Starting phenix.real_space_refine on Sun Apr 7 04:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/04_2024/8jwg_36682_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/04_2024/8jwg_36682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/04_2024/8jwg_36682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/04_2024/8jwg_36682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/04_2024/8jwg_36682_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwg_36682/04_2024/8jwg_36682_neut_updated.pdb" } resolution = 3.54 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= -0.003 sd= 0.054 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 6241 2.51 5 N 1583 2.21 5 O 1750 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1371": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9620 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9594 Classifications: {'peptide': 1192} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1165} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.55 Number of scatterers: 9620 At special positions: 0 Unit cell: (71.5, 111.1, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 6 9.00 O 1750 8.00 N 1583 7.00 C 6241 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: 4.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 3 sheets defined 57.4% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 removed outlier: 4.401A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.667A pdb=" N LYS A 55 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 56 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 63 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.726A pdb=" N SER A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 137 removed outlier: 3.609A pdb=" N LEU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 148 through 162 removed outlier: 4.426A pdb=" N LEU A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 190 removed outlier: 4.956A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 203 through 239 removed outlier: 3.662A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 251 through 304 removed outlier: 4.320A pdb=" N LYS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.770A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 337 through 357 removed outlier: 3.773A pdb=" N GLU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 472 through 476 removed outlier: 4.363A pdb=" N LYS A 476 " --> pdb=" O ASN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 488 removed outlier: 4.926A pdb=" N ASP A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 488 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 4.013A pdb=" N TYR A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.969A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 545 No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 677 through 680 No H-bonds generated for 'chain 'A' and resid 677 through 680' Processing helix chain 'A' and resid 686 through 693 Processing helix chain 'A' and resid 772 through 784 removed outlier: 4.063A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.515A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 4.379A pdb=" N ALA A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 812 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 815 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 848 removed outlier: 4.185A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 873 removed outlier: 4.286A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 880 Processing helix chain 'A' and resid 886 through 907 removed outlier: 3.808A pdb=" N ILE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN A 906 " --> pdb=" O THR A 902 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 907 " --> pdb=" O GLY A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.674A pdb=" N MET A 922 " --> pdb=" O PHE A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 944 removed outlier: 3.951A pdb=" N VAL A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 961 removed outlier: 3.981A pdb=" N GLU A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.937A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1034 removed outlier: 4.512A pdb=" N TYR A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A1019 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1054 removed outlier: 3.874A pdb=" N LEU A1052 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A1053 " --> pdb=" O GLY A1049 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1080 removed outlier: 3.636A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1097 removed outlier: 3.859A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1101 No H-bonds generated for 'chain 'A' and resid 1099 through 1101' Processing helix chain 'A' and resid 1170 through 1174 Processing helix chain 'A' and resid 1244 through 1247 No H-bonds generated for 'chain 'A' and resid 1244 through 1247' Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1278 through 1287 removed outlier: 3.698A pdb=" N LYS A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1296 No H-bonds generated for 'chain 'A' and resid 1294 through 1296' Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1314 through 1327 Processing helix chain 'A' and resid 1344 through 1359 Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 5.247A pdb=" N ARG A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1416 Processing sheet with id= A, first strand: chain 'A' and resid 1157 through 1161 removed outlier: 6.560A pdb=" N LYS A1380 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A1160 " --> pdb=" O LYS A1380 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A1382 " --> pdb=" O VAL A1160 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 1251 through 1253 removed outlier: 6.988A pdb=" N ILE A1332 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A1364 " --> pdb=" O LEU A1333 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 1126 through 1131 removed outlier: 6.679A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1065 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: 2.86 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2971 1.34 - 1.46: 1725 1.46 - 1.58: 5037 1.58 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 9800 Sorted by residual: bond pdb=" CAR YMZ A1500 " pdb=" NAP YMZ A1500 " ideal model delta sigma weight residual 1.298 1.374 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CAJ YMZ A1500 " pdb=" CAU YMZ A1500 " ideal model delta sigma weight residual 1.414 1.372 0.042 2.00e-02 2.50e+03 4.52e+00 bond pdb=" CAS YMZ A1500 " pdb=" CAW YMZ A1500 " ideal model delta sigma weight residual 1.518 1.560 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" CAN YMZ A1500 " pdb=" NAQ YMZ A1500 " ideal model delta sigma weight residual 1.457 1.415 0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" CAZ YMZ A1500 " pdb=" FAE YMZ A1500 " ideal model delta sigma weight residual 1.340 1.378 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 9795 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.38: 156 106.38 - 113.27: 5319 113.27 - 120.17: 3653 120.17 - 127.06: 4029 127.06 - 133.95: 55 Bond angle restraints: 13212 Sorted by residual: angle pdb=" C ASN A 440 " pdb=" N ASP A 441 " pdb=" CA ASP A 441 " ideal model delta sigma weight residual 122.08 128.80 -6.72 1.47e+00 4.63e-01 2.09e+01 angle pdb=" C ALA A 821 " pdb=" N ASN A 822 " pdb=" CA ASN A 822 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N LEU A1001 " pdb=" CA LEU A1001 " pdb=" C LEU A1001 " ideal model delta sigma weight residual 112.72 108.74 3.98 1.28e+00 6.10e-01 9.67e+00 angle pdb=" CA ASN A1106 " pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 112.60 115.57 -2.97 1.00e+00 1.00e+00 8.79e+00 angle pdb=" C SER A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta sigma weight residual 122.61 127.03 -4.42 1.56e+00 4.11e-01 8.04e+00 ... (remaining 13207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5720 17.92 - 35.84: 175 35.84 - 53.76: 18 53.76 - 71.68: 2 71.68 - 89.60: 3 Dihedral angle restraints: 5918 sinusoidal: 2413 harmonic: 3505 Sorted by residual: dihedral pdb=" CA TYR A1004 " pdb=" C TYR A1004 " pdb=" N PHE A1005 " pdb=" CA PHE A1005 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG A 776 " pdb=" C ARG A 776 " pdb=" N ILE A 777 " pdb=" CA ILE A 777 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ARG A 428 " pdb=" C ARG A 428 " pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 994 0.037 - 0.074: 376 0.074 - 0.111: 105 0.111 - 0.148: 33 0.148 - 0.185: 6 Chirality restraints: 1514 Sorted by residual: chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA ASN A 440 " pdb=" N ASN A 440 " pdb=" C ASN A 440 " pdb=" CB ASN A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CAX YMZ A1500 " pdb=" CAO YMZ A1500 " pdb=" CAW YMZ A1500 " pdb=" NAQ YMZ A1500 " both_signs ideal model delta sigma weight residual False -2.39 -2.56 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1511 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 290 " -0.019 2.00e-02 2.50e+03 1.38e-02 3.82e+00 pdb=" CG TYR A 290 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 290 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 290 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 290 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 290 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 290 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 290 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1257 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A1258 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1258 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1258 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 71 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 72 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.026 5.00e-02 4.00e+02 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1470 2.76 - 3.29: 10031 3.29 - 3.83: 14280 3.83 - 4.36: 17360 4.36 - 4.90: 29029 Nonbonded interactions: 72170 Sorted by model distance: nonbonded pdb=" O ASN A 822 " pdb=" ND2 ASN A 826 " model vdw 2.223 2.520 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.232 2.440 nonbonded pdb=" O PRO A 338 " pdb=" OG1 THR A 341 " model vdw 2.234 2.440 nonbonded pdb=" O LYS A 220 " pdb=" OG SER A 223 " model vdw 2.246 2.440 nonbonded pdb=" NE ARG A1116 " pdb=" OD2 ASP A1246 " model vdw 2.267 2.520 ... (remaining 72165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.005 0.076 9800 Z= 0.297 Angle : 0.721 6.724 13212 Z= 0.399 Chirality : 0.044 0.185 1514 Planarity : 0.004 0.049 1638 Dihedral : 9.433 89.598 3656 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.71 (0.20), residues: 1178 helix: -1.90 (0.16), residues: 658 sheet: -3.26 (0.73), residues: 34 loop : -3.12 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 186 HIS 0.010 0.002 HIS A 892 PHE 0.030 0.002 PHE A 926 TYR 0.033 0.002 TYR A 290 ARG 0.005 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8162 (tpp) cc_final: 0.7928 (tpp) REVERT: A 358 ASN cc_start: 0.6861 (m-40) cc_final: 0.6538 (t0) REVERT: A 793 PHE cc_start: 0.6511 (t80) cc_final: 0.6228 (t80) REVERT: A 880 ASP cc_start: 0.8342 (t70) cc_final: 0.8009 (t0) REVERT: A 1308 TYR cc_start: 0.7718 (m-80) cc_final: 0.7478 (m-80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2661 time to fit residues: 87.4210 Evaluate side-chains 111 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 HIS ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9800 Z= 0.354 Angle : 0.765 12.202 13212 Z= 0.407 Chirality : 0.050 0.199 1514 Planarity : 0.005 0.054 1638 Dihedral : 6.047 52.271 1307 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.51 % Allowed : 9.68 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.07 (0.21), residues: 1178 helix: -1.26 (0.17), residues: 688 sheet: -3.09 (0.68), residues: 36 loop : -3.09 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP A 452 HIS 0.006 0.001 HIS A 542 PHE 0.029 0.002 PHE A 257 TYR 0.026 0.002 TYR A 290 ARG 0.004 0.001 ARG A1110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8493 (tpp) cc_final: 0.8156 (tpp) REVERT: A 358 ASN cc_start: 0.7343 (m-40) cc_final: 0.6663 (t0) REVERT: A 377 LYS cc_start: 0.7764 (tttm) cc_final: 0.7543 (tttm) REVERT: A 542 HIS cc_start: 0.6454 (p-80) cc_final: 0.5867 (p-80) REVERT: A 690 MET cc_start: 0.5106 (mmm) cc_final: 0.4686 (ptp) REVERT: A 793 PHE cc_start: 0.7276 (t80) cc_final: 0.6943 (t80) REVERT: A 1397 HIS cc_start: 0.8211 (t70) cc_final: 0.7443 (p-80) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.2318 time to fit residues: 42.0614 Evaluate side-chains 118 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 ASN A 894 ASN A 998 ASN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9800 Z= 0.159 Angle : 0.604 12.721 13212 Z= 0.305 Chirality : 0.042 0.169 1514 Planarity : 0.003 0.048 1638 Dihedral : 5.326 48.936 1307 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.68 % Allowed : 11.64 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.23), residues: 1178 helix: -0.36 (0.19), residues: 676 sheet: -1.96 (0.80), residues: 35 loop : -2.57 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS A 898 PHE 0.018 0.001 PHE A1033 TYR 0.015 0.001 TYR A1266 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASN cc_start: 0.7214 (m-40) cc_final: 0.6608 (t0) REVERT: A 399 LEU cc_start: 0.7317 (tp) cc_final: 0.7030 (mm) REVERT: A 542 HIS cc_start: 0.6490 (p-80) cc_final: 0.6095 (p-80) REVERT: A 690 MET cc_start: 0.4638 (mmm) cc_final: 0.4180 (ptp) REVERT: A 988 GLU cc_start: 0.7593 (pp20) cc_final: 0.7208 (tm-30) REVERT: A 1150 THR cc_start: 0.8080 (p) cc_final: 0.7664 (t) REVERT: A 1335 LEU cc_start: 0.8912 (mt) cc_final: 0.8409 (tt) outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 0.2265 time to fit residues: 42.8015 Evaluate side-chains 112 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 11 optimal weight: 0.4980 chunk 51 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9800 Z= 0.145 Angle : 0.552 10.039 13212 Z= 0.283 Chirality : 0.041 0.166 1514 Planarity : 0.003 0.047 1638 Dihedral : 4.906 44.391 1307 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.33 % Allowed : 13.87 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.24), residues: 1178 helix: 0.10 (0.20), residues: 677 sheet: -1.50 (0.82), residues: 35 loop : -2.42 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 452 HIS 0.002 0.001 HIS A 898 PHE 0.021 0.001 PHE A 941 TYR 0.012 0.001 TYR A 290 ARG 0.002 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASN cc_start: 0.7364 (m-40) cc_final: 0.6615 (t0) REVERT: A 399 LEU cc_start: 0.7307 (tp) cc_final: 0.7038 (mm) REVERT: A 542 HIS cc_start: 0.6542 (p-80) cc_final: 0.6261 (p-80) REVERT: A 690 MET cc_start: 0.4734 (mmm) cc_final: 0.4229 (ptp) REVERT: A 813 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 988 GLU cc_start: 0.7725 (pp20) cc_final: 0.7411 (tm-30) REVERT: A 1150 THR cc_start: 0.8039 (p) cc_final: 0.7643 (t) REVERT: A 1308 TYR cc_start: 0.7644 (m-80) cc_final: 0.7351 (m-80) REVERT: A 1316 GLN cc_start: 0.7758 (mt0) cc_final: 0.7530 (mm110) REVERT: A 1335 LEU cc_start: 0.8875 (mt) cc_final: 0.8379 (tt) REVERT: A 1397 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7419 (p-80) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.2200 time to fit residues: 39.7338 Evaluate side-chains 118 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 813 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9800 Z= 0.155 Angle : 0.550 11.940 13212 Z= 0.280 Chirality : 0.041 0.161 1514 Planarity : 0.003 0.046 1638 Dihedral : 4.721 40.288 1307 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.51 % Allowed : 14.06 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.24), residues: 1178 helix: 0.22 (0.20), residues: 677 sheet: -1.28 (0.84), residues: 35 loop : -2.36 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 295 HIS 0.003 0.001 HIS A 898 PHE 0.016 0.001 PHE A 941 TYR 0.013 0.001 TYR A 290 ARG 0.002 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7526 (mmt) cc_final: 0.6990 (mmt) REVERT: A 358 ASN cc_start: 0.7383 (m-40) cc_final: 0.6583 (t0) REVERT: A 399 LEU cc_start: 0.7505 (tp) cc_final: 0.7178 (mm) REVERT: A 542 HIS cc_start: 0.6540 (p-80) cc_final: 0.6260 (p-80) REVERT: A 690 MET cc_start: 0.4805 (mmm) cc_final: 0.4271 (ptp) REVERT: A 813 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7572 (t80) REVERT: A 1150 THR cc_start: 0.8031 (p) cc_final: 0.7634 (t) REVERT: A 1335 LEU cc_start: 0.8861 (mt) cc_final: 0.8371 (tt) REVERT: A 1397 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7425 (p-80) outliers start: 27 outliers final: 19 residues processed: 133 average time/residue: 0.2054 time to fit residues: 39.7252 Evaluate side-chains 126 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 813 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 9800 Z= 0.378 Angle : 0.720 12.189 13212 Z= 0.378 Chirality : 0.049 0.198 1514 Planarity : 0.004 0.039 1638 Dihedral : 5.290 29.598 1307 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.54 % Allowed : 13.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.88 (0.23), residues: 1178 helix: -0.35 (0.19), residues: 688 sheet: -1.73 (0.71), residues: 50 loop : -2.61 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.008 0.001 HIS A 898 PHE 0.024 0.002 PHE A 78 TYR 0.028 0.002 TYR A 290 ARG 0.009 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7438 (tp) cc_final: 0.6977 (mm) REVERT: A 404 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8381 (tmtt) REVERT: A 542 HIS cc_start: 0.6549 (p-80) cc_final: 0.6254 (p-80) REVERT: A 690 MET cc_start: 0.4979 (mmm) cc_final: 0.4487 (ptp) REVERT: A 916 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7357 (tpp) REVERT: A 1150 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7818 (t) REVERT: A 1397 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7624 (p-80) outliers start: 38 outliers final: 30 residues processed: 131 average time/residue: 0.2082 time to fit residues: 39.9484 Evaluate side-chains 131 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9800 Z= 0.151 Angle : 0.574 12.872 13212 Z= 0.294 Chirality : 0.041 0.163 1514 Planarity : 0.003 0.039 1638 Dihedral : 4.685 26.260 1307 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.33 % Allowed : 15.64 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.24), residues: 1178 helix: 0.27 (0.20), residues: 672 sheet: -1.15 (0.81), residues: 40 loop : -2.26 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.004 0.001 HIS A 892 PHE 0.013 0.001 PHE A 941 TYR 0.019 0.001 TYR A 552 ARG 0.003 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7532 (mmt) cc_final: 0.7203 (mmp) REVERT: A 399 LEU cc_start: 0.7597 (tp) cc_final: 0.7248 (mm) REVERT: A 690 MET cc_start: 0.4987 (mmm) cc_final: 0.4482 (ptp) REVERT: A 916 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7254 (tpp) REVERT: A 1335 LEU cc_start: 0.8872 (mt) cc_final: 0.8381 (tt) REVERT: A 1397 HIS cc_start: 0.8225 (t70) cc_final: 0.7522 (p-80) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.2142 time to fit residues: 36.9874 Evaluate side-chains 120 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1320 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 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 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 9800 Z= 0.434 Angle : 0.762 12.167 13212 Z= 0.403 Chirality : 0.050 0.208 1514 Planarity : 0.004 0.042 1638 Dihedral : 5.332 21.744 1307 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.17 % Allowed : 15.46 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.98 (0.23), residues: 1178 helix: -0.43 (0.19), residues: 688 sheet: -1.47 (0.72), residues: 50 loop : -2.69 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 186 HIS 0.013 0.002 HIS A 542 PHE 0.025 0.002 PHE A 78 TYR 0.028 0.003 TYR A 290 ARG 0.004 0.001 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 399 LEU cc_start: 0.7480 (tp) cc_final: 0.7044 (mm) REVERT: A 690 MET cc_start: 0.5054 (mmm) cc_final: 0.4411 (ptp) REVERT: A 916 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7437 (tpp) REVERT: A 1150 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7782 (t) REVERT: A 1292 GLU cc_start: 0.8265 (pm20) cc_final: 0.8052 (pm20) REVERT: A 1397 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.7978 (t70) outliers start: 34 outliers final: 26 residues processed: 119 average time/residue: 0.2057 time to fit residues: 35.8483 Evaluate side-chains 125 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9800 Z= 0.159 Angle : 0.596 13.264 13212 Z= 0.304 Chirality : 0.041 0.154 1514 Planarity : 0.003 0.040 1638 Dihedral : 4.764 19.470 1307 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.33 % Allowed : 16.39 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.24), residues: 1178 helix: 0.22 (0.20), residues: 675 sheet: -1.01 (0.85), residues: 40 loop : -2.39 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1047 HIS 0.011 0.001 HIS A 542 PHE 0.016 0.001 PHE A 411 TYR 0.021 0.001 TYR A1097 ARG 0.002 0.000 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7565 (mmt) cc_final: 0.7214 (mmp) REVERT: A 399 LEU cc_start: 0.7622 (tp) cc_final: 0.7229 (mm) REVERT: A 690 MET cc_start: 0.5039 (mmm) cc_final: 0.4401 (ptp) REVERT: A 916 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7353 (tpp) REVERT: A 1150 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7681 (t) outliers start: 25 outliers final: 21 residues processed: 118 average time/residue: 0.2062 time to fit residues: 35.7433 Evaluate side-chains 123 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1320 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.0470 chunk 78 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9800 Z= 0.146 Angle : 0.575 12.854 13212 Z= 0.290 Chirality : 0.042 0.396 1514 Planarity : 0.003 0.040 1638 Dihedral : 4.336 18.666 1307 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.86 % Allowed : 16.95 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.24), residues: 1178 helix: 0.50 (0.20), residues: 686 sheet: -0.81 (0.87), residues: 40 loop : -2.30 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 295 HIS 0.012 0.001 HIS A 542 PHE 0.012 0.001 PHE A 941 TYR 0.020 0.001 TYR A1097 ARG 0.002 0.000 ARG A 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7466 (tp) cc_final: 0.7080 (mm) REVERT: A 690 MET cc_start: 0.5009 (mmm) cc_final: 0.4320 (ptp) REVERT: A 916 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7303 (tpp) REVERT: A 1335 LEU cc_start: 0.8822 (mt) cc_final: 0.8336 (tt) REVERT: A 1397 HIS cc_start: 0.8352 (t70) cc_final: 0.7667 (p-80) outliers start: 20 outliers final: 19 residues processed: 112 average time/residue: 0.2171 time to fit residues: 35.7026 Evaluate side-chains 119 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1320 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.0030 chunk 13 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.162334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.122131 restraints weight = 17918.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.127042 restraints weight = 6981.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.130035 restraints weight = 3768.626| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9800 Z= 0.147 Angle : 0.578 14.607 13212 Z= 0.290 Chirality : 0.041 0.294 1514 Planarity : 0.003 0.040 1638 Dihedral : 4.219 18.583 1307 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.86 % Allowed : 16.95 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.24), residues: 1178 helix: 0.72 (0.20), residues: 672 sheet: -0.64 (0.89), residues: 40 loop : -2.13 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 295 HIS 0.011 0.001 HIS A 542 PHE 0.012 0.001 PHE A 941 TYR 0.019 0.001 TYR A1097 ARG 0.001 0.000 ARG A1273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.26 seconds wall clock time: 39 minutes 25.44 seconds (2365.44 seconds total)