Starting phenix.real_space_refine on Sat Jun 21 22:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjp_50508/06_2025/9fjp_50508.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjp_50508/06_2025/9fjp_50508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjp_50508/06_2025/9fjp_50508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjp_50508/06_2025/9fjp_50508.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjp_50508/06_2025/9fjp_50508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjp_50508/06_2025/9fjp_50508.cif" } resolution = 3.2 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= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 15861 2.51 5 N 4524 2.21 5 O 4885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25376 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "b" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1765 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 217} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1056} Chain: "d" Number of atoms: 9951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9951 Classifications: {'peptide': 1269} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Chain: "e" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 654 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "f" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain: "O" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19232 SG CYS d 891 96.656 95.956 85.906 1.00 40.04 S ATOM 19806 SG CYS d 968 94.622 93.057 87.806 1.00 40.12 S ATOM 19848 SG CYS d 975 93.799 94.475 84.462 1.00 31.62 S ATOM 19866 SG CYS d 978 96.487 92.563 84.475 1.00 41.72 S ATOM 12652 SG CYS d 60 37.700 95.317 117.090 1.00 65.54 S ATOM 12670 SG CYS d 62 35.003 94.885 119.739 1.00 68.71 S ATOM 12779 SG CYS d 75 36.981 98.210 119.567 1.00 86.62 S ATOM 12805 SG CYS d 78 38.488 94.748 120.303 1.00 72.66 S Time building chain proxies: 15.34, per 1000 atoms: 0.60 Number of scatterers: 25376 At special positions: 0 Unit cell: (136.196, 125.852, 201.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 10 15.00 Mg 1 11.99 O 4885 8.00 N 4524 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " Number of angles added : 12 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5938 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 40 sheets defined 44.5% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'a' and resid 30 through 45 removed outlier: 3.680A pdb=" N SER a 44 " --> pdb=" O ARG a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 81 Processing helix chain 'a' and resid 108 through 110 No H-bonds generated for 'chain 'a' and resid 108 through 110' Processing helix chain 'a' and resid 148 through 156 removed outlier: 4.412A pdb=" N ALA a 154 " --> pdb=" O GLN a 151 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY a 156 " --> pdb=" O ARG a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 203 through 225 removed outlier: 4.290A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 46 removed outlier: 3.899A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 82 Processing helix chain 'b' and resid 108 through 110 No H-bonds generated for 'chain 'b' and resid 108 through 110' Processing helix chain 'b' and resid 203 through 224 removed outlier: 3.994A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 66 removed outlier: 3.769A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE c 61 " --> pdb=" O GLN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 78 Processing helix chain 'c' and resid 85 through 90 Processing helix chain 'c' and resid 118 through 126 Processing helix chain 'c' and resid 225 through 229 removed outlier: 3.671A pdb=" N ARG c 228 " --> pdb=" O ARG c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 234 through 241 Processing helix chain 'c' and resid 244 through 252 Processing helix chain 'c' and resid 256 through 265 Processing helix chain 'c' and resid 269 through 282 Processing helix chain 'c' and resid 288 through 301 Processing helix chain 'c' and resid 309 through 321 Processing helix chain 'c' and resid 334 through 351 Processing helix chain 'c' and resid 380 through 407 Processing helix chain 'c' and resid 413 through 417 Processing helix chain 'c' and resid 420 through 434 Processing helix chain 'c' and resid 444 through 453 Processing helix chain 'c' and resid 470 through 474 removed outlier: 3.560A pdb=" N ASP c 474 " --> pdb=" O GLU c 471 " (cutoff:3.500A) Processing helix chain 'c' and resid 476 through 480 removed outlier: 3.937A pdb=" N TYR c 480 " --> pdb=" O PRO c 477 " (cutoff:3.500A) Processing helix chain 'c' and resid 532 through 538 Processing helix chain 'c' and resid 564 through 566 No H-bonds generated for 'chain 'c' and resid 564 through 566' Processing helix chain 'c' and resid 582 through 587 removed outlier: 4.435A pdb=" N MET c 586 " --> pdb=" O PRO c 583 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL c 587 " --> pdb=" O ARG c 584 " (cutoff:3.500A) Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.810A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 596 through 600 Processing helix chain 'c' and resid 601 through 613 removed outlier: 3.897A pdb=" N ARG c 613 " --> pdb=" O ALA c 609 " (cutoff:3.500A) Processing helix chain 'c' and resid 629 through 639 removed outlier: 4.557A pdb=" N ARG c 633 " --> pdb=" O GLY c 629 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY c 639 " --> pdb=" O ALA c 635 " (cutoff:3.500A) Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 815 through 826 Processing helix chain 'c' and resid 921 through 926 removed outlier: 3.539A pdb=" N ARG c 925 " --> pdb=" O GLY c 921 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 960 through 964 removed outlier: 3.935A pdb=" N LEU c 964 " --> pdb=" O ASP c 961 " (cutoff:3.500A) Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.810A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1036 through 1041 removed outlier: 3.675A pdb=" N LYS c1040 " --> pdb=" O LEU c1036 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 removed outlier: 3.584A pdb=" N GLY c1080 " --> pdb=" O MET c1076 " (cutoff:3.500A) Processing helix chain 'c' and resid 1081 through 1091 removed outlier: 3.986A pdb=" N LEU c1085 " --> pdb=" O ALA c1081 " (cutoff:3.500A) Processing helix chain 'c' and resid 1095 through 1108 removed outlier: 3.939A pdb=" N VAL c1100 " --> pdb=" O THR c1096 " (cutoff:3.500A) Processing helix chain 'c' and resid 1118 through 1131 removed outlier: 3.523A pdb=" N LYS c1122 " --> pdb=" O PRO c1118 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU c1124 " --> pdb=" O SER c1120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU c1131 " --> pdb=" O GLU c1127 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 23 Processing helix chain 'd' and resid 84 through 90 removed outlier: 3.600A pdb=" N VAL d 87 " --> pdb=" O ARG d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 108 removed outlier: 3.756A pdb=" N PHE d 107 " --> pdb=" O HIS d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 119 Processing helix chain 'd' and resid 121 through 130 Processing helix chain 'd' and resid 140 through 147 Processing helix chain 'd' and resid 147 through 188 Processing helix chain 'd' and resid 190 through 228 Processing helix chain 'd' and resid 237 through 248 Processing helix chain 'd' and resid 257 through 268 Processing helix chain 'd' and resid 269 through 282 Processing helix chain 'd' and resid 285 through 306 removed outlier: 3.527A pdb=" N LEU d 290 " --> pdb=" O GLY d 286 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG d 291 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER d 305 " --> pdb=" O ALA d 301 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY d 306 " --> pdb=" O PHE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 308 through 311 removed outlier: 3.803A pdb=" N GLY d 311 " --> pdb=" O SER d 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 308 through 311' Processing helix chain 'd' and resid 321 through 325 Processing helix chain 'd' and resid 338 through 361 removed outlier: 4.162A pdb=" N ASP d 342 " --> pdb=" O SER d 338 " (cutoff:3.500A) Processing helix chain 'd' and resid 363 through 383 removed outlier: 3.524A pdb=" N VAL d 367 " --> pdb=" O PRO d 363 " (cutoff:3.500A) Processing helix chain 'd' and resid 402 through 406 Processing helix chain 'd' and resid 411 through 418 Processing helix chain 'd' and resid 445 through 452 Processing helix chain 'd' and resid 452 through 463 Processing helix chain 'd' and resid 468 through 479 Processing helix chain 'd' and resid 482 through 491 removed outlier: 4.069A pdb=" N VAL d 486 " --> pdb=" O GLN d 482 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE d 491 " --> pdb=" O LEU d 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 505 through 507 No H-bonds generated for 'chain 'd' and resid 505 through 507' Processing helix chain 'd' and resid 528 through 533 Processing helix chain 'd' and resid 548 through 558 Processing helix chain 'd' and resid 560 through 564 removed outlier: 3.522A pdb=" N ASN d 564 " --> pdb=" O SER d 561 " (cutoff:3.500A) Processing helix chain 'd' and resid 579 through 590 removed outlier: 3.860A pdb=" N THR d 583 " --> pdb=" O LEU d 579 " (cutoff:3.500A) Processing helix chain 'd' and resid 614 through 625 Processing helix chain 'd' and resid 643 through 651 removed outlier: 3.603A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) Processing helix chain 'd' and resid 667 through 675 Processing helix chain 'd' and resid 689 through 704 Processing helix chain 'd' and resid 705 through 725 removed outlier: 3.741A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.648A pdb=" N ILE d 745 " --> pdb=" O ARG d 741 " (cutoff:3.500A) Processing helix chain 'd' and resid 766 through 793 Processing helix chain 'd' and resid 797 through 805 Processing helix chain 'd' and resid 810 through 819 removed outlier: 3.708A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.090A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA d 864 " --> pdb=" O LEU d 860 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU d 865 " --> pdb=" O ALA d 861 " (cutoff:3.500A) Processing helix chain 'd' and resid 882 through 884 No H-bonds generated for 'chain 'd' and resid 882 through 884' Processing helix chain 'd' and resid 915 through 920 Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 964 through 968 Processing helix chain 'd' and resid 975 through 980 Processing helix chain 'd' and resid 994 through 1005 removed outlier: 3.893A pdb=" N VAL d 998 " --> pdb=" O ALA d 994 " (cutoff:3.500A) Processing helix chain 'd' and resid 1006 through 1008 No H-bonds generated for 'chain 'd' and resid 1006 through 1008' Processing helix chain 'd' and resid 1027 through 1036 Processing helix chain 'd' and resid 1117 through 1126 Processing helix chain 'd' and resid 1126 through 1146 removed outlier: 4.016A pdb=" N GLN d1145 " --> pdb=" O VAL d1141 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1162 removed outlier: 4.259A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) Processing helix chain 'd' and resid 1183 through 1196 removed outlier: 3.783A pdb=" N GLU d1196 " --> pdb=" O ARG d1192 " (cutoff:3.500A) Processing helix chain 'd' and resid 1209 through 1217 Processing helix chain 'd' and resid 1219 through 1227 removed outlier: 4.058A pdb=" N SER d1225 " --> pdb=" O LEU d1221 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE d1226 " --> pdb=" O SER d1222 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN d1227 " --> pdb=" O ALA d1223 " (cutoff:3.500A) Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1247 through 1255 Processing helix chain 'd' and resid 1260 through 1263 Processing helix chain 'd' and resid 1264 through 1269 Processing helix chain 'd' and resid 1275 through 1283 Processing helix chain 'e' and resid 39 through 45 Processing helix chain 'e' and resid 49 through 70 removed outlier: 3.916A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 101 Processing helix chain 'f' and resid 25 through 35 removed outlier: 3.722A pdb=" N GLY f 35 " --> pdb=" O LEU f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 65 removed outlier: 3.748A pdb=" N GLU f 63 " --> pdb=" O GLU f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 106 removed outlier: 5.022A pdb=" N ARG f 96 " --> pdb=" O GLU f 92 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU f 97 " --> pdb=" O ALA f 93 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL f 98 " --> pdb=" O ASN f 94 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL f 99 " --> pdb=" O LEU f 95 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG f 104 " --> pdb=" O SER f 100 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR f 105 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR f 106 " --> pdb=" O ALA f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 128 removed outlier: 3.507A pdb=" N LEU f 115 " --> pdb=" O PRO f 111 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU f 128 " --> pdb=" O ILE f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 157 removed outlier: 3.866A pdb=" N TYR f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP f 144 " --> pdb=" O THR f 140 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRP f 145 " --> pdb=" O TYR f 141 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 186 Processing helix chain 'f' and resid 190 through 199 Processing helix chain 'f' and resid 201 through 211 Processing helix chain 'f' and resid 229 through 234 removed outlier: 3.569A pdb=" N ILE f 234 " --> pdb=" O GLY f 231 " (cutoff:3.500A) Processing helix chain 'f' and resid 240 through 246 Processing helix chain 'f' and resid 246 through 262 removed outlier: 3.585A pdb=" N ALA f 260 " --> pdb=" O ARG f 256 " (cutoff:3.500A) Processing helix chain 'f' and resid 263 through 275 Processing helix chain 'f' and resid 283 through 292 Processing helix chain 'f' and resid 296 through 310 removed outlier: 4.324A pdb=" N GLN f 300 " --> pdb=" O GLU f 296 " (cutoff:3.500A) Processing helix chain 'f' and resid 312 through 319 removed outlier: 3.558A pdb=" N ASP f 316 " --> pdb=" O GLY f 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 13 removed outlier: 6.308A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 99 removed outlier: 7.434A pdb=" N GLU a 135 " --> pdb=" O ILE a 56 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE a 56 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU a 137 " --> pdb=" O ILE a 54 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE a 54 " --> pdb=" O GLU a 137 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL a 139 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 removed outlier: 3.544A pdb=" N THR a 117 " --> pdb=" O SER a 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'a' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'b' and resid 8 through 12 removed outlier: 6.597A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 93 through 100 removed outlier: 3.601A pdb=" N LYS b 99 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU b 134 " --> pdb=" O LYS b 99 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 100 removed outlier: 3.601A pdb=" N LYS b 99 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU b 134 " --> pdb=" O LYS b 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'b' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'c' and resid 39 through 40 removed outlier: 6.729A pdb=" N VAL c 39 " --> pdb=" O SER c 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'c' and resid 96 through 97 removed outlier: 3.560A pdb=" N SER c 104 " --> pdb=" O ILE c 140 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE c 134 " --> pdb=" O PRO c 110 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE c 112 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP c 156 " --> pdb=" O ALA c 131 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU c 133 " --> pdb=" O MET c 154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN c 150 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU c 146 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'c' and resid 376 through 379 removed outlier: 6.279A pdb=" N SER c 177 " --> pdb=" O SER c 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 184 through 191 removed outlier: 3.675A pdb=" N LEU c 212 " --> pdb=" O VAL c 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 223 through 224 Processing sheet with id=AB8, first strand: chain 'c' and resid 354 through 355 removed outlier: 3.505A pdb=" N VAL c 363 " --> pdb=" O MET c 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'c' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'c' and resid 541 through 542 Processing sheet with id=AC3, first strand: chain 'c' and resid 667 through 671 removed outlier: 7.084A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 676 through 677 removed outlier: 3.555A pdb=" N ALA c 676 " --> pdb=" O ALA c 684 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 687 through 688 Processing sheet with id=AC6, first strand: chain 'c' and resid 1007 through 1008 removed outlier: 7.602A pdb=" N LEU c 737 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE c 898 " --> pdb=" O LEU c 737 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 765 through 766 removed outlier: 3.624A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP c 761 " --> pdb=" O VAL c 865 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL c 865 " --> pdb=" O ASP c 761 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 768 through 769 removed outlier: 3.553A pdb=" N THR c 807 " --> pdb=" O ARG c 833 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.750A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.777A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 1066 through 1068 removed outlier: 3.789A pdb=" N GLN c1066 " --> pdb=" O VAL d 422 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL d 422 " --> pdb=" O GLN c1066 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 1133 through 1138 removed outlier: 3.502A pdb=" N ASP d1243 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 93 through 94 Processing sheet with id=AD5, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD6, first strand: chain 'd' and resid 234 through 235 removed outlier: 3.514A pdb=" N ILE d 235 " --> pdb=" O TYR d 134 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE d 136 " --> pdb=" O ALA d 255 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA d 255 " --> pdb=" O ILE d 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 327 through 330 removed outlier: 3.607A pdb=" N ARG d 334 " --> pdb=" O LEU d 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'd' and resid 897 through 900 removed outlier: 3.610A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 929 through 930 removed outlier: 7.121A pdb=" N ALA d 929 " --> pdb=" O ILE d 937 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 1075 through 1080 removed outlier: 3.913A pdb=" N VAL d1075 " --> pdb=" O ILE d1066 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE d1066 " --> pdb=" O VAL d1075 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 1180 through 1182 removed outlier: 3.516A pdb=" N ILE d1181 " --> pdb=" O VAL d1165 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL d1206 " --> pdb=" O ARG d1164 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE d1168 " --> pdb=" O ALA d1202 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA d1202 " --> pdb=" O ILE d1168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 1271 through 1274 1163 hydrogen bonds defined for protein. 3267 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: 18.54 Time building geometry restraints manager: 7.55 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: 8552 1.34 - 1.45: 2503 1.45 - 1.57: 14581 1.57 - 1.69: 19 1.69 - 1.81: 165 Bond restraints: 25820 Sorted by residual: bond pdb=" N GLY e 28 " pdb=" CA GLY e 28 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.97e+00 bond pdb=" C GLN f 280 " pdb=" O GLN f 280 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 3.77e+00 bond pdb=" N ASN c 29 " pdb=" CA ASN c 29 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET a 1 " pdb=" CA MET a 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N ALA f 24 " pdb=" CA ALA f 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 ... (remaining 25815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 33603 0.95 - 1.90: 1108 1.90 - 2.86: 123 2.86 - 3.81: 142 3.81 - 4.76: 22 Bond angle restraints: 34998 Sorted by residual: angle pdb=" CA VAL c 571 " pdb=" C VAL c 571 " pdb=" N PRO c 572 " ideal model delta sigma weight residual 116.57 119.44 -2.87 9.80e-01 1.04e+00 8.55e+00 angle pdb=" C3' DT O 54 " pdb=" C2' DT O 54 " pdb=" C1' DT O 54 " ideal model delta sigma weight residual 101.60 104.88 -3.28 1.50e+00 4.44e-01 4.77e+00 angle pdb=" C3' DG O 48 " pdb=" C2' DG O 48 " pdb=" C1' DG O 48 " ideal model delta sigma weight residual 101.60 104.83 -3.23 1.50e+00 4.44e-01 4.63e+00 angle pdb=" CA GLU f 227 " pdb=" CB GLU f 227 " pdb=" CG GLU f 227 " ideal model delta sigma weight residual 114.10 118.36 -4.26 2.00e+00 2.50e-01 4.54e+00 angle pdb=" O PHE f 233 " pdb=" C PHE f 233 " pdb=" N ILE f 234 " ideal model delta sigma weight residual 122.25 119.74 2.51 1.19e+00 7.06e-01 4.46e+00 ... (remaining 34993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 14852 17.50 - 35.00: 781 35.00 - 52.51: 149 52.51 - 70.01: 33 70.01 - 87.51: 6 Dihedral angle restraints: 15821 sinusoidal: 6584 harmonic: 9237 Sorted by residual: dihedral pdb=" CA PRO d 577 " pdb=" C PRO d 577 " pdb=" N ARG d 578 " pdb=" CA ARG d 578 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA MET d 688 " pdb=" C MET d 688 " pdb=" N HIS d 689 " pdb=" CA HIS d 689 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA THR c1090 " pdb=" C THR c1090 " pdb=" N ILE c1091 " pdb=" CA ILE c1091 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 15818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2498 0.029 - 0.058: 967 0.058 - 0.088: 231 0.088 - 0.117: 221 0.117 - 0.146: 55 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA ILE c1117 " pdb=" N ILE c1117 " pdb=" C ILE c1117 " pdb=" CB ILE c1117 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE a 193 " pdb=" N ILE a 193 " pdb=" C ILE a 193 " pdb=" CB ILE a 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE d 885 " pdb=" N ILE d 885 " pdb=" C ILE d 885 " pdb=" CB ILE d 885 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 3969 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU d 677 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO d 678 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO d 678 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO d 678 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN c 507 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO c 508 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO c 508 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO c 508 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN d 826 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO d 827 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO d 827 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO d 827 " -0.021 5.00e-02 4.00e+02 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 146 2.51 - 3.11: 19795 3.11 - 3.71: 37425 3.71 - 4.30: 52899 4.30 - 4.90: 90676 Nonbonded interactions: 200941 Sorted by model distance: nonbonded pdb=" OE2 GLU c1087 " pdb=" OG SER d 548 " model vdw 1.915 3.040 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 1.954 3.040 nonbonded pdb=" O SER c 182 " pdb=" OH TYR c 186 " model vdw 1.997 3.040 nonbonded pdb=" OG1 THR c 354 " pdb=" OE2 GLU c 362 " model vdw 2.015 3.040 nonbonded pdb=" OG SER d1170 " pdb=" O PHE d1175 " model vdw 2.026 3.040 ... (remaining 200936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 1 through 210 or (resid 211 through 212 and (name N or nam \ e CA or name C or name O )) or resid 213 through 226)) selection = (chain 'b' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.980 Check model and map are aligned: 0.220 Set scattering table: 0.240 Process input model: 75.930 Find NCS groups from input model: 0.860 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: 0.020 Load rotamer database and sin/cos tables:5.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25828 Z= 0.107 Angle : 0.488 16.414 35010 Z= 0.240 Chirality : 0.041 0.146 3972 Planarity : 0.003 0.048 4588 Dihedral : 11.308 87.510 9883 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.74 % Allowed : 4.63 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.82 (0.15), residues: 3214 helix: 1.72 (0.15), residues: 1257 sheet: -0.75 (0.27), residues: 367 loop : -0.00 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 938 HIS 0.003 0.001 HIS d 505 PHE 0.013 0.001 PHE c 107 TYR 0.010 0.001 TYR d1283 ARG 0.003 0.000 ARG d 353 Details of bonding type rmsd hydrogen bonds : bond 0.17062 ( 1155) hydrogen bonds : angle 6.45233 ( 3267) metal coordination : bond 0.04830 ( 8) metal coordination : angle 9.05075 ( 12) covalent geometry : bond 0.00226 (25820) covalent geometry : angle 0.45869 (34998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 420 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 129 ASN cc_start: 0.6761 (p0) cc_final: 0.6534 (p0) REVERT: b 152 ASN cc_start: 0.6738 (t0) cc_final: 0.6384 (t0) REVERT: c 55 ASP cc_start: 0.8124 (t70) cc_final: 0.7804 (t0) REVERT: c 96 ILE cc_start: 0.7917 (pt) cc_final: 0.7504 (mt) REVERT: c 366 GLU cc_start: 0.7360 (pm20) cc_final: 0.6969 (pm20) REVERT: c 577 ASP cc_start: 0.7897 (t0) cc_final: 0.7491 (t0) REVERT: d 37 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8455 (ttp-110) REVERT: d 265 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7787 (tt) REVERT: d 407 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8255 (pttm) REVERT: d 554 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: d 614 SER cc_start: 0.9017 (t) cc_final: 0.8767 (p) REVERT: d 983 MET cc_start: 0.8446 (mmt) cc_final: 0.8192 (mmt) REVERT: d 1008 THR cc_start: 0.8584 (m) cc_final: 0.8315 (p) REVERT: d 1012 MET cc_start: 0.6125 (mmt) cc_final: 0.5706 (mmt) outliers start: 20 outliers final: 4 residues processed: 435 average time/residue: 0.5521 time to fit residues: 360.4479 Evaluate side-chains 201 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 37 ARG Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 554 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 200 ASN b 36 ASN c 612 GLN d 22 GLN ** d 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 959 GLN f 148 GLN f 184 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.133951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092879 restraints weight = 43392.577| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.01 r_work: 0.3237 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25828 Z= 0.172 Angle : 0.596 11.411 35010 Z= 0.305 Chirality : 0.043 0.197 3972 Planarity : 0.004 0.044 4588 Dihedral : 7.205 66.438 3675 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.10 % Allowed : 9.08 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.70 (0.15), residues: 3214 helix: 1.57 (0.15), residues: 1275 sheet: -0.90 (0.26), residues: 381 loop : -0.01 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 223 HIS 0.007 0.001 HIS f 184 PHE 0.020 0.002 PHE d1186 TYR 0.020 0.001 TYR f 141 ARG 0.009 0.001 ARG d1204 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 1155) hydrogen bonds : angle 4.97777 ( 3267) metal coordination : bond 0.01150 ( 8) metal coordination : angle 5.77615 ( 12) covalent geometry : bond 0.00417 (25820) covalent geometry : angle 0.58667 (34998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 2.976 Fit side-chains REVERT: b 152 ASN cc_start: 0.6664 (t0) cc_final: 0.6231 (t0) REVERT: c 55 ASP cc_start: 0.8210 (t70) cc_final: 0.7979 (t0) REVERT: c 126 ASP cc_start: 0.7479 (t70) cc_final: 0.7146 (t70) REVERT: c 298 ASN cc_start: 0.8619 (m-40) cc_final: 0.8109 (t0) REVERT: c 396 MET cc_start: 0.8202 (tmm) cc_final: 0.7914 (tmm) REVERT: c 577 ASP cc_start: 0.7883 (t0) cc_final: 0.7347 (t0) REVERT: d 265 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7804 (tt) REVERT: d 407 LYS cc_start: 0.8556 (ptmt) cc_final: 0.8151 (pttm) REVERT: d 417 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7160 (tp) REVERT: d 1008 THR cc_start: 0.8785 (m) cc_final: 0.8454 (p) REVERT: d 1052 ARG cc_start: 0.8602 (ptm160) cc_final: 0.8402 (ttp80) REVERT: f 246 VAL cc_start: 0.7015 (m) cc_final: 0.6722 (m) outliers start: 57 outliers final: 33 residues processed: 249 average time/residue: 0.3635 time to fit residues: 146.9763 Evaluate side-chains 203 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 17 ASN Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 200 ASN Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 SER Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 458 LEU Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain c residue 1147 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 417 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 823 LEU Chi-restraints excluded: chain d residue 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 227 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 269 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN a 200 ASN b 36 ASN ** c 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 935 HIS d 687 GLN e 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094843 restraints weight = 43173.251| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.15 r_work: 0.3261 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25828 Z= 0.115 Angle : 0.512 7.080 35010 Z= 0.263 Chirality : 0.041 0.149 3972 Planarity : 0.004 0.043 4588 Dihedral : 7.047 66.830 3667 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.46 % Allowed : 11.07 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.82 (0.15), residues: 3214 helix: 1.69 (0.15), residues: 1275 sheet: -0.76 (0.25), residues: 410 loop : 0.04 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 144 HIS 0.003 0.000 HIS d1150 PHE 0.016 0.001 PHE d 107 TYR 0.015 0.001 TYR c 91 ARG 0.005 0.000 ARG d1204 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1155) hydrogen bonds : angle 4.61022 ( 3267) metal coordination : bond 0.00697 ( 8) metal coordination : angle 4.14690 ( 12) covalent geometry : bond 0.00256 (25820) covalent geometry : angle 0.50590 (34998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 2.666 Fit side-chains revert: symmetry clash REVERT: b 152 ASN cc_start: 0.6428 (t0) cc_final: 0.6014 (t0) REVERT: c 55 ASP cc_start: 0.8202 (t70) cc_final: 0.7935 (t0) REVERT: c 126 ASP cc_start: 0.7444 (t70) cc_final: 0.7085 (t70) REVERT: c 298 ASN cc_start: 0.8662 (m-40) cc_final: 0.8042 (t0) REVERT: c 366 GLU cc_start: 0.8029 (pm20) cc_final: 0.7058 (pm20) REVERT: c 577 ASP cc_start: 0.7819 (t0) cc_final: 0.7362 (t0) REVERT: d 265 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7733 (tt) REVERT: d 290 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6898 (mp) REVERT: d 407 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8187 (pttp) REVERT: d 417 LEU cc_start: 0.7435 (tt) cc_final: 0.7217 (tp) REVERT: d 983 MET cc_start: 0.8582 (mmt) cc_final: 0.8007 (mmt) REVERT: d 1008 THR cc_start: 0.8864 (m) cc_final: 0.8567 (p) REVERT: d 1218 ASP cc_start: 0.3962 (OUTLIER) cc_final: 0.3619 (t0) REVERT: e 73 GLU cc_start: 0.6088 (pm20) cc_final: 0.5887 (tp30) REVERT: f 246 VAL cc_start: 0.7054 (m) cc_final: 0.6800 (m) outliers start: 67 outliers final: 41 residues processed: 240 average time/residue: 0.3483 time to fit residues: 137.1973 Evaluate side-chains 207 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 127 MET Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 458 LEU Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 950 LYS Chi-restraints excluded: chain c residue 971 ILE Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 823 LEU Chi-restraints excluded: chain d residue 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1218 ASP Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 77 optimal weight: 0.0050 chunk 90 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 296 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 200 ASN b 36 ASN b 124 HIS c 232 GLN c 935 HIS d 239 ASN d 854 HIS ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 157 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.093738 restraints weight = 43423.463| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.15 r_work: 0.3242 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25828 Z= 0.127 Angle : 0.511 8.972 35010 Z= 0.260 Chirality : 0.041 0.147 3972 Planarity : 0.004 0.041 4588 Dihedral : 7.032 66.675 3667 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.79 % Allowed : 12.17 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.86 (0.15), residues: 3214 helix: 1.70 (0.15), residues: 1283 sheet: -0.66 (0.25), residues: 403 loop : 0.04 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 144 HIS 0.004 0.001 HIS d 94 PHE 0.026 0.001 PHE d1186 TYR 0.015 0.001 TYR c 91 ARG 0.004 0.000 ARG c1067 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1155) hydrogen bonds : angle 4.42637 ( 3267) metal coordination : bond 0.00724 ( 8) metal coordination : angle 4.03172 ( 12) covalent geometry : bond 0.00301 (25820) covalent geometry : angle 0.50532 (34998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 178 time to evaluate : 2.783 Fit side-chains revert: symmetry clash REVERT: c 55 ASP cc_start: 0.8200 (t70) cc_final: 0.7946 (t0) REVERT: c 211 TRP cc_start: 0.7151 (m-10) cc_final: 0.6938 (m-10) REVERT: c 298 ASN cc_start: 0.8664 (m-40) cc_final: 0.8113 (t0) REVERT: c 577 ASP cc_start: 0.7885 (t0) cc_final: 0.7352 (t0) REVERT: d 22 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: d 265 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7833 (tt) REVERT: d 342 ASP cc_start: 0.8141 (t0) cc_final: 0.7795 (t0) REVERT: d 360 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5975 (tt) REVERT: d 407 LYS cc_start: 0.8617 (ptmt) cc_final: 0.8180 (pttp) REVERT: d 417 LEU cc_start: 0.7555 (tt) cc_final: 0.7329 (tp) REVERT: d 983 MET cc_start: 0.8595 (mmt) cc_final: 0.7988 (mmt) REVERT: d 1008 THR cc_start: 0.8915 (m) cc_final: 0.8641 (p) REVERT: d 1012 MET cc_start: 0.6730 (tpp) cc_final: 0.6378 (tpp) REVERT: d 1041 ARG cc_start: 0.5950 (ttp80) cc_final: 0.5647 (ttp80) REVERT: d 1218 ASP cc_start: 0.3964 (OUTLIER) cc_final: 0.3659 (t0) REVERT: f 89 HIS cc_start: 0.7916 (t70) cc_final: 0.7652 (t-170) REVERT: f 246 VAL cc_start: 0.7133 (m) cc_final: 0.6808 (m) outliers start: 76 outliers final: 41 residues processed: 242 average time/residue: 0.3163 time to fit residues: 128.7367 Evaluate side-chains 207 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 458 LEU Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 971 ILE Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 360 LEU Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 823 LEU Chi-restraints excluded: chain d residue 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain d residue 1218 ASP Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 166 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN a 200 ASN b 36 ASN b 226 ASN c 232 GLN ** c 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 22 GLN d 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088328 restraints weight = 42908.993| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.19 r_work: 0.3087 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25828 Z= 0.250 Angle : 0.627 14.274 35010 Z= 0.318 Chirality : 0.045 0.152 3972 Planarity : 0.005 0.042 4588 Dihedral : 7.268 65.253 3667 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.57 % Allowed : 12.94 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.48 (0.15), residues: 3214 helix: 1.37 (0.15), residues: 1284 sheet: -0.77 (0.25), residues: 411 loop : -0.19 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 23 HIS 0.007 0.001 HIS d 505 PHE 0.033 0.002 PHE f 130 TYR 0.023 0.002 TYR c 657 ARG 0.005 0.001 ARG c 173 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 1155) hydrogen bonds : angle 4.59737 ( 3267) metal coordination : bond 0.01187 ( 8) metal coordination : angle 5.43845 ( 12) covalent geometry : bond 0.00616 (25820) covalent geometry : angle 0.61931 (34998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 168 time to evaluate : 3.168 Fit side-chains REVERT: c 55 ASP cc_start: 0.8215 (t70) cc_final: 0.7857 (t0) REVERT: c 126 ASP cc_start: 0.7557 (t70) cc_final: 0.7209 (t0) REVERT: c 172 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: c 298 ASN cc_start: 0.8589 (m-40) cc_final: 0.7919 (t0) REVERT: c 577 ASP cc_start: 0.8026 (t0) cc_final: 0.7680 (t0) REVERT: d 312 MET cc_start: 0.8898 (mtp) cc_final: 0.8680 (mtp) REVERT: d 342 ASP cc_start: 0.8205 (t0) cc_final: 0.7877 (t0) REVERT: d 360 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5884 (tt) REVERT: d 407 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8171 (pttp) REVERT: d 688 MET cc_start: 0.9058 (mmt) cc_final: 0.8617 (mmt) REVERT: d 1008 THR cc_start: 0.9053 (m) cc_final: 0.8739 (p) REVERT: d 1012 MET cc_start: 0.6550 (tpp) cc_final: 0.6116 (tpp) outliers start: 97 outliers final: 62 residues processed: 248 average time/residue: 0.3754 time to fit residues: 155.4021 Evaluate side-chains 219 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 200 ASN Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 172 GLU Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 520 VAL Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 926 MET Chi-restraints excluded: chain c residue 930 GLN Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain c residue 1138 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 248 TYR Chi-restraints excluded: chain d residue 260 SER Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 360 LEU Chi-restraints excluded: chain d residue 490 VAL Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 629 VAL Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 797 ASN Chi-restraints excluded: chain d residue 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1185 GLU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain d residue 1218 ASP Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1238 ILE Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 159 optimal weight: 0.7980 chunk 100 optimal weight: 0.0870 chunk 227 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 240 optimal weight: 0.6980 chunk 230 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 74 optimal weight: 0.0980 chunk 233 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN b 5 GLN b 36 ASN c 232 GLN c1086 GLN d 22 GLN ** d1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN f 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093828 restraints weight = 43285.744| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.12 r_work: 0.3232 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25828 Z= 0.100 Angle : 0.497 10.886 35010 Z= 0.255 Chirality : 0.040 0.145 3972 Planarity : 0.004 0.042 4588 Dihedral : 7.036 65.322 3667 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.68 % Allowed : 14.41 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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 (0.15), residues: 3214 helix: 1.67 (0.15), residues: 1289 sheet: -0.61 (0.25), residues: 406 loop : -0.03 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 23 HIS 0.003 0.000 HIS d 94 PHE 0.020 0.001 PHE d1186 TYR 0.019 0.001 TYR c 657 ARG 0.003 0.000 ARG d1052 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1155) hydrogen bonds : angle 4.33236 ( 3267) metal coordination : bond 0.00595 ( 8) metal coordination : angle 3.78672 ( 12) covalent geometry : bond 0.00225 (25820) covalent geometry : angle 0.49229 (34998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 2.998 Fit side-chains revert: symmetry clash REVERT: a 123 MET cc_start: 0.8098 (ttt) cc_final: 0.7893 (ttt) REVERT: c 55 ASP cc_start: 0.8255 (t70) cc_final: 0.7982 (t0) REVERT: c 298 ASN cc_start: 0.8602 (m-40) cc_final: 0.7940 (t0) REVERT: c 577 ASP cc_start: 0.7820 (t0) cc_final: 0.7413 (t0) REVERT: d 342 ASP cc_start: 0.8087 (t0) cc_final: 0.7874 (t0) REVERT: d 407 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8084 (pttp) REVERT: d 417 LEU cc_start: 0.7744 (tp) cc_final: 0.7389 (tt) REVERT: d 1008 THR cc_start: 0.8994 (m) cc_final: 0.8749 (p) REVERT: d 1012 MET cc_start: 0.6551 (tpp) cc_final: 0.6155 (tpp) REVERT: d 1218 ASP cc_start: 0.4010 (OUTLIER) cc_final: 0.3786 (t0) outliers start: 73 outliers final: 52 residues processed: 234 average time/residue: 0.3829 time to fit residues: 150.1556 Evaluate side-chains 211 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 5 GLN Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 520 VAL Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 869 VAL Chi-restraints excluded: chain c residue 971 ILE Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 490 VAL Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 629 VAL Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 797 ASN Chi-restraints excluded: chain d residue 823 LEU Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1185 GLU Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1218 ASP Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1238 ILE Chi-restraints excluded: chain d residue 1252 VAL Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 51 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 271 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 169 optimal weight: 0.0670 chunk 221 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 overall best weight: 3.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN a 200 ASN b 36 ASN c 232 GLN ** c 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088171 restraints weight = 43191.400| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.11 r_work: 0.3136 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25828 Z= 0.275 Angle : 0.631 13.142 35010 Z= 0.320 Chirality : 0.045 0.149 3972 Planarity : 0.005 0.043 4588 Dihedral : 7.236 64.496 3667 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.01 % Allowed : 14.60 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.49 (0.15), residues: 3214 helix: 1.38 (0.15), residues: 1286 sheet: -0.69 (0.25), residues: 411 loop : -0.21 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP d 23 HIS 0.006 0.001 HIS d 854 PHE 0.025 0.002 PHE d 107 TYR 0.020 0.002 TYR a 168 ARG 0.006 0.000 ARG b 6 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 1155) hydrogen bonds : angle 4.54096 ( 3267) metal coordination : bond 0.01198 ( 8) metal coordination : angle 5.31194 ( 12) covalent geometry : bond 0.00678 (25820) covalent geometry : angle 0.62294 (34998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 162 time to evaluate : 2.739 Fit side-chains revert: symmetry clash REVERT: c 55 ASP cc_start: 0.8262 (t70) cc_final: 0.7935 (t0) REVERT: c 126 ASP cc_start: 0.7537 (t70) cc_final: 0.7227 (t0) REVERT: c 298 ASN cc_start: 0.8596 (m-40) cc_final: 0.7915 (t0) REVERT: c 577 ASP cc_start: 0.7938 (t0) cc_final: 0.7702 (t0) REVERT: d 342 ASP cc_start: 0.8160 (t0) cc_final: 0.7938 (t0) REVERT: d 360 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6035 (tt) REVERT: d 451 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8591 (mp) REVERT: d 688 MET cc_start: 0.9041 (mmt) cc_final: 0.8615 (mmt) REVERT: d 1008 THR cc_start: 0.9017 (m) cc_final: 0.8777 (p) outliers start: 82 outliers final: 64 residues processed: 230 average time/residue: 0.3171 time to fit residues: 122.4343 Evaluate side-chains 218 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 520 VAL Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 781 LEU Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 869 VAL Chi-restraints excluded: chain c residue 926 MET Chi-restraints excluded: chain c residue 930 GLN Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 248 TYR Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 360 LEU Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 490 VAL Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 629 VAL Chi-restraints excluded: chain d residue 650 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 797 ASN Chi-restraints excluded: chain d residue 825 THR Chi-restraints excluded: chain d residue 836 VAL Chi-restraints excluded: chain d residue 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1162 LEU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain d residue 1218 ASP Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1252 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 311 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN a 200 ASN b 36 ASN c 232 GLN c 539 HIS e 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.131629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093569 restraints weight = 43775.380| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.96 r_work: 0.3208 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25828 Z= 0.213 Angle : 0.579 12.680 35010 Z= 0.294 Chirality : 0.043 0.148 3972 Planarity : 0.004 0.043 4588 Dihedral : 7.202 63.209 3667 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.09 % Allowed : 15.07 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.49 (0.15), residues: 3214 helix: 1.40 (0.15), residues: 1283 sheet: -0.60 (0.26), residues: 397 loop : -0.26 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 144 HIS 0.005 0.001 HIS d 94 PHE 0.022 0.002 PHE d 107 TYR 0.018 0.001 TYR a 168 ARG 0.004 0.000 ARG d 291 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1155) hydrogen bonds : angle 4.47756 ( 3267) metal coordination : bond 0.01041 ( 8) metal coordination : angle 4.88973 ( 12) covalent geometry : bond 0.00526 (25820) covalent geometry : angle 0.57156 (34998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 163 time to evaluate : 2.670 Fit side-chains REVERT: b 71 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: b 133 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7943 (ptmm) REVERT: c 55 ASP cc_start: 0.8325 (t70) cc_final: 0.7996 (t0) REVERT: c 126 ASP cc_start: 0.7550 (t70) cc_final: 0.7237 (t70) REVERT: c 298 ASN cc_start: 0.8537 (m-40) cc_final: 0.7886 (t0) REVERT: c 366 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: c 577 ASP cc_start: 0.7900 (t0) cc_final: 0.7639 (t0) REVERT: d 342 ASP cc_start: 0.8174 (t0) cc_final: 0.7918 (t0) REVERT: d 360 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5958 (tt) REVERT: d 404 ASP cc_start: 0.8474 (t0) cc_final: 0.8268 (t0) REVERT: d 1008 THR cc_start: 0.9036 (m) cc_final: 0.8796 (p) REVERT: f 306 MET cc_start: 0.6421 (ptm) cc_final: 0.6188 (ptp) outliers start: 84 outliers final: 66 residues processed: 233 average time/residue: 0.3306 time to fit residues: 128.7788 Evaluate side-chains 228 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 200 ASN Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 366 GLU Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 520 VAL Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 781 LEU Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 869 VAL Chi-restraints excluded: chain c residue 930 GLN Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain c residue 1138 LEU Chi-restraints excluded: chain d residue 6 PHE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 248 TYR Chi-restraints excluded: chain d residue 260 SER Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 360 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 629 VAL Chi-restraints excluded: chain d residue 650 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 797 ASN Chi-restraints excluded: chain d residue 836 VAL Chi-restraints excluded: chain d residue 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1162 LEU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1252 VAL Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 186 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 200 ASN ** b 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 ASN c 232 GLN c1077 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.132493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094687 restraints weight = 43892.542| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.07 r_work: 0.3204 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25828 Z= 0.152 Angle : 0.554 18.841 35010 Z= 0.279 Chirality : 0.042 0.228 3972 Planarity : 0.004 0.043 4588 Dihedral : 7.115 62.991 3667 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.65 % Allowed : 15.62 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.62 (0.15), residues: 3214 helix: 1.50 (0.15), residues: 1283 sheet: -0.54 (0.26), residues: 401 loop : -0.18 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 144 HIS 0.003 0.001 HIS d 505 PHE 0.021 0.001 PHE d 107 TYR 0.015 0.001 TYR a 168 ARG 0.011 0.000 ARG d 291 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1155) hydrogen bonds : angle 4.38820 ( 3267) metal coordination : bond 0.00852 ( 8) metal coordination : angle 4.48114 ( 12) covalent geometry : bond 0.00369 (25820) covalent geometry : angle 0.54801 (34998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 3.510 Fit side-chains REVERT: b 133 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7956 (ptmm) REVERT: c 55 ASP cc_start: 0.8367 (t70) cc_final: 0.8061 (t0) REVERT: c 107 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7498 (p90) REVERT: c 232 GLN cc_start: 0.5369 (OUTLIER) cc_final: 0.4920 (tt0) REVERT: c 271 ASP cc_start: 0.8615 (m-30) cc_final: 0.8138 (t0) REVERT: c 298 ASN cc_start: 0.8580 (m-40) cc_final: 0.7949 (t0) REVERT: c 366 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: c 527 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8202 (pp20) REVERT: c 577 ASP cc_start: 0.7811 (t0) cc_final: 0.7569 (t0) REVERT: d 342 ASP cc_start: 0.8123 (t0) cc_final: 0.7909 (t0) REVERT: d 360 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6056 (tt) REVERT: d 407 LYS cc_start: 0.8478 (ptmt) cc_final: 0.8034 (pttp) REVERT: d 688 MET cc_start: 0.8932 (mmt) cc_final: 0.8382 (mmt) REVERT: d 1008 THR cc_start: 0.9031 (m) cc_final: 0.8823 (p) REVERT: f 306 MET cc_start: 0.6554 (ptm) cc_final: 0.6296 (ptp) outliers start: 72 outliers final: 60 residues processed: 224 average time/residue: 0.5305 time to fit residues: 200.4788 Evaluate side-chains 225 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 232 GLN Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 366 GLU Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 520 VAL Chi-restraints excluded: chain c residue 527 GLU Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 869 VAL Chi-restraints excluded: chain c residue 926 MET Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain c residue 1138 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 248 TYR Chi-restraints excluded: chain d residue 260 SER Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 360 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 629 VAL Chi-restraints excluded: chain d residue 650 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 797 ASN Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1140 GLU Chi-restraints excluded: chain d residue 1162 LEU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1252 VAL Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 289 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 213 optimal weight: 0.2980 chunk 280 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 GLN b 36 ASN c 610 ASN d 22 GLN d 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096614 restraints weight = 43620.911| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.94 r_work: 0.3220 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25828 Z= 0.112 Angle : 0.528 15.025 35010 Z= 0.265 Chirality : 0.041 0.174 3972 Planarity : 0.004 0.043 4588 Dihedral : 6.998 62.662 3667 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.50 % Allowed : 15.81 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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 (0.15), residues: 3214 helix: 1.65 (0.15), residues: 1280 sheet: -0.48 (0.26), residues: 382 loop : -0.13 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP f 144 HIS 0.002 0.000 HIS d 854 PHE 0.020 0.001 PHE d 107 TYR 0.024 0.001 TYR c 344 ARG 0.010 0.000 ARG c 231 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1155) hydrogen bonds : angle 4.29009 ( 3267) metal coordination : bond 0.00655 ( 8) metal coordination : angle 3.85108 ( 12) covalent geometry : bond 0.00262 (25820) covalent geometry : angle 0.52322 (34998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 4.548 Fit side-chains REVERT: c 55 ASP cc_start: 0.8369 (t70) cc_final: 0.8057 (t0) REVERT: c 271 ASP cc_start: 0.8725 (m-30) cc_final: 0.8191 (t0) REVERT: c 298 ASN cc_start: 0.8493 (m-40) cc_final: 0.7871 (t0) REVERT: c 366 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: c 527 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8278 (pp20) REVERT: c 577 ASP cc_start: 0.7828 (t0) cc_final: 0.7565 (t70) REVERT: c 672 MET cc_start: 0.8554 (mtt) cc_final: 0.8313 (mtt) REVERT: d 342 ASP cc_start: 0.8115 (t0) cc_final: 0.7893 (t0) REVERT: d 360 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6113 (tt) REVERT: d 407 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7912 (pttp) REVERT: f 105 TYR cc_start: 0.8152 (m-80) cc_final: 0.7858 (m-10) REVERT: f 306 MET cc_start: 0.6277 (ptm) cc_final: 0.6030 (ptp) outliers start: 68 outliers final: 55 residues processed: 221 average time/residue: 0.4573 time to fit residues: 173.0821 Evaluate side-chains 215 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 9.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 5 GLN Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 257 ILE Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 346 VAL Chi-restraints excluded: chain c residue 366 GLU Chi-restraints excluded: chain c residue 373 PHE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 381 VAL Chi-restraints excluded: chain c residue 519 VAL Chi-restraints excluded: chain c residue 520 VAL Chi-restraints excluded: chain c residue 527 GLU Chi-restraints excluded: chain c residue 603 ASN Chi-restraints excluded: chain c residue 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 869 VAL Chi-restraints excluded: chain c residue 1057 LEU Chi-restraints excluded: chain c residue 1114 GLU Chi-restraints excluded: chain c residue 1120 SER Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 112 SER Chi-restraints excluded: chain d residue 129 ILE Chi-restraints excluded: chain d residue 260 SER Chi-restraints excluded: chain d residue 265 ILE Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 360 LEU Chi-restraints excluded: chain d residue 447 MET Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 VAL Chi-restraints excluded: chain d residue 629 VAL Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 797 ASN Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1162 LEU Chi-restraints excluded: chain d residue 1206 VAL Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1215 LEU Chi-restraints excluded: chain d residue 1219 SER Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1252 VAL Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 97 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 200 ASN b 36 ASN d 239 ASN d 369 ASN f 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093061 restraints weight = 42939.975| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.96 r_work: 0.3224 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 25828 Z= 0.165 Angle : 0.691 59.176 35010 Z= 0.375 Chirality : 0.041 0.210 3972 Planarity : 0.004 0.043 4588 Dihedral : 6.996 62.639 3667 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 15.96 % Favored : 81.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.68 % 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 (0.15), residues: 3214 helix: 1.63 (0.15), residues: 1280 sheet: -0.48 (0.26), residues: 382 loop : -0.13 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP f 144 HIS 0.003 0.001 HIS d 505 PHE 0.018 0.001 PHE d 107 TYR 0.021 0.001 TYR c 344 ARG 0.005 0.000 ARG c 231 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1155) hydrogen bonds : angle 4.28796 ( 3267) metal coordination : bond 0.00691 ( 8) metal coordination : angle 3.84209 ( 12) covalent geometry : bond 0.00370 (25820) covalent geometry : angle 0.68781 (34998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14151.60 seconds wall clock time: 254 minutes 21.47 seconds (15261.47 seconds total)