Starting phenix.real_space_refine on Fri Sep 19 10:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjp_50508/09_2025/9fjp_50508.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjp_50508/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fjp_50508/09_2025/9fjp_50508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjp_50508/09_2025/9fjp_50508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fjp_50508/09_2025/9fjp_50508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjp_50508/09_2025/9fjp_50508.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.06, per 1000 atoms: 0.20 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: 2.00 Conformation dependent library (CDL) restraints added in 868.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.03 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: 5.49 Time building geometry restraints manager: 2.55 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 24.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG d 353 TYR 0.010 0.001 TYR d1283 PHE 0.013 0.001 PHE c 107 TRP 0.009 0.001 TRP c 938 HIS 0.003 0.001 HIS d 505 Details of bonding type rmsd covalent geometry : bond 0.00226 (25820) covalent geometry : angle 0.45869 (34998) hydrogen bonds : bond 0.17062 ( 1155) hydrogen bonds : angle 6.45233 ( 3267) metal coordination : bond 0.04830 ( 8) metal coordination : angle 9.05075 ( 12) *********************** 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 : 0.939 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: 0.2063 time to fit residues: 133.1106 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 : 0.916 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.136142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.095407 restraints weight = 43456.992| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.00 r_work: 0.3284 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25828 Z= 0.130 Angle : 0.568 9.706 35010 Z= 0.293 Chirality : 0.042 0.173 3972 Planarity : 0.004 0.045 4588 Dihedral : 7.119 66.997 3675 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.80 % Allowed : 8.82 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3214 helix: 1.69 (0.15), residues: 1283 sheet: -0.76 (0.26), residues: 376 loop : 0.06 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d1204 TYR 0.020 0.001 TYR f 141 PHE 0.018 0.001 PHE d 107 TRP 0.012 0.001 TRP d 223 HIS 0.007 0.001 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00295 (25820) covalent geometry : angle 0.56022 (34998) hydrogen bonds : bond 0.04136 ( 1155) hydrogen bonds : angle 4.93183 ( 3267) metal coordination : bond 0.00936 ( 8) metal coordination : angle 5.18195 ( 12) *********************** 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 269 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: b 152 ASN cc_start: 0.6616 (t0) cc_final: 0.6212 (t0) REVERT: c 55 ASP cc_start: 0.8267 (t70) cc_final: 0.8044 (t0) REVERT: c 126 ASP cc_start: 0.7407 (t70) cc_final: 0.7068 (t70) REVERT: c 298 ASN cc_start: 0.8617 (m-40) cc_final: 0.8073 (t0) REVERT: c 396 MET cc_start: 0.8110 (tmm) cc_final: 0.7855 (tmm) REVERT: c 577 ASP cc_start: 0.7856 (t0) cc_final: 0.7346 (m-30) REVERT: d 265 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7579 (tt) REVERT: d 407 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8131 (pttm) REVERT: d 417 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7158 (tp) REVERT: d 614 SER cc_start: 0.8484 (t) cc_final: 0.8249 (m) REVERT: d 983 MET cc_start: 0.8392 (mmt) cc_final: 0.8065 (mmt) REVERT: d 1008 THR cc_start: 0.8749 (m) cc_final: 0.8391 (p) REVERT: d 1052 ARG cc_start: 0.8688 (ptm160) cc_final: 0.8488 (ttp80) REVERT: f 144 TRP cc_start: 0.7130 (m100) cc_final: 0.6803 (m100) REVERT: f 246 VAL cc_start: 0.7007 (m) cc_final: 0.6652 (m) outliers start: 49 outliers final: 31 residues processed: 256 average time/residue: 0.1704 time to fit residues: 70.4673 Evaluate side-chains 203 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 417 LEU Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 823 LEU Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain e residue 87 LEU 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 294 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 106 optimal weight: 0.0070 chunk 279 optimal weight: 4.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- 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 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 935 HIS d 267 ASN d 687 GLN e 69 ASN f 157 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.133228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092481 restraints weight = 43310.324| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.06 r_work: 0.3167 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25828 Z= 0.178 Angle : 0.561 8.808 35010 Z= 0.287 Chirality : 0.043 0.149 3972 Planarity : 0.004 0.040 4588 Dihedral : 7.115 66.901 3667 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.94 % Allowed : 10.62 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3214 helix: 1.58 (0.15), residues: 1272 sheet: -0.72 (0.26), residues: 375 loop : 0.01 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d1204 TYR 0.016 0.001 TYR c 530 PHE 0.016 0.002 PHE d1186 TRP 0.011 0.001 TRP c 938 HIS 0.004 0.001 HIS d 505 Details of bonding type rmsd covalent geometry : bond 0.00436 (25820) covalent geometry : angle 0.55428 (34998) hydrogen bonds : bond 0.04317 ( 1155) hydrogen bonds : angle 4.68502 ( 3267) metal coordination : bond 0.00975 ( 8) metal coordination : angle 4.62192 ( 12) *********************** 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 255 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 175 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: b 152 ASN cc_start: 0.6468 (t0) cc_final: 0.6062 (t0) REVERT: c 55 ASP cc_start: 0.8188 (t70) cc_final: 0.7893 (t0) REVERT: c 126 ASP cc_start: 0.7464 (t70) cc_final: 0.7111 (t70) REVERT: c 298 ASN cc_start: 0.8665 (m-40) cc_final: 0.8278 (t0) REVERT: c 577 ASP cc_start: 0.7972 (t0) cc_final: 0.7426 (t0) REVERT: c 791 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7586 (mmt90) REVERT: d 265 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7615 (tt) REVERT: d 267 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7979 (m110) REVERT: d 342 ASP cc_start: 0.8158 (t0) cc_final: 0.7769 (t0) REVERT: d 407 LYS cc_start: 0.8586 (ptmt) cc_final: 0.8143 (pttp) REVERT: d 417 LEU cc_start: 0.7526 (tt) cc_final: 0.7302 (tp) REVERT: d 1008 THR cc_start: 0.8895 (m) cc_final: 0.8561 (p) REVERT: d 1218 ASP cc_start: 0.4006 (OUTLIER) cc_final: 0.3802 (t70) REVERT: f 144 TRP cc_start: 0.7153 (m100) cc_final: 0.6846 (m100) outliers start: 80 outliers final: 44 residues processed: 241 average time/residue: 0.1676 time to fit residues: 66.2341 Evaluate side-chains 209 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 123 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 140 VAL 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 83 VAL Chi-restraints excluded: chain c residue 127 MET Chi-restraints excluded: chain c residue 149 SER 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 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 265 ILE Chi-restraints excluded: chain d residue 267 ASN Chi-restraints excluded: chain d residue 268 PHE Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 543 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 1206 VAL 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 243 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 232 GLN ** c 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 22 GLN d 239 ASN ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094317 restraints weight = 43374.773| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.02 r_work: 0.3246 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25828 Z= 0.112 Angle : 0.501 6.785 35010 Z= 0.257 Chirality : 0.041 0.148 3972 Planarity : 0.004 0.042 4588 Dihedral : 7.041 66.735 3667 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.65 % Allowed : 12.10 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3214 helix: 1.69 (0.15), residues: 1283 sheet: -0.69 (0.25), residues: 403 loop : 0.03 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d1204 TYR 0.018 0.001 TYR c 657 PHE 0.024 0.001 PHE d1186 TRP 0.011 0.001 TRP c 938 HIS 0.003 0.001 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00261 (25820) covalent geometry : angle 0.49645 (34998) hydrogen bonds : bond 0.03633 ( 1155) hydrogen bonds : angle 4.44386 ( 3267) metal coordination : bond 0.00641 ( 8) metal coordination : angle 3.74127 ( 12) *********************** 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 247 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 141 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7098 (mt-10) REVERT: c 55 ASP cc_start: 0.8191 (t70) cc_final: 0.7938 (t0) REVERT: c 211 TRP cc_start: 0.7198 (m-10) cc_final: 0.6956 (m-10) REVERT: c 298 ASN cc_start: 0.8661 (m-40) cc_final: 0.8122 (t0) REVERT: c 577 ASP cc_start: 0.7854 (t0) cc_final: 0.7331 (t0) REVERT: d 265 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7865 (tt) REVERT: d 342 ASP cc_start: 0.8104 (t0) cc_final: 0.7810 (t0) REVERT: d 360 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6010 (tt) REVERT: d 407 LYS cc_start: 0.8558 (ptmt) cc_final: 0.8131 (pttp) REVERT: d 417 LEU cc_start: 0.7612 (tt) cc_final: 0.7385 (tp) REVERT: d 983 MET cc_start: 0.8622 (mmt) cc_final: 0.8011 (mmt) REVERT: d 1008 THR cc_start: 0.8917 (m) cc_final: 0.8648 (p) REVERT: d 1012 MET cc_start: 0.6666 (tpp) cc_final: 0.6353 (tpp) REVERT: d 1218 ASP cc_start: 0.3981 (OUTLIER) cc_final: 0.3700 (t0) REVERT: f 89 HIS cc_start: 0.7871 (t70) cc_final: 0.7624 (t-170) REVERT: f 144 TRP cc_start: 0.7065 (m100) cc_final: 0.6762 (m100) outliers start: 72 outliers final: 43 residues processed: 233 average time/residue: 0.1404 time to fit residues: 55.1494 Evaluate side-chains 212 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 17 ASN 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 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 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 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 77 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** c 935 HIS d 368 ASN d 854 HIS d 959 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.127228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.086400 restraints weight = 43427.663| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.18 r_work: 0.3057 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 25828 Z= 0.372 Angle : 0.747 12.754 35010 Z= 0.378 Chirality : 0.049 0.211 3972 Planarity : 0.006 0.048 4588 Dihedral : 7.518 65.317 3667 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.71 % Allowed : 13.16 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 3214 helix: 1.01 (0.14), residues: 1279 sheet: -0.73 (0.25), residues: 416 loop : -0.44 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 173 TYR 0.027 0.002 TYR a 168 PHE 0.034 0.003 PHE c 107 TRP 0.032 0.002 TRP d 23 HIS 0.010 0.002 HIS e 106 Details of bonding type rmsd covalent geometry : bond 0.00932 (25820) covalent geometry : angle 0.73761 (34998) hydrogen bonds : bond 0.05525 ( 1155) hydrogen bonds : angle 4.87126 ( 3267) metal coordination : bond 0.01687 ( 8) metal coordination : angle 6.52671 ( 12) *********************** 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 272 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 171 time to evaluate : 0.991 Fit side-chains REVERT: b 71 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: c 55 ASP cc_start: 0.8299 (t70) cc_final: 0.7932 (t0) REVERT: c 126 ASP cc_start: 0.7711 (t70) cc_final: 0.7413 (t70) REVERT: c 298 ASN cc_start: 0.8606 (m-40) cc_final: 0.7961 (t0) REVERT: c 577 ASP cc_start: 0.8088 (t0) cc_final: 0.7759 (t0) REVERT: c 789 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8539 (mt) REVERT: d 342 ASP cc_start: 0.8206 (t0) cc_final: 0.7923 (t0) REVERT: d 360 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5926 (tt) REVERT: d 823 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7981 (pp) REVERT: d 1008 THR cc_start: 0.9062 (m) cc_final: 0.8753 (p) REVERT: d 1012 MET cc_start: 0.6517 (tpp) cc_final: 0.6245 (tpp) outliers start: 101 outliers final: 63 residues processed: 254 average time/residue: 0.1443 time to fit residues: 61.1424 Evaluate side-chains 220 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain b residue 95 MET 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 b residue 183 VAL Chi-restraints excluded: chain c residue 120 ASP Chi-restraints excluded: chain c residue 149 SER 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 626 VAL Chi-restraints excluded: chain c residue 653 VAL Chi-restraints excluded: chain c residue 660 VAL Chi-restraints excluded: chain c residue 666 THR Chi-restraints excluded: chain c residue 781 LEU Chi-restraints excluded: chain c residue 789 ILE 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 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 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 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 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 1252 VAL 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 92 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 301 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 5 GLN b 36 ASN c 232 GLN c 539 HIS c1077 GLN c1086 GLN e 69 ASN f 117 GLN f 148 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090160 restraints weight = 43000.520| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.21 r_work: 0.3126 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25828 Z= 0.131 Angle : 0.526 10.423 35010 Z= 0.271 Chirality : 0.041 0.183 3972 Planarity : 0.004 0.042 4588 Dihedral : 7.187 64.117 3667 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.54 % Allowed : 14.89 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.15), residues: 3214 helix: 1.45 (0.15), residues: 1284 sheet: -0.78 (0.25), residues: 425 loop : -0.18 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d1204 TYR 0.018 0.001 TYR f 141 PHE 0.024 0.001 PHE f 130 TRP 0.015 0.001 TRP f 144 HIS 0.004 0.001 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00310 (25820) covalent geometry : angle 0.52033 (34998) hydrogen bonds : bond 0.03819 ( 1155) hydrogen bonds : angle 4.48382 ( 3267) metal coordination : bond 0.00756 ( 8) metal coordination : angle 4.08357 ( 12) *********************** 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 240 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 1.018 Fit side-chains REVERT: a 1 MET cc_start: 0.5917 (mpp) cc_final: 0.5084 (mpp) REVERT: c 55 ASP cc_start: 0.8255 (t70) cc_final: 0.7946 (t0) REVERT: c 126 ASP cc_start: 0.7608 (t70) cc_final: 0.7246 (t0) REVERT: c 298 ASN cc_start: 0.8587 (m-40) cc_final: 0.7967 (t0) REVERT: c 366 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: c 577 ASP cc_start: 0.7924 (t0) cc_final: 0.7546 (t0) REVERT: d 342 ASP cc_start: 0.8091 (t0) cc_final: 0.7827 (t0) REVERT: d 360 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5909 (tt) REVERT: d 407 LYS cc_start: 0.8490 (ptmt) cc_final: 0.8021 (pttp) REVERT: d 417 LEU cc_start: 0.7792 (tp) cc_final: 0.7382 (tt) REVERT: d 1008 THR cc_start: 0.9000 (m) cc_final: 0.8731 (p) outliers start: 69 outliers final: 49 residues processed: 229 average time/residue: 0.1572 time to fit residues: 59.0684 Evaluate side-chains 210 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 5 GLN Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 65 THR 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 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 626 VAL Chi-restraints excluded: chain c residue 640 ASP Chi-restraints excluded: chain c residue 803 VAL Chi-restraints excluded: chain c residue 930 GLN Chi-restraints excluded: chain c residue 1031 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 d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE 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 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 919 SER Chi-restraints excluded: chain d residue 1034 LEU Chi-restraints excluded: chain d residue 1162 LEU Chi-restraints excluded: chain d residue 1185 GLU Chi-restraints excluded: chain d residue 1207 LEU Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1238 ILE 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 184 optimal weight: 6.9990 chunk 8 optimal weight: 0.0270 chunk 186 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 174 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.0644 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090237 restraints weight = 42591.520| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.87 r_work: 0.3235 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25828 Z= 0.121 Angle : 0.517 13.868 35010 Z= 0.264 Chirality : 0.041 0.163 3972 Planarity : 0.004 0.042 4588 Dihedral : 7.085 64.283 3667 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.61 % Allowed : 15.26 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 3214 helix: 1.58 (0.15), residues: 1284 sheet: -0.61 (0.25), residues: 407 loop : -0.14 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 291 TYR 0.013 0.001 TYR a 168 PHE 0.019 0.001 PHE d1186 TRP 0.016 0.001 TRP f 144 HIS 0.003 0.001 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00287 (25820) covalent geometry : angle 0.51230 (34998) hydrogen bonds : bond 0.03651 ( 1155) hydrogen bonds : angle 4.37002 ( 3267) metal coordination : bond 0.00680 ( 8) metal coordination : angle 3.71966 ( 12) *********************** 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 239 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.5969 (mpp) cc_final: 0.5247 (mpp) REVERT: c 55 ASP cc_start: 0.8497 (t70) cc_final: 0.8210 (t0) REVERT: c 126 ASP cc_start: 0.7746 (t70) cc_final: 0.7372 (t70) REVERT: c 298 ASN cc_start: 0.8623 (m-40) cc_final: 0.7989 (t0) REVERT: c 366 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: c 577 ASP cc_start: 0.8035 (t0) cc_final: 0.7735 (t0) REVERT: d 342 ASP cc_start: 0.8288 (t0) cc_final: 0.8030 (t0) REVERT: d 360 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6145 (tt) REVERT: d 407 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8135 (pttp) REVERT: d 417 LEU cc_start: 0.7836 (tp) cc_final: 0.7427 (tt) REVERT: d 1008 THR cc_start: 0.9001 (m) cc_final: 0.8769 (p) outliers start: 71 outliers final: 54 residues processed: 228 average time/residue: 0.1426 time to fit residues: 54.3616 Evaluate side-chains 214 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 65 THR 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 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 1031 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 d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE 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 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 614 SER 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 909 THR 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 1229 THR Chi-restraints excluded: chain d residue 1238 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 d 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094132 restraints weight = 43681.662| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.78 r_work: 0.3200 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25828 Z= 0.186 Angle : 0.567 12.828 35010 Z= 0.288 Chirality : 0.043 0.146 3972 Planarity : 0.004 0.042 4588 Dihedral : 7.133 63.787 3667 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 15.66 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.15), residues: 3214 helix: 1.50 (0.15), residues: 1283 sheet: -0.59 (0.26), residues: 398 loop : -0.21 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 291 TYR 0.017 0.001 TYR a 168 PHE 0.018 0.001 PHE d1186 TRP 0.016 0.001 TRP f 144 HIS 0.004 0.001 HIS d 505 Details of bonding type rmsd covalent geometry : bond 0.00455 (25820) covalent geometry : angle 0.56204 (34998) hydrogen bonds : bond 0.04049 ( 1155) hydrogen bonds : angle 4.41139 ( 3267) metal coordination : bond 0.00910 ( 8) metal coordination : angle 4.27410 ( 12) *********************** 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 231 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 0.895 Fit side-chains REVERT: b 65 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7786 (m) REVERT: c 55 ASP cc_start: 0.8343 (t70) cc_final: 0.8017 (t0) REVERT: c 126 ASP cc_start: 0.7606 (t70) cc_final: 0.7253 (t70) REVERT: c 298 ASN cc_start: 0.8560 (m-40) cc_final: 0.7909 (t0) REVERT: c 366 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: c 527 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: c 577 ASP cc_start: 0.7867 (t0) cc_final: 0.7644 (t0) REVERT: d 360 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6035 (tt) REVERT: d 407 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8029 (pttp) REVERT: d 1008 THR cc_start: 0.9027 (m) cc_final: 0.8821 (p) REVERT: f 306 MET cc_start: 0.6304 (ptm) cc_final: 0.6049 (ptp) outliers start: 74 outliers final: 59 residues processed: 216 average time/residue: 0.1617 time to fit residues: 57.8585 Evaluate side-chains 219 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 65 THR 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 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 926 MET Chi-restraints excluded: chain c residue 930 GLN Chi-restraints excluded: chain c residue 1031 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 d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE 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 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 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 909 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 253 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN a 200 ASN b 5 GLN b 36 ASN d 22 GLN d 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.134524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097056 restraints weight = 43733.468| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.82 r_work: 0.3267 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25828 Z= 0.110 Angle : 0.523 19.847 35010 Z= 0.262 Chirality : 0.041 0.198 3972 Planarity : 0.004 0.042 4588 Dihedral : 7.004 63.149 3667 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 15.85 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3214 helix: 1.60 (0.15), residues: 1292 sheet: -0.40 (0.27), residues: 373 loop : -0.13 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 291 TYR 0.013 0.001 TYR c 91 PHE 0.024 0.001 PHE d 107 TRP 0.017 0.001 TRP f 144 HIS 0.003 0.000 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00254 (25820) covalent geometry : angle 0.51954 (34998) hydrogen bonds : bond 0.03456 ( 1155) hydrogen bonds : angle 4.28515 ( 3267) metal coordination : bond 0.00612 ( 8) metal coordination : angle 3.39390 ( 12) *********************** 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 238 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 168 time to evaluate : 1.112 Fit side-chains REVERT: b 65 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7803 (m) REVERT: b 133 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7938 (ptmm) REVERT: c 55 ASP cc_start: 0.8517 (t70) cc_final: 0.8241 (t0) REVERT: c 62 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: c 126 ASP cc_start: 0.7737 (t70) cc_final: 0.7429 (t70) REVERT: c 298 ASN cc_start: 0.8491 (m-40) cc_final: 0.7857 (t0) REVERT: c 366 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: c 527 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8394 (pp20) REVERT: c 577 ASP cc_start: 0.8041 (t0) cc_final: 0.7729 (t0) REVERT: d 360 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5968 (tt) REVERT: d 407 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7889 (pttp) REVERT: d 1008 THR cc_start: 0.9037 (m) cc_final: 0.8796 (p) REVERT: f 105 TYR cc_start: 0.8135 (m-80) cc_final: 0.7849 (m-10) REVERT: f 306 MET cc_start: 0.6279 (ptm) cc_final: 0.6020 (ptp) outliers start: 70 outliers final: 54 residues processed: 223 average time/residue: 0.1658 time to fit residues: 60.8497 Evaluate side-chains 217 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 5 GLN Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 65 THR 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 62 GLU 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 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 803 VAL Chi-restraints excluded: chain c residue 1031 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 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 261 ILE Chi-restraints excluded: chain d residue 265 ILE 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 629 VAL Chi-restraints excluded: chain d residue 650 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 909 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 284 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 5 GLN a 17 ASN a 200 ASN b 36 ASN ** c 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097459 restraints weight = 43702.420| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.81 r_work: 0.3250 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 25828 Z= 0.174 Angle : 0.764 59.200 35010 Z= 0.434 Chirality : 0.045 0.998 3972 Planarity : 0.005 0.159 4588 Dihedral : 7.001 63.127 3667 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.35 % Allowed : 16.03 % Favored : 81.62 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.15), residues: 3214 helix: 1.57 (0.15), residues: 1292 sheet: -0.39 (0.27), residues: 373 loop : -0.12 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 291 TYR 0.046 0.001 TYR c 344 PHE 0.045 0.001 PHE c 187 TRP 0.016 0.001 TRP f 144 HIS 0.003 0.000 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00400 (25820) covalent geometry : angle 0.76160 (34998) hydrogen bonds : bond 0.03518 ( 1155) hydrogen bonds : angle 4.29980 ( 3267) metal coordination : bond 0.00643 ( 8) metal coordination : angle 3.38692 ( 12) ********************** 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 222 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 158 time to evaluate : 1.090 Fit side-chains REVERT: b 65 THR cc_start: 0.8006 (t) cc_final: 0.7775 (m) REVERT: b 133 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7912 (ptmm) REVERT: c 55 ASP cc_start: 0.8301 (t70) cc_final: 0.8008 (t0) REVERT: c 62 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: c 126 ASP cc_start: 0.7567 (t70) cc_final: 0.7269 (t70) REVERT: c 298 ASN cc_start: 0.8483 (m-40) cc_final: 0.7851 (t0) REVERT: c 366 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: c 527 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8253 (pp20) REVERT: c 577 ASP cc_start: 0.7818 (t0) cc_final: 0.7526 (t0) REVERT: d 360 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5997 (tt) REVERT: d 407 LYS cc_start: 0.8362 (ptmt) cc_final: 0.7853 (pttm) REVERT: d 1008 THR cc_start: 0.9032 (m) cc_final: 0.8823 (p) REVERT: f 105 TYR cc_start: 0.8125 (m-80) cc_final: 0.7838 (m-10) REVERT: f 306 MET cc_start: 0.6283 (ptm) cc_final: 0.6032 (ptp) outliers start: 64 outliers final: 54 residues processed: 210 average time/residue: 0.1710 time to fit residues: 59.0553 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 : 1.013 ------------------------------------------------------------------------------- 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 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 62 GLU 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 393 MET 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 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 1031 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 d residue 16 THR Chi-restraints excluded: chain d residue 34 ILE 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 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 629 VAL Chi-restraints excluded: chain d residue 650 LEU Chi-restraints excluded: chain d residue 731 VAL Chi-restraints excluded: chain d residue 909 THR 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 1185 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 150 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 250 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 288 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 ASN ** c 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.134279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096351 restraints weight = 43598.571| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.10 r_work: 0.3263 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 25828 Z= 0.174 Angle : 0.764 59.200 35010 Z= 0.434 Chirality : 0.045 0.998 3972 Planarity : 0.005 0.159 4588 Dihedral : 7.001 63.127 3667 Min Nonbonded Distance : 0.955 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.17 % Allowed : 16.07 % Favored : 81.76 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.15), residues: 3214 helix: 1.57 (0.15), residues: 1292 sheet: -0.39 (0.27), residues: 373 loop : -0.12 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 291 TYR 0.046 0.001 TYR c 344 PHE 0.045 0.001 PHE c 187 TRP 0.016 0.001 TRP f 144 HIS 0.003 0.000 HIS f 184 Details of bonding type rmsd covalent geometry : bond 0.00400 (25820) covalent geometry : angle 0.76160 (34998) hydrogen bonds : bond 0.03518 ( 1155) hydrogen bonds : angle 4.29980 ( 3267) metal coordination : bond 0.00643 ( 8) metal coordination : angle 3.38692 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6152.92 seconds wall clock time: 105 minutes 55.86 seconds (6355.86 seconds total)