 1.45 - 1.57: 27407 1.57 - 1.69: 0 1.69 - 1.81: 476 Bond restraints: 47788 Sorted by residual: bond pdb=" N LYS B3131 " pdb=" CA LYS B3131 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.23e-02 6.61e+03 1.20e+01 bond pdb=" C LEU B4212 " pdb=" N PRO B4213 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.22e+00 bond pdb=" N PHE B3132 " pdb=" CA PHE B3132 " ideal model delta sigma weight residual 1.453 1.481 -0.029 1.31e-02 5.83e+03 4.81e+00 bond pdb=" N ILE B3129 " pdb=" CA ILE B3129 " ideal model delta sigma weight residual 1.461 1.484 -0.024 1.19e-02 7.06e+03 3.95e+00 bond pdb=" N THR B3128 " pdb=" CA THR B3128 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.30e-02 5.92e+03 3.84e+00 ... (remaining 47783 not shown) Histogram of bond angle deviations from ideal: 95.61 - 104.00: 767 104.00 - 112.39: 26195 112.39 - 120.78: 23133 120.78 - 129.17: 14449 129.17 - 137.57: 375 Bond angle restraints: 64919 Sorted by residual: angle pdb=" N PHE B3132 " pdb=" CA PHE B3132 " pdb=" C PHE B3132 " ideal model delta sigma weight residual 110.53 99.60 10.93 1.29e+00 6.01e-01 7.17e+01 angle pdb=" N THR B3128 " pdb=" CA THR B3128 " pdb=" C THR B3128 " ideal model delta sigma weight residual 113.55 105.43 8.12 1.26e+00 6.30e-01 4.15e+01 angle pdb=" N LEU B3133 " pdb=" CA LEU B3133 " pdb=" C LEU B3133 " ideal model delta sigma weight residual 111.74 103.91 7.83 1.35e+00 5.49e-01 3.36e+01 angle pdb=" CA PHE B3132 " pdb=" C PHE B3132 " pdb=" O PHE B3132 " ideal model delta sigma weight residual 121.94 115.87 6.07 1.15e+00 7.56e-01 2.79e+01 angle pdb=" C LEU A1847 " pdb=" CA LEU A1847 " pdb=" CB LEU A1847 " ideal model delta sigma weight residual 115.79 109.77 6.02 1.19e+00 7.06e-01 2.56e+01 ... (remaining 64914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 26442 17.99 - 35.98: 2081 35.98 - 53.97: 345 53.97 - 71.96: 76 71.96 - 89.96: 37 Dihedral angle restraints: 28981 sinusoidal: 11338 harmonic: 17643 Sorted by residual: dihedral pdb=" CA PRO A1043 " pdb=" C PRO A1043 " pdb=" N PRO A1044 " pdb=" CA PRO A1044 " ideal model delta harmonic sigma weight residual 180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C PHE B3132 " pdb=" N PHE B3132 " pdb=" CA PHE B3132 " pdb=" CB PHE B3132 " ideal model delta harmonic sigma weight residual -122.60 -111.80 -10.80 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA GLU A4177 " pdb=" C GLU A4177 " pdb=" N ARG A4178 " pdb=" CA ARG A4178 " ideal model delta harmonic sigma weight residual -180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 28978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 7368 0.085 - 0.169: 454 0.169 - 0.254: 2 0.254 - 0.338: 1 0.338 - 0.423: 1 Chirality restraints: 7826 Sorted by residual: chirality pdb=" CA PHE B3132 " pdb=" N PHE B3132 " pdb=" C PHE B3132 " pdb=" CB PHE B3132 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA LEU B3133 " pdb=" N LEU B3133 " pdb=" C LEU B3133 " pdb=" CB LEU B3133 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE B3129 " pdb=" N ILE B3129 " pdb=" C ILE B3129 " pdb=" CB ILE B3129 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 7823 not shown) Planarity restraints: 8158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B3127 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C SER B3127 " 0.060 2.00e-02 2.50e+03 pdb=" O SER B3127 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B3128 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1450 " 0.007 2.00e-02 2.50e+03 1.87e-02 8.71e+00 pdb=" CG TRP A1450 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A1450 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A1450 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A1450 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1450 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1450 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1450 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1450 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1450 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B1042 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B1043 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B1043 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1043 " 0.028 5.00e-02 4.00e+02 ... (remaining 8155 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 690 2.68 - 3.23: 45859 3.23 - 3.79: 73463 3.79 - 4.34: 94217 4.34 - 4.90: 154187 Nonbonded interactions: 368416 Sorted by model distance: nonbonded pdb=" O GLU B3787 " pdb=" OG1 THR B3791 " model vdw 2.120 2.440 nonbonded pdb=" OG SER A1500 " pdb=" OH TYR A1974 " model vdw 2.162 2.440 nonbonded pdb=" O LEU B1093 " pdb=" OH TYR B1217 " model vdw 2.165 2.440 nonbonded pdb=" OE1 GLU A1052 " pdb=" NH1 ARG A1056 " model vdw 2.166 2.520 nonbonded pdb=" O HIS A1103 " pdb=" NH2 ARG A1305 " model vdw 2.183 2.520 ... (remaining 368411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 55 through 3134 or resid 3158 through 4502)) selection = (chain 'B' and (resid 55 through 1226 or resid 1290 through 1530 or resid 1770 t \ hrough 2420 or resid 2577 through 2600 or resid 2629 through 2944 or resid 2976 \ through 4502)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.780 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 121.490 Find NCS groups from input model: 3.680 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 0.043 47788 Z= 0.164 Angle : 0.550 10.926 64919 Z= 0.284 Chirality : 0.039 0.423 7826 Planarity : 0.004 0.051 8158 Dihedral : 13.627 89.956 17459 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.11), residues: 5915 helix: 1.63 (0.10), residues: 2974 sheet: 0.20 (0.29), residues: 371 loop : -0.44 (0.13), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A1450 HIS 0.009 0.001 HIS A2065 PHE 0.029 0.001 PHE B1031 TYR 0.019 0.001 TYR B3065 ARG 0.004 0.000 ARG A4378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 560 time to evaluate : 5.191 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 309 MET cc_start: 0.0583 (tmm) cc_final: -0.0647 (mmm) REVERT: A 501 MET cc_start: 0.0981 (ttm) cc_final: 0.0631 (tpp) REVERT: A 1321 MET cc_start: 0.3033 (mpp) cc_final: 0.2638 (mpp) REVERT: A 1482 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 1485 LEU cc_start: 0.8543 (tp) cc_final: 0.8258 (tp) REVERT: A 1488 MET cc_start: 0.7487 (tpp) cc_final: 0.7204 (mmm) REVERT: A 1504 ASP cc_start: 0.7223 (t0) cc_final: 0.6690 (t0) REVERT: A 1783 MET cc_start: 0.3352 (mpp) cc_final: 0.2551 (tpp) REVERT: A 1916 MET cc_start: 0.4828 (pmm) cc_final: 0.2516 (tmm) REVERT: A 2021 GLU cc_start: 0.6679 (mp0) cc_final: 0.6224 (mp0) REVERT: A 2073 LYS cc_start: 0.7238 (tptt) cc_final: 0.6713 (tttm) REVERT: A 2167 MET cc_start: 0.8310 (tpp) cc_final: 0.7938 (tpp) REVERT: A 2787 GLN cc_start: 0.7999 (tp40) cc_final: 0.7743 (tp40) REVERT: A 3876 THR cc_start: 0.7810 (m) cc_final: 0.7446 (p) REVERT: A 4218 ARG cc_start: 0.6256 (tmt-80) cc_final: 0.5785 (tmt-80) REVERT: A 4440 MET cc_start: 0.6348 (mpp) cc_final: 0.5409 (ptm) REVERT: A 4489 TYR cc_start: 0.5309 (t80) cc_final: 0.4626 (t80) REVERT: B 327 MET cc_start: 0.3806 (pmm) cc_final: 0.3564 (mtp) REVERT: B 1017 PHE cc_start: 0.5218 (m-80) cc_final: 0.4843 (m-80) REVERT: B 1030 ARG cc_start: 0.6968 (tpm170) cc_final: 0.6696 (mmt180) REVERT: B 1100 MET cc_start: 0.5685 (mtp) cc_final: 0.5243 (mmm) REVERT: B 1324 PHE cc_start: 0.7336 (m-80) cc_final: 0.7072 (m-80) REVERT: B 1350 SER cc_start: 0.8301 (t) cc_final: 0.8016 (p) REVERT: B 1852 VAL cc_start: 0.7892 (t) cc_final: 0.7600 (p) REVERT: B 1857 LYS cc_start: 0.6094 (tptt) cc_final: 0.5469 (ttmm) REVERT: B 1879 TYR cc_start: 0.8656 (m-80) cc_final: 0.8253 (m-80) REVERT: B 2015 ILE cc_start: 0.8179 (pt) cc_final: 0.7929 (mp) REVERT: B 2032 ASP cc_start: 0.7961 (t0) cc_final: 0.7654 (m-30) REVERT: B 2589 LEU cc_start: 0.8783 (mt) cc_final: 0.8519 (mm) REVERT: B 2822 GLU cc_start: 0.7086 (pp20) cc_final: 0.6734 (tm-30) REVERT: B 3090 ASP cc_start: 0.8028 (t70) cc_final: 0.7784 (t0) REVERT: B 3130 MET cc_start: 0.8549 (mmm) cc_final: 0.8293 (mmp) REVERT: B 3308 SER cc_start: 0.8744 (t) cc_final: 0.8290 (p) REVERT: B 3444 PRO cc_start: 0.7563 (Cg_exo) cc_final: 0.7206 (Cg_endo) REVERT: B 3698 ILE cc_start: 0.8329 (mm) cc_final: 0.8082 (mp) REVERT: B 3760 GLU cc_start: 0.7207 (pt0) cc_final: 0.7002 (tt0) REVERT: D 57 MET cc_start: 0.0729 (mmp) cc_final: -0.1270 (ptp) REVERT: D 92 THR cc_start: 0.2788 (m) cc_final: 0.2522 (t) outliers start: 5 outliers final: 3 residues processed: 563 average time/residue: 1.4644 time to fit residues: 1036.2805 Evaluate side-chains 361 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 358 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3129 ILE Chi-restraints excluded: chain B residue 3134 ASP Chi-restraints excluded: chain B residue 3871 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 9.9990 chunk 459 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 474 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 353 optimal weight: 50.0000 chunk 550 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4215 HIS A4245 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1121 GLN B1347 HIS ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2105 ASN B2108 GLN ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2565 GLN B2735 ASN B3002 ASN ** B3493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3776 ASN ** B3790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 47788 Z= 0.280 Angle : 0.591 17.423 64919 Z= 0.290 Chirality : 0.041 0.182 7826 Planarity : 0.004 0.054 8158 Dihedral : 4.195 58.617 6376 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.55 % Allowed : 8.12 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 5915 helix: 1.61 (0.09), residues: 3022 sheet: 0.09 (0.28), residues: 391 loop : -0.60 (0.13), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B2710 HIS 0.013 0.001 HIS A2654 PHE 0.025 0.001 PHE A1508 TYR 0.021 0.001 TYR A2181 ARG 0.008 0.000 ARG A4086 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 374 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.4714 (tpt) cc_final: 0.3718 (ptm) REVERT: A 309 MET cc_start: 0.0783 (tmm) cc_final: 0.0547 (ptm) REVERT: A 501 MET cc_start: 0.1106 (ttm) cc_final: 0.0736 (tpp) REVERT: A 1321 MET cc_start: 0.3081 (mpp) cc_final: 0.2750 (mpp) REVERT: A 1482 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 1488 MET cc_start: 0.7580 (tpp) cc_final: 0.7322 (mmm) REVERT: A 1504 ASP cc_start: 0.7299 (t0) cc_final: 0.6723 (t0) REVERT: A 1783 MET cc_start: 0.3439 (mpp) cc_final: 0.2548 (tpp) REVERT: A 1916 MET cc_start: 0.4696 (pmm) cc_final: 0.2469 (tmm) REVERT: A 2021 GLU cc_start: 0.6688 (mp0) cc_final: 0.6178 (mp0) REVERT: A 2073 LYS cc_start: 0.7335 (tptt) cc_final: 0.6774 (tttm) REVERT: A 2787 GLN cc_start: 0.8111 (tp40) cc_final: 0.7743 (tp40) REVERT: A 4218 ARG cc_start: 0.6313 (tmt-80) cc_final: 0.5710 (tmt-80) REVERT: A 4440 MET cc_start: 0.6229 (mpp) cc_final: 0.5452 (ptm) REVERT: A 4489 TYR cc_start: 0.5288 (t80) cc_final: 0.4484 (t80) REVERT: B 327 MET cc_start: 0.3901 (pmm) cc_final: 0.3686 (mtp) REVERT: B 1017 PHE cc_start: 0.5260 (m-80) cc_final: 0.4925 (m-80) REVERT: B 1030 ARG cc_start: 0.6824 (tpm170) cc_final: 0.6523 (mmt180) REVERT: B 1100 MET cc_start: 0.5631 (mtp) cc_final: 0.5307 (mmm) REVERT: B 1305 ARG cc_start: 0.6543 (ptt90) cc_final: 0.6040 (ptp90) REVERT: B 1324 PHE cc_start: 0.7355 (m-80) cc_final: 0.7067 (m-80) REVERT: B 1358 TRP cc_start: 0.6848 (t-100) cc_final: 0.6552 (t-100) REVERT: B 1842 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8562 (pt) REVERT: B 1857 LYS cc_start: 0.6020 (tptt) cc_final: 0.5660 (ttmm) REVERT: B 2030 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 2032 ASP cc_start: 0.7930 (t0) cc_final: 0.7618 (m-30) REVERT: B 2596 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: B 2822 GLU cc_start: 0.7002 (pp20) cc_final: 0.6680 (tm-30) REVERT: B 3090 ASP cc_start: 0.8084 (t70) cc_final: 0.7806 (t0) REVERT: B 3130 MET cc_start: 0.8661 (mmm) cc_final: 0.8415 (mmp) REVERT: B 3308 SER cc_start: 0.8767 (t) cc_final: 0.8227 (p) REVERT: B 3698 ILE cc_start: 0.8375 (mm) cc_final: 0.8121 (mp) REVERT: B 3760 GLU cc_start: 0.7352 (pt0) cc_final: 0.7043 (pt0) REVERT: C 99 MET cc_start: -0.0780 (ttt) cc_final: -0.1050 (ttp) REVERT: D 57 MET cc_start: 0.0806 (mmp) cc_final: -0.1285 (ptp) REVERT: D 87 GLU cc_start: 0.2317 (mm-30) cc_final: 0.1977 (mm-30) REVERT: D 91 MET cc_start: 0.3348 (OUTLIER) cc_final: 0.2476 (mpp) outliers start: 82 outliers final: 39 residues processed: 420 average time/residue: 1.5116 time to fit residues: 810.7001 Evaluate side-chains 376 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 333 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1436 MET Chi-restraints excluded: chain A residue 1968 SER Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2366 ARG Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2590 GLU Chi-restraints excluded: chain A residue 3181 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3693 VAL Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3873 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1829 ARG Chi-restraints excluded: chain B residue 1842 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2030 LEU Chi-restraints excluded: chain B residue 2110 LEU Chi-restraints excluded: chain B residue 2128 SER Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2872 THR Chi-restraints excluded: chain B residue 2874 SER Chi-restraints excluded: chain B residue 3071 SER Chi-restraints excluded: chain B residue 3134 ASP Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3759 ILE Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3843 VAL Chi-restraints excluded: chain B residue 3869 VAL Chi-restraints excluded: chain B residue 3871 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain D residue 91 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 305 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 458 optimal weight: 0.8980 chunk 374 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 551 optimal weight: 5.9990 chunk 595 optimal weight: 30.0000 chunk 490 optimal weight: 4.9990 chunk 546 optimal weight: 30.0000 chunk 187 optimal weight: 0.9990 chunk 442 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1519 ASN ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2126 GLN A2787 GLN A2830 GLN A3055 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3177 GLN A3503 HIS A3803 ASN A4215 HIS B 151 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3424 ASN ** B3493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 47788 Z= 0.248 Angle : 0.560 12.138 64919 Z= 0.273 Chirality : 0.040 0.173 7826 Planarity : 0.004 0.053 8158 Dihedral : 4.154 53.692 6374 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 10.78 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5915 helix: 1.62 (0.09), residues: 3007 sheet: 0.17 (0.27), residues: 400 loop : -0.65 (0.13), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B2710 HIS 0.008 0.001 HIS A2654 PHE 0.027 0.001 PHE B1108 TYR 0.023 0.001 TYR A2181 ARG 0.007 0.000 ARG A4236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 355 time to evaluate : 4.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.4063 (tpt) cc_final: 0.3384 (ptm) REVERT: A 309 MET cc_start: 0.0891 (tmm) cc_final: 0.0630 (ptm) REVERT: A 501 MET cc_start: 0.1139 (ttm) cc_final: 0.0755 (tpp) REVERT: A 830 MET cc_start: -0.2004 (ttm) cc_final: -0.2866 (tpp) REVERT: A 1504 ASP cc_start: 0.7254 (t0) cc_final: 0.6659 (t0) REVERT: A 1512 MET cc_start: 0.4952 (tpp) cc_final: 0.4746 (tmm) REVERT: A 1783 MET cc_start: 0.3434 (mpp) cc_final: 0.2541 (tpp) REVERT: A 1916 MET cc_start: 0.4565 (pmm) cc_final: 0.2359 (tmm) REVERT: A 1962 LYS cc_start: 0.7329 (ptmm) cc_final: 0.7107 (pttp) REVERT: A 2021 GLU cc_start: 0.6684 (mp0) cc_final: 0.6165 (mp0) REVERT: A 2073 LYS cc_start: 0.7334 (tptt) cc_final: 0.6755 (tttm) REVERT: A 2349 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: A 2787 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7704 (tp40) REVERT: A 3254 SER cc_start: 0.9171 (p) cc_final: 0.8882 (t) REVERT: A 3818 GLU cc_start: 0.7297 (pm20) cc_final: 0.7012 (pm20) REVERT: A 4218 ARG cc_start: 0.6307 (tmt-80) cc_final: 0.5856 (tmt-80) REVERT: A 4240 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 4408 MET cc_start: 0.4206 (tpt) cc_final: 0.3647 (tpt) REVERT: A 4440 MET cc_start: 0.6194 (mpp) cc_final: 0.5449 (ptm) REVERT: B 1017 PHE cc_start: 0.5289 (m-80) cc_final: 0.4998 (m-80) REVERT: B 1030 ARG cc_start: 0.6621 (tpm170) cc_final: 0.6370 (mmt180) REVERT: B 1100 MET cc_start: 0.5448 (mtp) cc_final: 0.5021 (mtm) REVERT: B 1305 ARG cc_start: 0.6632 (ptt90) cc_final: 0.6398 (pmm-80) REVERT: B 1324 PHE cc_start: 0.7419 (m-80) cc_final: 0.7083 (m-80) REVERT: B 1857 LYS cc_start: 0.6179 (tptt) cc_final: 0.5790 (ttmm) REVERT: B 1975 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: B 2032 ASP cc_start: 0.8151 (t0) cc_final: 0.7776 (m-30) REVERT: B 2596 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: B 2822 GLU cc_start: 0.7091 (pp20) cc_final: 0.6754 (tm-30) REVERT: B 3090 ASP cc_start: 0.8047 (t70) cc_final: 0.7764 (t0) REVERT: B 3273 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6836 (mm-30) REVERT: B 3308 SER cc_start: 0.8808 (t) cc_final: 0.8284 (p) REVERT: B 3698 ILE cc_start: 0.8345 (mm) cc_final: 0.8098 (mp) REVERT: B 3760 GLU cc_start: 0.7396 (pt0) cc_final: 0.7118 (pt0) REVERT: B 3999 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: D 57 MET cc_start: 0.0836 (mmp) cc_final: -0.1385 (ptp) REVERT: D 87 GLU cc_start: 0.2456 (mm-30) cc_final: 0.2153 (mm-30) REVERT: D 91 MET cc_start: 0.3297 (OUTLIER) cc_final: 0.2462 (mpp) outliers start: 107 outliers final: 43 residues processed: 415 average time/residue: 1.3754 time to fit residues: 730.1903 Evaluate side-chains 381 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 332 time to evaluate : 4.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2366 ARG Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2855 THR Chi-restraints excluded: chain A residue 3181 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3558 SER Chi-restraints excluded: chain A residue 3693 VAL Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3873 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4240 GLU Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1829 ARG Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2110 LEU Chi-restraints excluded: chain B residue 2128 SER Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2872 THR Chi-restraints excluded: chain B residue 3052 MET Chi-restraints excluded: chain B residue 3071 SER Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3278 VAL Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3843 VAL Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4385 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 553 optimal weight: 30.0000 chunk 585 optimal weight: 30.0000 chunk 289 optimal weight: 3.9990 chunk 524 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN A4215 HIS ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 HIS ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 HIS ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3754 GLN B3859 HIS C 119 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47788 Z= 0.262 Angle : 0.562 12.743 64919 Z= 0.273 Chirality : 0.040 0.251 7826 Planarity : 0.004 0.054 8158 Dihedral : 4.073 21.622 6370 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.32 % Allowed : 12.62 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 5915 helix: 1.62 (0.09), residues: 3005 sheet: 0.07 (0.27), residues: 408 loop : -0.70 (0.13), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B2710 HIS 0.008 0.001 HIS A2654 PHE 0.019 0.001 PHE B1407 TYR 0.018 0.001 TYR A2181 ARG 0.005 0.000 ARG A4086 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 338 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.0540 (tmm) cc_final: 0.0292 (ptm) REVERT: A 501 MET cc_start: 0.1122 (ttm) cc_final: 0.0734 (tpp) REVERT: A 1504 ASP cc_start: 0.7257 (t0) cc_final: 0.6717 (t0) REVERT: A 1783 MET cc_start: 0.3475 (mpp) cc_final: 0.2563 (tpp) REVERT: A 1916 MET cc_start: 0.4462 (pmm) cc_final: 0.2363 (tmm) REVERT: A 2021 GLU cc_start: 0.6645 (mp0) cc_final: 0.6390 (mp0) REVERT: A 2073 LYS cc_start: 0.7352 (tptt) cc_final: 0.6766 (tttm) REVERT: A 2349 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: A 2714 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7948 (p) REVERT: A 3254 SER cc_start: 0.9157 (p) cc_final: 0.8878 (t) REVERT: A 3682 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 3818 GLU cc_start: 0.7270 (pm20) cc_final: 0.6938 (pm20) REVERT: A 3824 MET cc_start: 0.7883 (tmm) cc_final: 0.7657 (ttt) REVERT: A 4218 ARG cc_start: 0.6358 (tmt-80) cc_final: 0.5906 (tmt-80) REVERT: A 4240 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 4408 MET cc_start: 0.4025 (tpt) cc_final: 0.3721 (tpt) REVERT: A 4440 MET cc_start: 0.6132 (mpp) cc_final: 0.5499 (ptm) REVERT: B 1017 PHE cc_start: 0.5270 (m-80) cc_final: 0.4996 (m-80) REVERT: B 1100 MET cc_start: 0.5439 (mtp) cc_final: 0.5082 (mmm) REVERT: B 1842 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8602 (pt) REVERT: B 1857 LYS cc_start: 0.6210 (tptt) cc_final: 0.5879 (ttmm) REVERT: B 1998 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6521 (tt) REVERT: B 2032 ASP cc_start: 0.8224 (t0) cc_final: 0.7798 (m-30) REVERT: B 2413 GLN cc_start: 0.8515 (tt0) cc_final: 0.8289 (tt0) REVERT: B 2596 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: B 2822 GLU cc_start: 0.7049 (pp20) cc_final: 0.6754 (tm-30) REVERT: B 3090 ASP cc_start: 0.8008 (t70) cc_final: 0.7721 (t0) REVERT: B 3308 SER cc_start: 0.8810 (t) cc_final: 0.8294 (p) REVERT: B 3698 ILE cc_start: 0.8342 (mm) cc_final: 0.8094 (mp) REVERT: B 3760 GLU cc_start: 0.7432 (pt0) cc_final: 0.7160 (pt0) REVERT: B 3825 PHE cc_start: 0.6825 (t80) cc_final: 0.6174 (t80) REVERT: B 3999 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.5582 (m-80) REVERT: B 4085 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: D 57 MET cc_start: 0.0650 (mmp) cc_final: -0.1470 (ptp) REVERT: D 87 GLU cc_start: 0.2509 (mm-30) cc_final: 0.2180 (mm-30) REVERT: D 91 MET cc_start: 0.3389 (OUTLIER) cc_final: 0.2564 (mpp) REVERT: D 118 ASN cc_start: 0.1845 (m-40) cc_final: 0.1561 (t0) outliers start: 123 outliers final: 55 residues processed: 420 average time/residue: 1.3649 time to fit residues: 737.7199 Evaluate side-chains 387 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 322 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 1780 ILE Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2366 ARG Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2590 GLU Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2855 THR Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3181 VAL Chi-restraints excluded: chain A residue 3218 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3558 SER Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3693 VAL Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3873 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4240 GLU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1829 ARG Chi-restraints excluded: chain B residue 1842 LEU Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1958 ARG Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2099 VAL Chi-restraints excluded: chain B residue 2110 LEU Chi-restraints excluded: chain B residue 2128 SER Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2872 THR Chi-restraints excluded: chain B residue 2874 SER Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3052 MET Chi-restraints excluded: chain B residue 3071 SER Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3278 VAL Chi-restraints excluded: chain B residue 3359 LEU Chi-restraints excluded: chain B residue 3512 ASP Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3843 VAL Chi-restraints excluded: chain B residue 3869 VAL Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 487 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 8 optimal weight: 0.2980 chunk 436 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 499 optimal weight: 8.9990 chunk 404 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 299 optimal weight: 0.2980 chunk 525 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2126 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 HIS ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 47788 Z= 0.224 Angle : 0.552 13.037 64919 Z= 0.266 Chirality : 0.039 0.269 7826 Planarity : 0.004 0.054 8158 Dihedral : 4.017 21.475 6370 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.52 % Allowed : 13.36 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 5915 helix: 1.69 (0.10), residues: 3012 sheet: 0.00 (0.27), residues: 410 loop : -0.68 (0.13), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B2710 HIS 0.007 0.001 HIS A2654 PHE 0.033 0.001 PHE B1108 TYR 0.022 0.001 TYR A2181 ARG 0.008 0.000 ARG A4236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 339 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.1023 (ttm) cc_final: 0.0598 (tpp) REVERT: A 1439 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6387 (mm) REVERT: A 1504 ASP cc_start: 0.7212 (t0) cc_final: 0.6679 (t0) REVERT: A 1512 MET cc_start: 0.6129 (tmm) cc_final: 0.5220 (ttm) REVERT: A 1783 MET cc_start: 0.3519 (mpp) cc_final: 0.2547 (tpp) REVERT: A 1916 MET cc_start: 0.4412 (pmm) cc_final: 0.2313 (tmm) REVERT: A 1968 SER cc_start: 0.7679 (OUTLIER) cc_final: 0.7161 (p) REVERT: A 2021 GLU cc_start: 0.6641 (mp0) cc_final: 0.6356 (mp0) REVERT: A 2073 LYS cc_start: 0.7342 (tptt) cc_final: 0.6730 (tttm) REVERT: A 2349 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: A 2714 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7934 (p) REVERT: A 3254 SER cc_start: 0.9197 (p) cc_final: 0.8893 (t) REVERT: A 3682 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 3818 GLU cc_start: 0.7311 (pm20) cc_final: 0.6876 (pm20) REVERT: A 4218 ARG cc_start: 0.6347 (tmt-80) cc_final: 0.5889 (tmt-80) REVERT: A 4236 ARG cc_start: 0.7336 (ttm110) cc_final: 0.7134 (ttp-110) REVERT: A 4237 MET cc_start: 0.7869 (mmm) cc_final: 0.7640 (mmt) REVERT: A 4240 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 4440 MET cc_start: 0.6254 (mpp) cc_final: 0.5577 (ptm) REVERT: B 1017 PHE cc_start: 0.5272 (m-80) cc_final: 0.5002 (m-80) REVERT: B 1100 MET cc_start: 0.5468 (mtp) cc_final: 0.4927 (mtm) REVERT: B 1412 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7386 (OUTLIER) REVERT: B 1856 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7683 (ttp) REVERT: B 1971 PHE cc_start: 0.7420 (t80) cc_final: 0.7146 (m-80) REVERT: B 1998 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6534 (tt) REVERT: B 2032 ASP cc_start: 0.8210 (t0) cc_final: 0.7755 (m-30) REVERT: B 2586 MET cc_start: 0.8211 (mmt) cc_final: 0.7891 (mmp) REVERT: B 2596 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: B 2822 GLU cc_start: 0.6980 (pp20) cc_final: 0.6706 (tm-30) REVERT: B 3090 ASP cc_start: 0.8009 (t70) cc_final: 0.7704 (t0) REVERT: B 3308 SER cc_start: 0.8827 (t) cc_final: 0.8319 (p) REVERT: B 3760 GLU cc_start: 0.7437 (pt0) cc_final: 0.7194 (pt0) REVERT: B 3825 PHE cc_start: 0.6778 (t80) cc_final: 0.6131 (t80) REVERT: B 3999 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5575 (m-80) REVERT: B 4085 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: B 4229 ASP cc_start: 0.5054 (OUTLIER) cc_final: 0.4185 (t0) REVERT: D 57 MET cc_start: 0.0491 (mmp) cc_final: -0.1717 (ptp) REVERT: D 87 GLU cc_start: 0.2547 (mm-30) cc_final: 0.2210 (mm-30) REVERT: D 91 MET cc_start: 0.3364 (OUTLIER) cc_final: 0.2560 (mpp) outliers start: 134 outliers final: 61 residues processed: 429 average time/residue: 1.3238 time to fit residues: 741.0379 Evaluate side-chains 394 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 320 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1780 ILE Chi-restraints excluded: chain A residue 1968 SER Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2182 VAL Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2366 ARG Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2855 THR Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3052 MET Chi-restraints excluded: chain A residue 3181 VAL Chi-restraints excluded: chain A residue 3218 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3343 ASP Chi-restraints excluded: chain A residue 3537 VAL Chi-restraints excluded: chain A residue 3558 SER Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3693 VAL Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3873 VAL Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4240 GLU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1829 ARG Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1856 MET Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1958 ARG Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2099 VAL Chi-restraints excluded: chain B residue 2110 LEU Chi-restraints excluded: chain B residue 2128 SER Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2135 LEU Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2872 THR Chi-restraints excluded: chain B residue 2874 SER Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3052 MET Chi-restraints excluded: chain B residue 3071 SER Chi-restraints excluded: chain B residue 3273 GLU Chi-restraints excluded: chain B residue 3512 ASP Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3843 VAL Chi-restraints excluded: chain B residue 3869 VAL Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain B residue 4229 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 197 optimal weight: 3.9990 chunk 527 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 343 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 586 optimal weight: 20.0000 chunk 486 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 307 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2126 GLN A2578 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 HIS ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1784 HIS ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3553 HIS ** B3754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4332 ASN D 118 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 47788 Z= 0.359 Angle : 0.618 12.718 64919 Z= 0.300 Chirality : 0.042 0.282 7826 Planarity : 0.004 0.055 8158 Dihedral : 4.255 24.026 6370 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 13.98 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.11), residues: 5915 helix: 1.44 (0.09), residues: 3017 sheet: -0.27 (0.26), residues: 422 loop : -0.77 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B2710 HIS 0.008 0.001 HIS A2654 PHE 0.025 0.002 PHE B3766 TYR 0.024 0.002 TYR A2181 ARG 0.005 0.001 ARG A1479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 334 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.0897 (ttm) cc_final: 0.0483 (tpp) REVERT: A 1439 LEU cc_start: 0.6911 (mm) cc_final: 0.6457 (mm) REVERT: A 1504 ASP cc_start: 0.7332 (t0) cc_final: 0.6701 (t0) REVERT: A 1512 MET cc_start: 0.6256 (tmm) cc_final: 0.5185 (ttm) REVERT: A 1783 MET cc_start: 0.3666 (mpp) cc_final: 0.2552 (tpp) REVERT: A 1968 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 2021 GLU cc_start: 0.6720 (mp0) cc_final: 0.6201 (mp0) REVERT: A 2073 LYS cc_start: 0.7346 (tptt) cc_final: 0.6750 (tttm) REVERT: A 2169 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8328 (m) REVERT: A 2349 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: A 2714 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7985 (p) REVERT: A 3191 ARG cc_start: 0.6924 (ptt90) cc_final: 0.6234 (ptt90) REVERT: A 3254 SER cc_start: 0.9190 (p) cc_final: 0.8916 (t) REVERT: A 3682 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8219 (tt) REVERT: A 3818 GLU cc_start: 0.7309 (pm20) cc_final: 0.6847 (pm20) REVERT: A 4218 ARG cc_start: 0.6431 (tmt-80) cc_final: 0.5924 (tmt-80) REVERT: A 4440 MET cc_start: 0.6296 (mpp) cc_final: 0.5513 (ptm) REVERT: B 1100 MET cc_start: 0.5587 (mtp) cc_final: 0.5168 (mtm) REVERT: B 1512 MET cc_start: 0.6695 (tpt) cc_final: 0.6401 (tpt) REVERT: B 1856 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7585 (ttp) REVERT: B 1971 PHE cc_start: 0.7441 (t80) cc_final: 0.7102 (m-80) REVERT: B 1998 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6579 (tt) REVERT: B 2032 ASP cc_start: 0.8273 (t0) cc_final: 0.7857 (m-30) REVERT: B 2100 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 2565 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6528 (pp30) REVERT: B 2589 LEU cc_start: 0.8751 (mt) cc_final: 0.8414 (mm) REVERT: B 2596 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: B 2822 GLU cc_start: 0.6999 (pp20) cc_final: 0.6707 (tm-30) REVERT: B 3090 ASP cc_start: 0.8093 (t70) cc_final: 0.7754 (t0) REVERT: B 3308 SER cc_start: 0.8817 (t) cc_final: 0.8306 (p) REVERT: B 3487 LEU cc_start: 0.8943 (tp) cc_final: 0.8666 (tm) REVERT: B 3510 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7000 (tp30) REVERT: B 3624 LYS cc_start: 0.7435 (tmmt) cc_final: 0.7142 (ttpp) REVERT: B 3760 GLU cc_start: 0.7567 (pt0) cc_final: 0.7287 (pt0) REVERT: B 3825 PHE cc_start: 0.6981 (t80) cc_final: 0.6250 (t80) REVERT: B 3999 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: B 4077 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4086 (pmt) REVERT: B 4085 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: B 4229 ASP cc_start: 0.5078 (OUTLIER) cc_final: 0.4198 (t0) REVERT: D 87 GLU cc_start: 0.2576 (mm-30) cc_final: 0.2259 (mm-30) REVERT: D 91 MET cc_start: 0.3299 (OUTLIER) cc_final: 0.2458 (mpp) outliers start: 155 outliers final: 77 residues processed: 444 average time/residue: 1.3194 time to fit residues: 769.3141 Evaluate side-chains 411 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 319 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1780 ILE Chi-restraints excluded: chain A residue 1968 SER Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2172 VAL Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2182 VAL Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2366 ARG Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2748 THR Chi-restraints excluded: chain A residue 2753 VAL Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2855 THR Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3181 VAL Chi-restraints excluded: chain A residue 3218 VAL Chi-restraints excluded: chain A residue 3248 VAL Chi-restraints excluded: chain A residue 3343 ASP Chi-restraints excluded: chain A residue 3537 VAL Chi-restraints excluded: chain A residue 3558 SER Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3676 MET Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3693 VAL Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3873 VAL Chi-restraints excluded: chain A residue 4008 LEU Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4188 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1856 MET Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1911 ASP Chi-restraints excluded: chain B residue 1958 ARG Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2010 ASN Chi-restraints excluded: chain B residue 2099 VAL Chi-restraints excluded: chain B residue 2100 LEU Chi-restraints excluded: chain B residue 2110 LEU Chi-restraints excluded: chain B residue 2128 SER Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2135 LEU Chi-restraints excluded: chain B residue 2565 GLN Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2872 THR Chi-restraints excluded: chain B residue 2874 SER Chi-restraints excluded: chain B residue 2877 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3052 MET Chi-restraints excluded: chain B residue 3071 SER Chi-restraints excluded: chain B residue 3229 LEU Chi-restraints excluded: chain B residue 3273 GLU Chi-restraints excluded: chain B residue 3278 VAL Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3343 ASP Chi-restraints excluded: chain B residue 3512 ASP Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3843 VAL Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4077 MET Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain B residue 4229 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 565 optimal weight: 0.0570 chunk 66 optimal weight: 20.0000 chunk 334 optimal weight: 50.0000 chunk 428 optimal weight: 10.0000 chunk 331 optimal weight: 0.0050 chunk 493 optimal weight: 0.9980 chunk 327 optimal weight: 30.0000 chunk 584 optimal weight: 0.0770 chunk 365 optimal weight: 40.0000 chunk 356 optimal weight: 6.9990 chunk 269 optimal weight: 0.0270 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2084 GLN A2126 GLN A2578 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN A4202 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 HIS ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1989 ASN ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2379 GLN ** B4332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 47788 Z= 0.136 Angle : 0.536 12.111 64919 Z= 0.257 Chirality : 0.038 0.284 7826 Planarity : 0.004 0.054 8158 Dihedral : 3.902 22.850 6370 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 15.39 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.11), residues: 5915 helix: 1.85 (0.10), residues: 3009 sheet: -0.08 (0.27), residues: 398 loop : -0.67 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B2710 HIS 0.009 0.001 HIS A2654 PHE 0.028 0.001 PHE B3644 TYR 0.012 0.001 TYR A1451 ARG 0.009 0.000 ARG A4236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 356 time to evaluate : 4.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.0821 (ttm) cc_final: 0.0405 (tpp) REVERT: A 1321 MET cc_start: 0.3245 (mpp) cc_final: 0.2972 (mpp) REVERT: A 1439 LEU cc_start: 0.6718 (mm) cc_final: 0.6381 (mm) REVERT: A 1504 ASP cc_start: 0.7149 (t0) cc_final: 0.6568 (t0) REVERT: A 1512 MET cc_start: 0.6156 (tmm) cc_final: 0.5126 (ttm) REVERT: A 1783 MET cc_start: 0.3550 (mpp) cc_final: 0.2600 (tpp) REVERT: A 2021 GLU cc_start: 0.6645 (mp0) cc_final: 0.6313 (mp0) REVERT: A 2073 LYS cc_start: 0.7301 (tptt) cc_final: 0.6704 (tttm) REVERT: A 2714 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7969 (p) REVERT: A 3123 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7052 (mtt-85) REVERT: A 3191 ARG cc_start: 0.6888 (ptt90) cc_final: 0.6251 (ptt90) REVERT: A 3229 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8575 (tt) REVERT: A 3433 ASP cc_start: 0.8299 (t70) cc_final: 0.7930 (t0) REVERT: A 3682 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8150 (tt) REVERT: A 3818 GLU cc_start: 0.7245 (pm20) cc_final: 0.6791 (pm20) REVERT: A 4218 ARG cc_start: 0.6432 (tmt-80) cc_final: 0.5832 (tmt-80) REVERT: A 4236 ARG cc_start: 0.7476 (ttm110) cc_final: 0.7135 (ptp90) REVERT: A 4385 MET cc_start: 0.3361 (tpt) cc_final: 0.1013 (ptm) REVERT: A 4440 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5527 (ptm) REVERT: B 1100 MET cc_start: 0.5606 (mtp) cc_final: 0.5333 (mmm) REVERT: B 1207 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7146 (mmtt) REVERT: B 1998 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6575 (tt) REVERT: B 2032 ASP cc_start: 0.8232 (t0) cc_final: 0.7822 (m-30) REVERT: B 2565 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6498 (pp30) REVERT: B 2586 MET cc_start: 0.8163 (mmt) cc_final: 0.7871 (mmp) REVERT: B 2589 LEU cc_start: 0.8741 (mt) cc_final: 0.8385 (mm) REVERT: B 2596 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: B 2822 GLU cc_start: 0.6986 (pp20) cc_final: 0.6694 (tm-30) REVERT: B 3090 ASP cc_start: 0.7990 (t70) cc_final: 0.7690 (OUTLIER) REVERT: B 3308 SER cc_start: 0.8827 (t) cc_final: 0.8312 (p) REVERT: B 3487 LEU cc_start: 0.8550 (tp) cc_final: 0.8301 (tm) REVERT: B 3760 GLU cc_start: 0.7494 (pt0) cc_final: 0.7175 (pt0) REVERT: B 3825 PHE cc_start: 0.6637 (t80) cc_final: 0.5977 (t80) REVERT: B 3999 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: B 4085 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: D 57 MET cc_start: 0.0553 (mmp) cc_final: -0.1370 (ptp) REVERT: D 87 GLU cc_start: 0.2545 (mm-30) cc_final: 0.2208 (mm-30) REVERT: D 91 MET cc_start: 0.3324 (OUTLIER) cc_final: 0.2548 (mpp) outliers start: 95 outliers final: 35 residues processed: 427 average time/residue: 1.4106 time to fit residues: 778.6659 Evaluate side-chains 376 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 331 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 2054 PHE Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2182 VAL Chi-restraints excluded: chain A residue 2578 GLN Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3123 ARG Chi-restraints excluded: chain A residue 3229 LEU Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 4008 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4440 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1204 THR Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1911 ASP Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2010 ASN Chi-restraints excluded: chain B residue 2565 GLN Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2874 SER Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3343 ASP Chi-restraints excluded: chain B residue 3512 ASP Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3824 MET Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 361 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 348 optimal weight: 0.1980 chunk 175 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 371 optimal weight: 2.9990 chunk 397 optimal weight: 0.7980 chunk 288 optimal weight: 0.0270 chunk 54 optimal weight: 50.0000 chunk 459 optimal weight: 7.9990 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2578 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1989 ASN ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3754 GLN ** B4332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 47788 Z= 0.179 Angle : 0.549 14.285 64919 Z= 0.260 Chirality : 0.039 0.307 7826 Planarity : 0.004 0.053 8158 Dihedral : 3.862 22.826 6370 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.87 % Allowed : 15.60 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.11), residues: 5915 helix: 1.87 (0.10), residues: 3020 sheet: 0.03 (0.27), residues: 406 loop : -0.64 (0.13), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B2710 HIS 0.006 0.001 HIS A2654 PHE 0.036 0.001 PHE B1108 TYR 0.025 0.001 TYR A2181 ARG 0.009 0.000 ARG A4236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 330 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.0844 (ttm) cc_final: 0.0425 (tpp) REVERT: A 1439 LEU cc_start: 0.6716 (mm) cc_final: 0.6325 (mm) REVERT: A 1504 ASP cc_start: 0.7250 (t0) cc_final: 0.6659 (t0) REVERT: A 1512 MET cc_start: 0.6224 (tmm) cc_final: 0.5088 (ttm) REVERT: A 1783 MET cc_start: 0.3567 (mpp) cc_final: 0.2555 (tpp) REVERT: A 1916 MET cc_start: 0.3982 (pmm) cc_final: 0.1842 (tmm) REVERT: A 2021 GLU cc_start: 0.6633 (mp0) cc_final: 0.6317 (mp0) REVERT: A 2073 LYS cc_start: 0.7300 (tptt) cc_final: 0.6678 (tttm) REVERT: A 2169 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 2640 ASN cc_start: 0.6869 (m-40) cc_final: 0.6585 (m-40) REVERT: A 2714 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7988 (p) REVERT: A 2845 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 3191 ARG cc_start: 0.6896 (ptt90) cc_final: 0.6291 (ptt90) REVERT: A 3254 SER cc_start: 0.9157 (p) cc_final: 0.8843 (t) REVERT: A 3682 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 3818 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: A 4218 ARG cc_start: 0.6361 (tmt-80) cc_final: 0.5717 (tmt-80) REVERT: A 4385 MET cc_start: 0.3332 (tpt) cc_final: 0.1067 (ptm) REVERT: A 4440 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5455 (ptm) REVERT: B 1174 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6199 (tt) REVERT: B 1207 LYS cc_start: 0.7417 (mtpt) cc_final: 0.7095 (mmpt) REVERT: B 1412 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7156 (OUTLIER) REVERT: B 1971 PHE cc_start: 0.7491 (t80) cc_final: 0.7214 (m-80) REVERT: B 1998 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6556 (tt) REVERT: B 2032 ASP cc_start: 0.8250 (t0) cc_final: 0.7858 (m-30) REVERT: B 2565 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6462 (pp30) REVERT: B 2586 MET cc_start: 0.8216 (mmt) cc_final: 0.7915 (mmp) REVERT: B 2589 LEU cc_start: 0.8690 (mt) cc_final: 0.8398 (mm) REVERT: B 2596 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: B 2822 GLU cc_start: 0.6979 (pp20) cc_final: 0.6719 (tm-30) REVERT: B 3090 ASP cc_start: 0.8006 (t70) cc_final: 0.7746 (t0) REVERT: B 3308 SER cc_start: 0.8836 (t) cc_final: 0.8329 (p) REVERT: B 3487 LEU cc_start: 0.8623 (tp) cc_final: 0.8380 (tm) REVERT: B 3510 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6989 (tp30) REVERT: B 3760 GLU cc_start: 0.7495 (pt0) cc_final: 0.7254 (pt0) REVERT: B 3825 PHE cc_start: 0.6707 (t80) cc_final: 0.6002 (t80) REVERT: B 3999 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.5523 (m-80) REVERT: B 4085 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: D 57 MET cc_start: 0.0594 (mmp) cc_final: -0.1322 (ptp) REVERT: D 91 MET cc_start: 0.3240 (OUTLIER) cc_final: 0.2439 (mpp) outliers start: 99 outliers final: 48 residues processed: 398 average time/residue: 1.3632 time to fit residues: 708.2829 Evaluate side-chains 382 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 321 time to evaluate : 4.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2182 VAL Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2578 GLN Chi-restraints excluded: chain A residue 2590 GLU Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2845 GLU Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3818 GLU Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3870 LEU Chi-restraints excluded: chain A residue 4008 LEU Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4440 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 1109 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1204 THR Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1911 ASP Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2010 ASN Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2099 VAL Chi-restraints excluded: chain B residue 2135 LEU Chi-restraints excluded: chain B residue 2565 GLN Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2874 SER Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3218 VAL Chi-restraints excluded: chain B residue 3273 GLU Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3824 MET Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 531 optimal weight: 8.9990 chunk 559 optimal weight: 8.9990 chunk 510 optimal weight: 9.9990 chunk 544 optimal weight: 20.0000 chunk 327 optimal weight: 30.0000 chunk 237 optimal weight: 8.9990 chunk 427 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 491 optimal weight: 9.9990 chunk 514 optimal weight: 5.9990 chunk 542 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2578 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1989 ASN ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2379 GLN ** B4332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 47788 Z= 0.343 Angle : 0.632 13.708 64919 Z= 0.305 Chirality : 0.042 0.394 7826 Planarity : 0.004 0.054 8158 Dihedral : 4.178 29.457 6370 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.87 % Allowed : 15.96 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5915 helix: 1.62 (0.09), residues: 3008 sheet: -0.30 (0.27), residues: 409 loop : -0.74 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B2710 HIS 0.009 0.001 HIS B1103 PHE 0.041 0.002 PHE A4164 TYR 0.020 0.002 TYR A2181 ARG 0.013 0.001 ARG A4236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 323 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.0853 (ttm) cc_final: 0.0409 (tpp) REVERT: A 1321 MET cc_start: 0.3031 (mpp) cc_final: 0.2674 (mpp) REVERT: A 1439 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6368 (mm) REVERT: A 1504 ASP cc_start: 0.7307 (t0) cc_final: 0.6698 (t0) REVERT: A 1512 MET cc_start: 0.6321 (tmm) cc_final: 0.5157 (ttm) REVERT: A 1783 MET cc_start: 0.3600 (mpp) cc_final: 0.2559 (tpp) REVERT: A 2021 GLU cc_start: 0.6676 (mp0) cc_final: 0.6364 (mp0) REVERT: A 2073 LYS cc_start: 0.7342 (tptt) cc_final: 0.6725 (tttm) REVERT: A 2169 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8282 (m) REVERT: A 2714 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 3191 ARG cc_start: 0.6913 (ptt90) cc_final: 0.6238 (ptt90) REVERT: A 3254 SER cc_start: 0.9165 (p) cc_final: 0.8887 (t) REVERT: A 3682 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 3818 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: A 4178 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6689 (mtp-110) REVERT: A 4218 ARG cc_start: 0.6421 (tmt-80) cc_final: 0.5884 (tmt-80) REVERT: A 4385 MET cc_start: 0.3280 (tpt) cc_final: 0.0840 (ptm) REVERT: A 4440 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.5478 (ptm) REVERT: B 1174 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6014 (tt) REVERT: B 1412 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7287 (OUTLIER) REVERT: B 1512 MET cc_start: 0.6653 (tpt) cc_final: 0.6371 (tpt) REVERT: B 1971 PHE cc_start: 0.7513 (t80) cc_final: 0.7197 (m-80) REVERT: B 1998 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6604 (tt) REVERT: B 2032 ASP cc_start: 0.8260 (t0) cc_final: 0.7867 (m-30) REVERT: B 2100 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8484 (tt) REVERT: B 2167 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8471 (tpt) REVERT: B 2565 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6506 (pp30) REVERT: B 2589 LEU cc_start: 0.8736 (mt) cc_final: 0.8422 (mm) REVERT: B 2596 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: B 2822 GLU cc_start: 0.6996 (pp20) cc_final: 0.6729 (tm-30) REVERT: B 3090 ASP cc_start: 0.8109 (t70) cc_final: 0.7790 (t0) REVERT: B 3308 SER cc_start: 0.8824 (t) cc_final: 0.8326 (p) REVERT: B 3487 LEU cc_start: 0.8930 (tp) cc_final: 0.8673 (tm) REVERT: B 3510 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7064 (tp30) REVERT: B 3624 LYS cc_start: 0.7391 (tmmt) cc_final: 0.7100 (ttpp) REVERT: B 3760 GLU cc_start: 0.7586 (pt0) cc_final: 0.7325 (pt0) REVERT: B 3825 PHE cc_start: 0.6954 (t80) cc_final: 0.6164 (t80) REVERT: B 3999 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: B 4085 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: D 57 MET cc_start: 0.0707 (mmp) cc_final: -0.1329 (ptp) REVERT: D 87 GLU cc_start: 0.2475 (mm-30) cc_final: 0.2142 (mm-30) REVERT: D 91 MET cc_start: 0.3331 (OUTLIER) cc_final: 0.2473 (mpp) outliers start: 99 outliers final: 53 residues processed: 391 average time/residue: 1.3799 time to fit residues: 704.5493 Evaluate side-chains 390 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 321 time to evaluate : 4.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2182 VAL Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2590 GLU Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3818 GLU Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 4008 LEU Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4178 ARG Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4440 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1109 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1204 THR Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1427 VAL Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1911 ASP Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2010 ASN Chi-restraints excluded: chain B residue 2099 VAL Chi-restraints excluded: chain B residue 2100 LEU Chi-restraints excluded: chain B residue 2135 LEU Chi-restraints excluded: chain B residue 2167 MET Chi-restraints excluded: chain B residue 2565 GLN Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3208 CYS Chi-restraints excluded: chain B residue 3218 VAL Chi-restraints excluded: chain B residue 3273 GLU Chi-restraints excluded: chain B residue 3278 VAL Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3343 ASP Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3824 MET Chi-restraints excluded: chain B residue 3967 LEU Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 357 optimal weight: 30.0000 chunk 575 optimal weight: 50.0000 chunk 351 optimal weight: 0.0270 chunk 273 optimal weight: 0.9990 chunk 400 optimal weight: 4.9990 chunk 603 optimal weight: 5.9990 chunk 555 optimal weight: 6.9990 chunk 480 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 294 optimal weight: 40.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2578 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN A3975 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1989 ASN ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47788 Z= 0.202 Angle : 0.575 14.407 64919 Z= 0.273 Chirality : 0.040 0.495 7826 Planarity : 0.004 0.054 8158 Dihedral : 4.021 23.522 6370 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.56 % Allowed : 16.37 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 5915 helix: 1.77 (0.10), residues: 3027 sheet: -0.10 (0.27), residues: 402 loop : -0.71 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B2710 HIS 0.007 0.001 HIS B1103 PHE 0.027 0.001 PHE D 21 TYR 0.022 0.001 TYR B1457 ARG 0.012 0.000 ARG A4236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 324 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.0952 (ttm) cc_final: 0.0506 (tpp) REVERT: A 1321 MET cc_start: 0.2927 (mpp) cc_final: 0.2661 (mpp) REVERT: A 1439 LEU cc_start: 0.6763 (mm) cc_final: 0.6347 (mm) REVERT: A 1504 ASP cc_start: 0.7226 (t0) cc_final: 0.6635 (t0) REVERT: A 1512 MET cc_start: 0.6279 (tmm) cc_final: 0.5064 (ttm) REVERT: A 1783 MET cc_start: 0.3578 (mpp) cc_final: 0.2583 (tpp) REVERT: A 2021 GLU cc_start: 0.6684 (mp0) cc_final: 0.6355 (mp0) REVERT: A 2073 LYS cc_start: 0.7312 (tptt) cc_final: 0.6704 (tttm) REVERT: A 2169 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 2349 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: A 2714 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 3254 SER cc_start: 0.9179 (p) cc_final: 0.8872 (t) REVERT: A 3682 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 3818 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: A 4218 ARG cc_start: 0.6465 (tmt-80) cc_final: 0.5955 (tmt-80) REVERT: A 4385 MET cc_start: 0.3236 (tpt) cc_final: 0.0851 (ptm) REVERT: A 4440 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5492 (ptm) REVERT: B 1174 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6001 (tt) REVERT: B 1192 LEU cc_start: 0.8541 (tp) cc_final: 0.8327 (tm) REVERT: B 1412 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7219 (OUTLIER) REVERT: B 1512 MET cc_start: 0.6604 (tpt) cc_final: 0.6324 (tpt) REVERT: B 1971 PHE cc_start: 0.7497 (t80) cc_final: 0.7201 (m-80) REVERT: B 1998 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6634 (tt) REVERT: B 2032 ASP cc_start: 0.8230 (t0) cc_final: 0.7851 (m-30) REVERT: B 2565 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6466 (pp30) REVERT: B 2586 MET cc_start: 0.8280 (mmt) cc_final: 0.7888 (mmp) REVERT: B 2596 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: B 2822 GLU cc_start: 0.6996 (pp20) cc_final: 0.6724 (tm-30) REVERT: B 3090 ASP cc_start: 0.8046 (t70) cc_final: 0.7730 (OUTLIER) REVERT: B 3308 SER cc_start: 0.8788 (t) cc_final: 0.8303 (p) REVERT: B 3487 LEU cc_start: 0.8799 (tp) cc_final: 0.8527 (tm) REVERT: B 3510 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7061 (tp30) REVERT: B 3760 GLU cc_start: 0.7584 (pt0) cc_final: 0.7316 (pt0) REVERT: B 3824 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7480 (ptm) REVERT: B 3825 PHE cc_start: 0.6813 (t80) cc_final: 0.5999 (t80) REVERT: B 3999 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: B 4085 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: D 57 MET cc_start: 0.0607 (mmp) cc_final: -0.1346 (ptp) REVERT: D 87 GLU cc_start: 0.2589 (mm-30) cc_final: 0.2215 (mm-30) REVERT: D 91 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.2416 (mpp) outliers start: 83 outliers final: 48 residues processed: 387 average time/residue: 1.3890 time to fit residues: 700.1516 Evaluate side-chains 379 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 318 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1103 HIS Chi-restraints excluded: chain A residue 1780 ILE Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2180 ASP Chi-restraints excluded: chain A residue 2182 VAL Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2391 ASP Chi-restraints excluded: chain A residue 2578 GLN Chi-restraints excluded: chain A residue 2590 GLU Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2937 ASN Chi-restraints excluded: chain A residue 3682 LEU Chi-restraints excluded: chain A residue 3752 THR Chi-restraints excluded: chain A residue 3818 GLU Chi-restraints excluded: chain A residue 3830 CYS Chi-restraints excluded: chain A residue 3840 THR Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 4008 LEU Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4188 VAL Chi-restraints excluded: chain A residue 4440 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1109 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain B residue 1204 THR Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain B residue 1427 VAL Chi-restraints excluded: chain B residue 1527 VAL Chi-restraints excluded: chain B residue 1812 LEU Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1911 ASP Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1998 LEU Chi-restraints excluded: chain B residue 2003 LYS Chi-restraints excluded: chain B residue 2010 ASN Chi-restraints excluded: chain B residue 2099 VAL Chi-restraints excluded: chain B residue 2135 LEU Chi-restraints excluded: chain B residue 2565 GLN Chi-restraints excluded: chain B residue 2596 GLN Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 3006 MET Chi-restraints excluded: chain B residue 3218 VAL Chi-restraints excluded: chain B residue 3273 GLU Chi-restraints excluded: chain B residue 3343 ASP Chi-restraints excluded: chain B residue 3619 SER Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3824 MET Chi-restraints excluded: chain B residue 3999 TYR Chi-restraints excluded: chain B residue 4085 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 99 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 381 optimal weight: 7.9990 chunk 512 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 443 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 481 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 494 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2578 GLN ** A3161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3803 ASN A3975 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1989 ASN ** B2370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4332 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 = 0.4665 r_free = 0.4665 target = 0.217175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140346 restraints weight = 74168.460| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.68 r_work: 0.3465 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.218 47788 Z= 0.219 Angle : 0.662 59.108 64919 Z= 0.337 Chirality : 0.040 0.570 7826 Planarity : 0.004 0.054 8158 Dihedral : 4.024 24.156 6370 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.28 % Allowed : 16.69 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 5915 helix: 1.78 (0.10), residues: 3027 sheet: -0.10 (0.27), residues: 402 loop : -0.70 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B2710 HIS 0.009 0.001 HIS B1103 PHE 0.019 0.001 PHE A4164 TYR 0.020 0.001 TYR B1457 ARG 0.009 0.000 ARG A4236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14025.71 seconds wall clock time: 250 minutes 38.51 seconds (15038.51 seconds total)