Starting phenix.real_space_refine on Thu Mar 5 16:38:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pp4_13579/03_2026/7pp4_13579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pp4_13579/03_2026/7pp4_13579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pp4_13579/03_2026/7pp4_13579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pp4_13579/03_2026/7pp4_13579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pp4_13579/03_2026/7pp4_13579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pp4_13579/03_2026/7pp4_13579.map" } resolution = 3.84 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= -0.004 sd= 0.046 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 87 5.16 5 C 14928 2.51 5 N 4233 2.21 5 O 4565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23816 Number of models: 1 Model: "" Number of chains: 7 Chain: "a" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1700 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 208} Chain: "b" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1749 Classifications: {'peptide': 230} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 215} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8640 Classifications: {'peptide': 1112} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1049} 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: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1119 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} 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 19145 SG CYS d 891 53.286 82.541 99.359 1.00 41.50 S ATOM 19719 SG CYS d 968 56.209 82.943 96.563 1.00 46.68 S ATOM 19761 SG CYS d 975 54.610 79.648 97.691 1.00 39.55 S ATOM 19779 SG CYS d 978 52.612 81.879 95.678 1.00 42.32 S ATOM 12565 SG CYS d 60 121.649 72.008 93.859 1.00112.36 S ATOM 12583 SG CYS d 62 124.257 73.067 94.827 1.00113.61 S ATOM 12692 SG CYS d 75 122.413 73.710 97.707 1.00114.67 S ATOM 12718 SG CYS d 78 121.212 75.331 95.336 1.00112.81 S Time building chain proxies: 5.21, per 1000 atoms: 0.22 Number of scatterers: 23816 At special positions: 0 Unit cell: (151.8, 185.9, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 87 16.00 Mg 1 11.99 O 4565 8.00 N 4233 7.00 C 14928 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " Number of angles added : 12 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 44 sheets defined 41.3% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.913A pdb=" N SER a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) 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 153 Processing helix chain 'a' and resid 203 through 224 removed outlier: 3.533A pdb=" N ALA a 207 " --> pdb=" O SER a 203 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG a 223 " --> pdb=" O PHE a 219 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU a 224 " --> pdb=" O GLY a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 45 removed outlier: 3.983A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (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 148 through 153 Processing helix chain 'b' and resid 203 through 225 removed outlier: 3.948A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU b 225 " --> pdb=" O LEU b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 66 removed outlier: 3.827A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 4.115A 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 84 through 94 removed outlier: 3.660A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 125 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 removed outlier: 3.680A pdb=" N GLU c 297 " --> pdb=" O GLN c 293 " (cutoff:3.500A) 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 removed outlier: 3.564A pdb=" N VAL c 399 " --> pdb=" O ARG c 395 " (cutoff:3.500A) Processing helix chain 'c' and resid 413 through 418 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 Processing helix chain 'c' and resid 532 through 538 Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.595A pdb=" N MET c 593 " --> pdb=" O ALA c 590 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 590 through 594' Processing helix chain 'c' and resid 601 through 613 removed outlier: 3.775A pdb=" N ARG c 613 " --> pdb=" O ALA c 609 " (cutoff:3.500A) Processing helix chain 'c' and resid 631 through 637 Processing helix chain 'c' and resid 730 through 732 No H-bonds generated for 'chain 'c' and resid 730 through 732' Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 814 through 825 removed outlier: 3.900A pdb=" N ARG c 819 " --> pdb=" O THR c 815 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU c 820 " --> pdb=" O PRO c 816 " (cutoff:3.500A) Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.172A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 removed outlier: 3.553A pdb=" N LEU c 932 " --> pdb=" O ILE c 928 " (cutoff:3.500A) Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.611A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1069 through 1080 removed outlier: 3.563A pdb=" N CYS c1073 " --> pdb=" O GLY c1069 " (cutoff:3.500A) Processing helix chain 'c' and resid 1082 through 1091 Processing helix chain 'c' and resid 1095 through 1108 Processing helix chain 'c' and resid 1118 through 1129 Processing helix chain 'd' and resid 16 through 24 Processing helix chain 'd' and resid 84 through 91 removed outlier: 4.214A pdb=" N ARG d 91 " --> pdb=" O ARG d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 108 removed outlier: 3.792A pdb=" N PHE d 107 " --> pdb=" O HIS d 103 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS d 108 " --> pdb=" O ILE d 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 103 through 108' 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 removed outlier: 3.515A pdb=" N GLU d 147 " --> pdb=" O MET d 143 " (cutoff:3.500A) 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 removed outlier: 3.551A pdb=" N TYR d 241 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 257 through 268 removed outlier: 3.516A pdb=" N ILE d 261 " --> pdb=" O GLY d 257 " (cutoff:3.500A) Processing helix chain 'd' and resid 270 through 283 Processing helix chain 'd' and resid 285 through 306 removed outlier: 4.148A pdb=" N ARG d 291 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY d 306 " --> pdb=" O PHE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 308 through 311 Processing helix chain 'd' and resid 339 through 361 Processing helix chain 'd' and resid 363 through 383 removed outlier: 3.609A pdb=" N VAL d 367 " --> pdb=" O PRO d 363 " (cutoff:3.500A) Processing helix chain 'd' and resid 401 through 406 Processing helix chain 'd' and resid 411 through 416 removed outlier: 3.523A pdb=" N ASN d 416 " --> pdb=" O ARG d 412 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 452 removed outlier: 3.912A pdb=" N GLU d 450 " --> pdb=" O LEU d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 452 through 463 Processing helix chain 'd' and resid 468 through 479 Processing helix chain 'd' and resid 483 through 491 removed outlier: 3.700A 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 525 through 527 No H-bonds generated for 'chain 'd' and resid 525 through 527' Processing helix chain 'd' and resid 528 through 533 removed outlier: 3.532A pdb=" N PHE d 532 " --> pdb=" O VAL d 528 " (cutoff:3.500A) Processing helix chain 'd' and resid 548 through 558 Processing helix chain 'd' and resid 560 through 564 removed outlier: 3.592A pdb=" N ASN d 563 " --> pdb=" O LEU d 560 " (cutoff:3.500A) Processing helix chain 'd' and resid 580 through 590 Processing helix chain 'd' and resid 614 through 625 Processing helix chain 'd' and resid 643 through 651 removed outlier: 4.074A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE d 651 " --> pdb=" O GLU d 647 " (cutoff:3.500A) Processing helix chain 'd' and resid 668 through 675 Processing helix chain 'd' and resid 689 through 704 Processing helix chain 'd' and resid 705 through 726 removed outlier: 4.023A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG d 726 " --> pdb=" O TYR d 722 " (cutoff:3.500A) Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.672A 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: 3.743A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.551A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA d 868 " --> pdb=" O ALA d 864 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER d 881 " --> pdb=" O LEU d 877 " (cutoff:3.500A) Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 975 through 980 Processing helix chain 'd' and resid 995 through 1005 Processing helix chain 'd' and resid 1006 through 1010 Processing helix chain 'd' and resid 1027 through 1037 Processing helix chain 'd' and resid 1117 through 1126 Processing helix chain 'd' and resid 1126 through 1145 removed outlier: 3.885A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN d1145 " --> pdb=" O VAL d1141 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1162 removed outlier: 4.055A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN d1160 " --> pdb=" O VAL d1156 " (cutoff:3.500A) Processing helix chain 'd' and resid 1183 through 1196 Processing helix chain 'd' and resid 1209 through 1216 removed outlier: 3.668A pdb=" N ALA d1216 " --> pdb=" O LYS d1212 " (cutoff:3.500A) Processing helix chain 'd' and resid 1219 through 1227 Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1248 through 1255 Processing helix chain 'd' and resid 1260 through 1263 Processing helix chain 'd' and resid 1264 through 1269 removed outlier: 3.692A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1283 removed outlier: 4.485A pdb=" N TYR d1283 " --> pdb=" O ARG d1279 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 47 removed outlier: 3.996A pdb=" N LEU e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG e 46 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 70 removed outlier: 3.560A pdb=" N VAL e 54 " --> pdb=" O LYS e 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 73 No H-bonds generated for 'chain 'e' and resid 71 through 73' Processing helix chain 'e' and resid 90 through 100 Processing helix chain 'f' and resid 25 through 35 Processing helix chain 'f' and resid 44 through 65 Processing helix chain 'f' and resid 73 through 94 removed outlier: 3.621A pdb=" N ASN f 94 " --> pdb=" O LEU f 90 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 105 removed outlier: 3.692A pdb=" N TYR f 105 " --> pdb=" O LEU f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 128 removed outlier: 3.745A pdb=" N GLU f 128 " --> pdb=" O ILE f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 158 removed outlier: 3.987A pdb=" N TYR f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 9 through 13 removed outlier: 3.688A pdb=" N LEU a 9 " --> pdb=" O GLU a 24 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU a 24 " --> pdb=" O LEU a 9 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE a 189 " --> pdb=" O THR a 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS a 173 " --> pdb=" O GLU a 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 100 removed outlier: 3.660A pdb=" N LEU a 138 " --> pdb=" O MET a 95 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER a 53 " --> pdb=" O VAL a 139 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU a 141 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL a 51 " --> pdb=" O GLU a 141 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY a 143 " --> pdb=" O ALA a 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA a 49 " --> pdb=" O GLY a 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 removed outlier: 3.576A pdb=" N SER a 86 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR a 117 " --> pdb=" O SER a 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 removed outlier: 3.555A pdb=" N GLY a 103 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU a 128 " --> pdb=" O GLY a 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA a 126 " --> pdb=" O VAL a 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.714A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.714A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS b 173 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 93 through 97 removed outlier: 6.204A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE b 54 " --> pdb=" O ILE b 162 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE b 162 " --> pdb=" O ILE b 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 97 removed outlier: 3.891A pdb=" N VAL b 147 " --> pdb=" O SER b 166 " (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 removed outlier: 4.130A pdb=" N ALA b 126 " --> pdb=" O VAL b 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 96 through 97 removed outlier: 4.777A pdb=" N LEU c 105 " --> pdb=" O ILE c 140 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE c 140 " --> pdb=" O LEU c 105 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE c 107 " --> pdb=" O GLU c 138 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU c 138 " --> pdb=" O PHE c 107 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP c 109 " --> pdb=" O THR c 136 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR c 136 " --> pdb=" O ASP c 109 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP c 156 " --> pdb=" O ALA c 131 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU c 133 " --> pdb=" O MET c 154 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU c 146 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.588A pdb=" N GLN c 178 " --> pdb=" O ARG c 379 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER c 177 " --> pdb=" O SER c 456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 184 through 191 Processing sheet with id=AB6, first strand: chain 'c' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'c' and resid 354 through 355 removed outlier: 3.600A pdb=" N VAL c 363 " --> pdb=" O MET c 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 529 through 531 Processing sheet with id=AB9, first strand: chain 'c' and resid 558 through 559 removed outlier: 3.602A pdb=" N VAL c 559 " --> pdb=" O VAL c 571 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL c 571 " --> pdb=" O VAL c 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'c' and resid 667 through 671 removed outlier: 6.952A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 676 through 677 removed outlier: 3.548A pdb=" N ALA c 676 " --> pdb=" O ALA c 684 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA c 684 " --> pdb=" O ALA c 676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'c' and resid 687 through 688 removed outlier: 3.523A pdb=" N ASP c 704 " --> pdb=" O CYS c 687 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.170A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU c 719 " --> pdb=" O MET c1028 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE c 915 " --> pdb=" O ASN c 718 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU c 917 " --> pdb=" O LEU c 720 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA c 722 " --> pdb=" O LEU c 917 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE c 735 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE c 898 " --> pdb=" O ILE c 735 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU c 737 " --> pdb=" O ILE c 898 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.170A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 748 through 752 removed outlier: 6.710A pdb=" N VAL c 865 " --> pdb=" O ASP c 761 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP c 761 " --> pdb=" O VAL c 865 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 748 through 752 removed outlier: 4.028A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.888A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 806 through 808 Processing sheet with id=AD1, first strand: chain 'c' and resid 906 through 907 removed outlier: 3.577A pdb=" N PHE c 906 " --> pdb=" O PHE c1011 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.789A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET d 541 " --> pdb=" O SER d 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 7.737A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 1133 through 1135 Processing sheet with id=AD5, first strand: chain 'd' and resid 9 through 10 Processing sheet with id=AD6, first strand: chain 'd' and resid 93 through 94 Processing sheet with id=AD7, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD8, first strand: chain 'd' and resid 134 through 135 removed outlier: 3.767A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE d 235 " --> pdb=" O TYR d 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.833A pdb=" N SER d 138 " --> pdb=" O THR d 253 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 443 through 444 removed outlier: 5.384A pdb=" N LEU d 443 " --> pdb=" O VAL d 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.536A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU d 637 " --> pdb=" O TRP d 662 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 611 through 612 removed outlier: 3.536A pdb=" N TYR d 612 " --> pdb=" O LYS d 634 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 898 through 900 removed outlier: 3.742A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 902 through 903 Processing sheet with id=AE6, first strand: chain 'd' and resid 1075 through 1080 removed outlier: 4.244A pdb=" N VAL d1075 " --> pdb=" O ILE d1066 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE d1066 " --> pdb=" O VAL d1075 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY d1051 " --> pdb=" O VAL d1105 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL d1105 " --> pdb=" O GLY d1051 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 1181 through 1182 removed outlier: 3.751A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 1272 through 1274 1008 hydrogen bonds defined for protein. 2847 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: 5.29 Time building geometry restraints manager: 2.46 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: 8171 1.34 - 1.46: 2681 1.46 - 1.57: 13214 1.57 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 24219 Sorted by residual: bond pdb=" N VAL d 974 " pdb=" CA VAL d 974 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.76e+00 bond pdb=" N ASP d 539 " pdb=" CA ASP d 539 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.27e-02 6.20e+03 7.54e+00 bond pdb=" N THR d 970 " pdb=" CA THR d 970 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.21e+00 bond pdb=" N ARG f 67 " pdb=" CA ARG f 67 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.64e+00 bond pdb=" N CYS d 891 " pdb=" CA CYS d 891 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.33e-02 5.65e+03 5.64e+00 ... (remaining 24214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 32383 1.66 - 3.32: 329 3.32 - 4.98: 85 4.98 - 6.64: 1 6.64 - 8.30: 1 Bond angle restraints: 32799 Sorted by residual: angle pdb=" CA ASP d 539 " pdb=" C ASP d 539 " pdb=" O ASP d 539 " ideal model delta sigma weight residual 121.56 116.63 4.93 1.09e+00 8.42e-01 2.04e+01 angle pdb=" C ASP d 535 " pdb=" CA ASP d 535 " pdb=" CB ASP d 535 " ideal model delta sigma weight residual 109.37 117.67 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N ASP d 535 " pdb=" CA ASP d 535 " pdb=" C ASP d 535 " ideal model delta sigma weight residual 109.40 103.06 6.34 1.63e+00 3.76e-01 1.51e+01 angle pdb=" CA ASP d 535 " pdb=" CB ASP d 535 " pdb=" CG ASP d 535 " ideal model delta sigma weight residual 112.60 116.45 -3.85 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA ARG f 67 " pdb=" C ARG f 67 " pdb=" O ARG f 67 " ideal model delta sigma weight residual 120.82 116.86 3.96 1.05e+00 9.07e-01 1.42e+01 ... (remaining 32794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 14235 17.79 - 35.58: 539 35.58 - 53.37: 60 53.37 - 71.16: 14 71.16 - 88.95: 4 Dihedral angle restraints: 14852 sinusoidal: 6103 harmonic: 8749 Sorted by residual: dihedral pdb=" CA GLN d 882 " pdb=" C GLN d 882 " pdb=" N ASP d 883 " pdb=" CA ASP d 883 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 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 -164.59 -15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" N ARG d 478 " pdb=" CA ARG d 478 " pdb=" CB ARG d 478 " pdb=" CG ARG d 478 " ideal model delta sinusoidal sigma weight residual -60.00 -119.83 59.83 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 14849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2439 0.029 - 0.057: 792 0.057 - 0.086: 218 0.086 - 0.115: 219 0.115 - 0.144: 55 Chirality restraints: 3723 Sorted by residual: chirality pdb=" CA VAL c 561 " pdb=" N VAL c 561 " pdb=" C VAL c 561 " pdb=" CB VAL c 561 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE d 832 " pdb=" N ILE d 832 " pdb=" C ILE d 832 " pdb=" CB ILE d 832 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 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 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 3720 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL c 571 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO c 572 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO c 572 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO c 572 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG b 6 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO b 7 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO b 7 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 7 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU c1125 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU c1125 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU c1125 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS c1126 " -0.009 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 172 2.52 - 3.12: 19429 3.12 - 3.71: 35072 3.71 - 4.31: 47040 4.31 - 4.90: 79982 Nonbonded interactions: 181695 Sorted by model distance: nonbonded pdb=" O PRO d 326 " pdb=" OG1 THR d 337 " model vdw 1.926 3.040 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 2.036 3.040 nonbonded pdb=" OG SER d1170 " pdb=" O PHE d1175 " model vdw 2.064 3.040 nonbonded pdb=" OH TYR d 241 " pdb=" O GLY d 254 " model vdw 2.067 3.040 nonbonded pdb=" O ARG d1054 " pdb=" OG1 THR d1065 " model vdw 2.119 3.040 ... (remaining 181690 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 4 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 4 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.230 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 24227 Z= 0.138 Angle : 0.572 43.002 32811 Z= 0.271 Chirality : 0.040 0.144 3723 Planarity : 0.003 0.045 4332 Dihedral : 9.428 88.947 9232 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.39 % Allowed : 3.89 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 3045 helix: 1.70 (0.16), residues: 1119 sheet: -1.46 (0.29), residues: 348 loop : -0.95 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 372 TYR 0.017 0.001 TYR f 141 PHE 0.016 0.001 PHE d 107 TRP 0.007 0.001 TRP f 145 HIS 0.003 0.000 HIS f 89 Details of bonding type rmsd covalent geometry : bond 0.00244 (24219) covalent geometry : angle 0.47586 (32799) hydrogen bonds : bond 0.19263 ( 988) hydrogen bonds : angle 6.57006 ( 2847) metal coordination : bond 0.07907 ( 8) metal coordination : angle 16.60548 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 478 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 ASN cc_start: 0.7790 (p0) cc_final: 0.7510 (p0) REVERT: c 122 CYS cc_start: 0.8093 (m) cc_final: 0.7798 (m) REVERT: c 165 THR cc_start: 0.8343 (p) cc_final: 0.8115 (p) REVERT: c 396 MET cc_start: 0.8182 (tmm) cc_final: 0.7630 (tmm) REVERT: c 661 MET cc_start: 0.7628 (tpp) cc_final: 0.7010 (tpp) REVERT: c 902 GLU cc_start: 0.6994 (pt0) cc_final: 0.6773 (pt0) REVERT: d 12 ILE cc_start: 0.9239 (mt) cc_final: 0.9004 (tt) REVERT: d 1155 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7656 (mm-30) REVERT: e 29 TYR cc_start: 0.8097 (p90) cc_final: 0.7792 (p90) REVERT: e 49 SER cc_start: 0.8202 (p) cc_final: 0.7850 (m) REVERT: e 78 TYR cc_start: 0.7578 (m-80) cc_final: 0.7333 (m-10) REVERT: f 154 MET cc_start: 0.6152 (mmm) cc_final: 0.5951 (tpt) outliers start: 10 outliers final: 3 residues processed: 485 average time/residue: 0.2039 time to fit residues: 145.1061 Evaluate side-chains 266 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain d residue 60 CYS Chi-restraints excluded: chain f residue 30 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 612 GLN d 145 HIS d 207 GLN ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 687 GLN e 88 GLN f 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.071267 restraints weight = 66777.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.073501 restraints weight = 37457.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075006 restraints weight = 25711.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.075914 restraints weight = 20131.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076453 restraints weight = 17291.806| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24227 Z= 0.163 Angle : 0.630 8.897 32811 Z= 0.321 Chirality : 0.044 0.177 3723 Planarity : 0.004 0.054 4332 Dihedral : 3.936 39.486 3367 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.67 % Allowed : 9.44 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 3045 helix: 1.47 (0.16), residues: 1144 sheet: -1.27 (0.27), residues: 351 loop : -0.96 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG f 81 TYR 0.018 0.001 TYR d 251 PHE 0.018 0.002 PHE c 139 TRP 0.006 0.001 TRP d1220 HIS 0.006 0.001 HIS b 61 Details of bonding type rmsd covalent geometry : bond 0.00365 (24219) covalent geometry : angle 0.62703 (32799) hydrogen bonds : bond 0.04683 ( 988) hydrogen bonds : angle 5.11694 ( 2847) metal coordination : bond 0.00877 ( 8) metal coordination : angle 3.45576 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 123 MET cc_start: 0.8281 (tmm) cc_final: 0.8011 (tmm) REVERT: c 122 CYS cc_start: 0.8595 (m) cc_final: 0.7982 (m) REVERT: c 165 THR cc_start: 0.9056 (p) cc_final: 0.8728 (t) REVERT: c 188 ASP cc_start: 0.7480 (m-30) cc_final: 0.7193 (p0) REVERT: c 393 MET cc_start: 0.7972 (tpp) cc_final: 0.7724 (tpp) REVERT: c 396 MET cc_start: 0.8273 (tmm) cc_final: 0.7550 (tmm) REVERT: c 607 MET cc_start: 0.8749 (tpp) cc_final: 0.8524 (tpp) REVERT: c 611 MET cc_start: 0.8614 (tpp) cc_final: 0.8400 (tpp) REVERT: c 724 MET cc_start: 0.8652 (ptm) cc_final: 0.8424 (ppp) REVERT: c 1103 TYR cc_start: 0.8758 (t80) cc_final: 0.8476 (t80) REVERT: d 310 MET cc_start: 0.8387 (mpp) cc_final: 0.8021 (tmm) REVERT: d 373 MET cc_start: 0.7796 (mtp) cc_final: 0.7551 (mmm) REVERT: d 820 MET cc_start: 0.8374 (mmm) cc_final: 0.8005 (mmm) REVERT: d 837 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8614 (mtmm) REVERT: d 966 LEU cc_start: 0.8084 (tt) cc_final: 0.7856 (tp) REVERT: d 1155 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8559 (tp30) REVERT: d 1235 ASP cc_start: 0.8716 (t0) cc_final: 0.8305 (m-30) REVERT: e 29 TYR cc_start: 0.8600 (p90) cc_final: 0.7892 (p90) REVERT: f 48 LEU cc_start: 0.7516 (mm) cc_final: 0.7161 (mp) REVERT: f 92 GLU cc_start: 0.8409 (tp30) cc_final: 0.7865 (tm-30) REVERT: f 94 ASN cc_start: 0.8842 (m-40) cc_final: 0.8557 (m-40) outliers start: 43 outliers final: 15 residues processed: 321 average time/residue: 0.1555 time to fit residues: 79.8884 Evaluate side-chains 253 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 939 CYS Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1030 ILE Chi-restraints excluded: chain d residue 60 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 208 ILE Chi-restraints excluded: chain d residue 317 VAL Chi-restraints excluded: chain d residue 369 ASN Chi-restraints excluded: chain d residue 377 SER Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 503 THR Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 837 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 42 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 295 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 329 GLN d 505 HIS ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069481 restraints weight = 66846.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071561 restraints weight = 37963.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072968 restraints weight = 26493.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073871 restraints weight = 20985.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074471 restraints weight = 18080.698| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24227 Z= 0.205 Angle : 0.625 10.699 32811 Z= 0.318 Chirality : 0.044 0.200 3723 Planarity : 0.004 0.052 4332 Dihedral : 4.137 35.241 3364 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.25 % Allowed : 11.27 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 3045 helix: 1.26 (0.16), residues: 1140 sheet: -1.41 (0.26), residues: 389 loop : -0.97 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 282 TYR 0.018 0.002 TYR d 251 PHE 0.016 0.002 PHE c 107 TRP 0.008 0.001 TRP d1220 HIS 0.006 0.001 HIS d 94 Details of bonding type rmsd covalent geometry : bond 0.00472 (24219) covalent geometry : angle 0.62223 (32799) hydrogen bonds : bond 0.04880 ( 988) hydrogen bonds : angle 5.00259 ( 2847) metal coordination : bond 0.00943 ( 8) metal coordination : angle 3.23456 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8614 (pp) REVERT: c 122 CYS cc_start: 0.8580 (m) cc_final: 0.7992 (m) REVERT: c 157 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: c 165 THR cc_start: 0.8972 (p) cc_final: 0.8726 (t) REVERT: c 188 ASP cc_start: 0.7649 (m-30) cc_final: 0.7447 (p0) REVERT: c 396 MET cc_start: 0.8305 (tmm) cc_final: 0.7633 (tmm) REVERT: c 689 ILE cc_start: 0.9401 (pt) cc_final: 0.9035 (tp) REVERT: c 724 MET cc_start: 0.8605 (ptm) cc_final: 0.8337 (ppp) REVERT: c 1103 TYR cc_start: 0.8773 (t80) cc_final: 0.8532 (t80) REVERT: d 155 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.6027 (ttt) REVERT: d 244 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8307 (mm) REVERT: d 310 MET cc_start: 0.8275 (mpp) cc_final: 0.8021 (tmm) REVERT: d 312 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8370 (mmm) REVERT: d 554 GLU cc_start: 0.8726 (tp30) cc_final: 0.8446 (tp30) REVERT: d 1155 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8079 (mm-30) REVERT: d 1235 ASP cc_start: 0.8753 (t0) cc_final: 0.8288 (m-30) REVERT: e 29 TYR cc_start: 0.8584 (p90) cc_final: 0.7886 (p90) REVERT: e 41 ASP cc_start: 0.8329 (p0) cc_final: 0.7633 (p0) REVERT: e 42 GLU cc_start: 0.8513 (mp0) cc_final: 0.7804 (mp0) REVERT: f 25 ASP cc_start: 0.8421 (t0) cc_final: 0.7972 (t0) REVERT: f 28 ARG cc_start: 0.7751 (tpp-160) cc_final: 0.7330 (mmp80) REVERT: f 31 LEU cc_start: 0.9007 (mm) cc_final: 0.8553 (tt) REVERT: f 92 GLU cc_start: 0.8538 (tp30) cc_final: 0.7758 (tm-30) outliers start: 58 outliers final: 27 residues processed: 294 average time/residue: 0.1591 time to fit residues: 74.3032 Evaluate side-chains 257 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 939 CYS Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1030 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 60 CYS Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 155 MET Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 253 THR Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 317 VAL Chi-restraints excluded: chain d residue 327 MET Chi-restraints excluded: chain d residue 377 SER Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 518 GLU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 785 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 1008 THR Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 82 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 679 ASN d 349 ASN f 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069168 restraints weight = 66864.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071320 restraints weight = 37665.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072785 restraints weight = 25986.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073720 restraints weight = 20391.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074300 restraints weight = 17499.753| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24227 Z= 0.155 Angle : 0.575 9.473 32811 Z= 0.293 Chirality : 0.042 0.162 3723 Planarity : 0.004 0.050 4332 Dihedral : 4.097 32.179 3364 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.18 % Allowed : 12.86 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 3045 helix: 1.27 (0.16), residues: 1143 sheet: -1.36 (0.26), residues: 383 loop : -0.97 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 386 TYR 0.014 0.001 TYR e 56 PHE 0.013 0.001 PHE c 107 TRP 0.009 0.001 TRP c 938 HIS 0.003 0.001 HIS d 94 Details of bonding type rmsd covalent geometry : bond 0.00356 (24219) covalent geometry : angle 0.57324 (32799) hydrogen bonds : bond 0.04423 ( 988) hydrogen bonds : angle 4.81235 ( 2847) metal coordination : bond 0.00603 ( 8) metal coordination : angle 2.30688 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 MET cc_start: 0.8627 (mmt) cc_final: 0.8307 (mmm) REVERT: b 172 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8598 (pp) REVERT: c 122 CYS cc_start: 0.8619 (m) cc_final: 0.7992 (m) REVERT: c 157 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: c 165 THR cc_start: 0.9055 (p) cc_final: 0.8803 (t) REVERT: c 188 ASP cc_start: 0.7607 (m-30) cc_final: 0.7371 (p0) REVERT: c 366 GLU cc_start: 0.8938 (pm20) cc_final: 0.8736 (pm20) REVERT: c 393 MET cc_start: 0.7869 (tpp) cc_final: 0.7500 (tpp) REVERT: c 396 MET cc_start: 0.8284 (tmm) cc_final: 0.7597 (tmm) REVERT: c 607 MET cc_start: 0.8765 (tpp) cc_final: 0.8114 (tpp) REVERT: c 611 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8055 (mpp) REVERT: c 661 MET cc_start: 0.8460 (tpp) cc_final: 0.8083 (mmt) REVERT: c 689 ILE cc_start: 0.9469 (pt) cc_final: 0.9103 (tp) REVERT: c 724 MET cc_start: 0.8567 (ptm) cc_final: 0.8346 (ppp) REVERT: c 891 ASN cc_start: 0.9476 (OUTLIER) cc_final: 0.8930 (p0) REVERT: c 1103 TYR cc_start: 0.8765 (t80) cc_final: 0.8548 (t80) REVERT: d 148 LEU cc_start: 0.7083 (mt) cc_final: 0.6053 (pp) REVERT: d 244 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8274 (mm) REVERT: d 256 MET cc_start: 0.8375 (ptm) cc_final: 0.7380 (mtm) REVERT: d 310 MET cc_start: 0.8256 (mpp) cc_final: 0.7993 (tmm) REVERT: d 312 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8474 (mmm) REVERT: d 554 GLU cc_start: 0.8776 (tp30) cc_final: 0.8416 (tp30) REVERT: d 614 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8977 (m) REVERT: d 688 MET cc_start: 0.8314 (tpp) cc_final: 0.8021 (tpp) REVERT: d 754 ASP cc_start: 0.8285 (t0) cc_final: 0.7942 (t0) REVERT: d 820 MET cc_start: 0.8509 (mmm) cc_final: 0.8018 (mmm) REVERT: d 966 LEU cc_start: 0.8448 (tp) cc_final: 0.8221 (tt) REVERT: d 1235 ASP cc_start: 0.8790 (t0) cc_final: 0.8368 (m-30) REVERT: e 29 TYR cc_start: 0.8556 (p90) cc_final: 0.7874 (p90) REVERT: f 25 ASP cc_start: 0.8550 (t0) cc_final: 0.8047 (t0) REVERT: f 28 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7274 (mmp80) REVERT: f 92 GLU cc_start: 0.8586 (tp30) cc_final: 0.7788 (tm-30) REVERT: f 105 TYR cc_start: 0.8694 (t80) cc_final: 0.8492 (t80) outliers start: 56 outliers final: 27 residues processed: 278 average time/residue: 0.1520 time to fit residues: 67.8428 Evaluate side-chains 253 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 95 MET Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 611 MET Chi-restraints excluded: chain c residue 758 ASP Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 939 CYS Chi-restraints excluded: chain c residue 952 VAL Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1030 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 317 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 518 GLU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 901 LEU Chi-restraints excluded: chain d residue 1008 THR Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain e residue 42 GLU Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 102 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 294 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 679 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066609 restraints weight = 67221.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068621 restraints weight = 38983.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069972 restraints weight = 27425.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.070833 restraints weight = 21810.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071360 restraints weight = 18924.781| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 24227 Z= 0.329 Angle : 0.728 9.921 32811 Z= 0.374 Chirality : 0.046 0.171 3723 Planarity : 0.005 0.061 4332 Dihedral : 4.628 21.937 3363 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.99 % Allowed : 14.02 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3045 helix: 0.78 (0.15), residues: 1148 sheet: -1.47 (0.26), residues: 381 loop : -1.21 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 208 TYR 0.021 0.002 TYR a 176 PHE 0.028 0.002 PHE c 107 TRP 0.010 0.002 TRP d 723 HIS 0.007 0.001 HIS d 94 Details of bonding type rmsd covalent geometry : bond 0.00748 (24219) covalent geometry : angle 0.72542 (32799) hydrogen bonds : bond 0.05658 ( 988) hydrogen bonds : angle 5.27149 ( 2847) metal coordination : bond 0.01433 ( 8) metal coordination : angle 3.23949 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 222 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8592 (pp) REVERT: c 122 CYS cc_start: 0.8568 (m) cc_final: 0.8052 (m) REVERT: c 157 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: c 165 THR cc_start: 0.9074 (p) cc_final: 0.8870 (t) REVERT: c 188 ASP cc_start: 0.7643 (m-30) cc_final: 0.7375 (p0) REVERT: c 393 MET cc_start: 0.7879 (tpp) cc_final: 0.7448 (tpp) REVERT: c 396 MET cc_start: 0.8359 (tmm) cc_final: 0.7659 (tmm) REVERT: c 689 ILE cc_start: 0.9476 (pt) cc_final: 0.9218 (tp) REVERT: c 724 MET cc_start: 0.8690 (ptm) cc_final: 0.8323 (ppp) REVERT: c 891 ASN cc_start: 0.9537 (OUTLIER) cc_final: 0.9048 (p0) REVERT: c 1103 TYR cc_start: 0.8885 (t80) cc_final: 0.8638 (t80) REVERT: d 244 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8481 (mm) REVERT: d 285 LYS cc_start: 0.7561 (tmtt) cc_final: 0.7306 (tmtt) REVERT: d 312 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8529 (mtm) REVERT: d 373 MET cc_start: 0.8382 (mtp) cc_final: 0.8125 (mmm) REVERT: d 554 GLU cc_start: 0.8932 (tp30) cc_final: 0.8566 (tp30) REVERT: d 614 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.9061 (m) REVERT: d 688 MET cc_start: 0.8300 (tpp) cc_final: 0.8022 (tpp) REVERT: d 750 GLU cc_start: 0.8603 (pp20) cc_final: 0.7801 (pp20) REVERT: d 820 MET cc_start: 0.8792 (mmm) cc_final: 0.8313 (mmm) REVERT: d 1235 ASP cc_start: 0.8893 (t0) cc_final: 0.8447 (m-30) REVERT: e 33 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8902 (pp) REVERT: e 41 ASP cc_start: 0.8401 (p0) cc_final: 0.7713 (p0) REVERT: e 42 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: e 105 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7748 (mp0) REVERT: f 92 GLU cc_start: 0.8547 (tp30) cc_final: 0.7821 (tm-30) REVERT: f 105 TYR cc_start: 0.8858 (t80) cc_final: 0.8641 (t80) outliers start: 77 outliers final: 53 residues processed: 283 average time/residue: 0.1514 time to fit residues: 69.7016 Evaluate side-chains 269 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 296 LEU Chi-restraints excluded: chain c residue 423 VAL Chi-restraints excluded: chain c residue 577 ASP Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 582 SER Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 758 ASP Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 939 CYS Chi-restraints excluded: chain c residue 952 VAL Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1030 ILE Chi-restraints excluded: chain c residue 1102 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 253 THR Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 317 VAL Chi-restraints excluded: chain d residue 377 SER Chi-restraints excluded: chain d residue 378 VAL Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 518 GLU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 713 VAL Chi-restraints excluded: chain d residue 733 MET Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 785 VAL Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 874 THR Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 937 ILE Chi-restraints excluded: chain d residue 1008 THR Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 42 GLU Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 224 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 693 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.069345 restraints weight = 66780.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.071506 restraints weight = 37464.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072896 restraints weight = 25766.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.073898 restraints weight = 20321.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074470 restraints weight = 17335.547| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24227 Z= 0.123 Angle : 0.569 9.177 32811 Z= 0.289 Chirality : 0.042 0.184 3723 Planarity : 0.004 0.053 4332 Dihedral : 4.192 19.899 3363 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.21 % Allowed : 15.66 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3045 helix: 1.20 (0.16), residues: 1136 sheet: -1.13 (0.27), residues: 358 loop : -1.05 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG c 208 TYR 0.012 0.001 TYR c 731 PHE 0.014 0.001 PHE d1061 TRP 0.012 0.001 TRP d1220 HIS 0.003 0.001 HIS d 854 Details of bonding type rmsd covalent geometry : bond 0.00276 (24219) covalent geometry : angle 0.56814 (32799) hydrogen bonds : bond 0.04300 ( 988) hydrogen bonds : angle 4.72652 ( 2847) metal coordination : bond 0.00292 ( 8) metal coordination : angle 2.01776 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8523 (pp) REVERT: c 122 CYS cc_start: 0.8638 (m) cc_final: 0.8004 (m) REVERT: c 157 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: c 165 THR cc_start: 0.9092 (p) cc_final: 0.8851 (t) REVERT: c 188 ASP cc_start: 0.7646 (m-30) cc_final: 0.7387 (p0) REVERT: c 383 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7398 (mm-30) REVERT: c 393 MET cc_start: 0.7901 (tpp) cc_final: 0.7543 (tpp) REVERT: c 396 MET cc_start: 0.8267 (tmm) cc_final: 0.7550 (tmm) REVERT: c 611 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7805 (mpp) REVERT: c 661 MET cc_start: 0.8519 (tpp) cc_final: 0.8081 (mmt) REVERT: c 689 ILE cc_start: 0.9464 (pt) cc_final: 0.9123 (tp) REVERT: c 724 MET cc_start: 0.8618 (ptm) cc_final: 0.8385 (ppp) REVERT: c 891 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.8935 (p0) REVERT: c 1103 TYR cc_start: 0.8781 (t80) cc_final: 0.8534 (t80) REVERT: d 148 LEU cc_start: 0.7154 (mt) cc_final: 0.6109 (pp) REVERT: d 152 GLU cc_start: 0.7548 (pp20) cc_final: 0.7187 (pp20) REVERT: d 244 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8295 (mm) REVERT: d 256 MET cc_start: 0.8408 (ptm) cc_final: 0.7501 (mtp) REVERT: d 285 LYS cc_start: 0.7404 (tmtt) cc_final: 0.7175 (tmtt) REVERT: d 312 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: d 493 GLU cc_start: 0.7687 (mp0) cc_final: 0.7484 (mp0) REVERT: d 554 GLU cc_start: 0.8824 (tp30) cc_final: 0.8133 (tp30) REVERT: d 614 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8911 (m) REVERT: d 688 MET cc_start: 0.8112 (tpp) cc_final: 0.7907 (tpp) REVERT: d 820 MET cc_start: 0.8676 (mmm) cc_final: 0.8214 (mmm) REVERT: d 1112 MET cc_start: 0.5253 (mmm) cc_final: 0.4968 (tpp) REVERT: d 1208 MET cc_start: 0.8881 (pmm) cc_final: 0.8354 (pmm) REVERT: d 1235 ASP cc_start: 0.8824 (t0) cc_final: 0.8365 (m-30) REVERT: e 30 ASP cc_start: 0.8781 (t0) cc_final: 0.8481 (t0) REVERT: e 33 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8854 (pp) REVERT: e 105 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7553 (mp0) REVERT: f 92 GLU cc_start: 0.8442 (tp30) cc_final: 0.7650 (tm-30) REVERT: f 105 TYR cc_start: 0.8830 (t80) cc_final: 0.8630 (t80) outliers start: 57 outliers final: 32 residues processed: 286 average time/residue: 0.1568 time to fit residues: 71.5391 Evaluate side-chains 261 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 611 MET Chi-restraints excluded: chain c residue 758 ASP Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 693 GLN Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 974 VAL Chi-restraints excluded: chain d residue 1120 GLU Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain d residue 1264 ILE Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 42 GLU Chi-restraints excluded: chain e residue 94 ILE Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 199 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 158 optimal weight: 0.0270 chunk 98 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 298 ASN c 679 ASN d1125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.069883 restraints weight = 67029.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.072056 restraints weight = 37714.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.073480 restraints weight = 25975.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074456 restraints weight = 20451.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075093 restraints weight = 17525.721| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24227 Z= 0.116 Angle : 0.563 11.686 32811 Z= 0.284 Chirality : 0.042 0.163 3723 Planarity : 0.004 0.052 4332 Dihedral : 4.020 20.875 3363 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.29 % Allowed : 15.97 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3045 helix: 1.29 (0.16), residues: 1136 sheet: -0.95 (0.28), residues: 340 loop : -1.00 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 350 TYR 0.019 0.001 TYR e 29 PHE 0.014 0.001 PHE d1061 TRP 0.011 0.001 TRP c 938 HIS 0.002 0.001 HIS b 124 Details of bonding type rmsd covalent geometry : bond 0.00260 (24219) covalent geometry : angle 0.56133 (32799) hydrogen bonds : bond 0.04007 ( 988) hydrogen bonds : angle 4.57359 ( 2847) metal coordination : bond 0.00253 ( 8) metal coordination : angle 1.98288 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 78 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8540 (tt) REVERT: b 172 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8548 (pp) REVERT: c 122 CYS cc_start: 0.8674 (m) cc_final: 0.8127 (m) REVERT: c 157 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: c 165 THR cc_start: 0.9041 (p) cc_final: 0.8821 (t) REVERT: c 188 ASP cc_start: 0.7634 (m-30) cc_final: 0.7374 (p0) REVERT: c 383 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7353 (mm-30) REVERT: c 393 MET cc_start: 0.7879 (tpp) cc_final: 0.7528 (tpp) REVERT: c 396 MET cc_start: 0.8276 (tmm) cc_final: 0.7554 (tmm) REVERT: c 611 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7940 (mpp) REVERT: c 689 ILE cc_start: 0.9462 (pt) cc_final: 0.9123 (tp) REVERT: c 724 MET cc_start: 0.8614 (ptm) cc_final: 0.8377 (ppp) REVERT: c 891 ASN cc_start: 0.9436 (OUTLIER) cc_final: 0.8909 (p0) REVERT: c 1091 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8928 (tt) REVERT: c 1103 TYR cc_start: 0.8819 (t80) cc_final: 0.8607 (t80) REVERT: d 148 LEU cc_start: 0.7098 (mt) cc_final: 0.6032 (pp) REVERT: d 152 GLU cc_start: 0.7608 (pp20) cc_final: 0.7305 (pp20) REVERT: d 256 MET cc_start: 0.8370 (ptm) cc_final: 0.8015 (mtp) REVERT: d 285 LYS cc_start: 0.7360 (tmtt) cc_final: 0.7008 (tptp) REVERT: d 312 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8226 (mmm) REVERT: d 373 MET cc_start: 0.8169 (mmm) cc_final: 0.7780 (tmm) REVERT: d 493 GLU cc_start: 0.7735 (mp0) cc_final: 0.7484 (mp0) REVERT: d 554 GLU cc_start: 0.8759 (tp30) cc_final: 0.8050 (tp30) REVERT: d 614 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8938 (m) REVERT: d 757 GLU cc_start: 0.8705 (tp30) cc_final: 0.8362 (tp30) REVERT: d 820 MET cc_start: 0.8617 (mmm) cc_final: 0.8204 (mmm) REVERT: d 966 LEU cc_start: 0.8245 (tp) cc_final: 0.6878 (mt) REVERT: d 1208 MET cc_start: 0.8869 (pmm) cc_final: 0.8292 (pmm) REVERT: d 1235 ASP cc_start: 0.8785 (t0) cc_final: 0.8338 (m-30) REVERT: e 30 ASP cc_start: 0.8878 (t0) cc_final: 0.8605 (t0) REVERT: e 33 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8842 (pp) REVERT: e 41 ASP cc_start: 0.8295 (p0) cc_final: 0.7740 (p0) REVERT: e 42 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: e 105 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7612 (mp0) REVERT: f 48 LEU cc_start: 0.7369 (tp) cc_final: 0.7071 (mt) REVERT: f 92 GLU cc_start: 0.8509 (tp30) cc_final: 0.7629 (tm-30) outliers start: 59 outliers final: 38 residues processed: 293 average time/residue: 0.1554 time to fit residues: 73.5174 Evaluate side-chains 273 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 95 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 582 SER Chi-restraints excluded: chain c residue 611 MET Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 679 ASN Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 952 VAL Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1091 ILE Chi-restraints excluded: chain c residue 1102 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 901 LEU Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 974 VAL Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain d residue 1264 ILE Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 42 GLU Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 75 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.067411 restraints weight = 66967.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.069503 restraints weight = 38254.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.070919 restraints weight = 26549.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.071845 restraints weight = 20933.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072426 restraints weight = 17970.353| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24227 Z= 0.214 Angle : 0.628 10.233 32811 Z= 0.320 Chirality : 0.043 0.219 3723 Planarity : 0.004 0.051 4332 Dihedral : 4.265 21.270 3363 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.60 % Allowed : 16.24 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3045 helix: 1.07 (0.15), residues: 1146 sheet: -1.08 (0.27), residues: 352 loop : -1.11 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 218 TYR 0.030 0.002 TYR f 105 PHE 0.019 0.002 PHE c 252 TRP 0.009 0.001 TRP d1220 HIS 0.011 0.001 HIS c 680 Details of bonding type rmsd covalent geometry : bond 0.00487 (24219) covalent geometry : angle 0.62649 (32799) hydrogen bonds : bond 0.04727 ( 988) hydrogen bonds : angle 4.79836 ( 2847) metal coordination : bond 0.00785 ( 8) metal coordination : angle 2.45209 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8538 (pp) REVERT: c 122 CYS cc_start: 0.8622 (m) cc_final: 0.8046 (m) REVERT: c 157 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: c 165 THR cc_start: 0.9075 (p) cc_final: 0.8869 (t) REVERT: c 188 ASP cc_start: 0.7619 (m-30) cc_final: 0.7334 (p0) REVERT: c 393 MET cc_start: 0.7870 (tpp) cc_final: 0.7517 (tpp) REVERT: c 396 MET cc_start: 0.8291 (tmm) cc_final: 0.7618 (tmm) REVERT: c 661 MET cc_start: 0.8501 (tpp) cc_final: 0.7990 (mmt) REVERT: c 689 ILE cc_start: 0.9490 (pt) cc_final: 0.9182 (tp) REVERT: c 724 MET cc_start: 0.8644 (ptm) cc_final: 0.8272 (ppp) REVERT: c 891 ASN cc_start: 0.9503 (OUTLIER) cc_final: 0.9008 (p0) REVERT: c 1091 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8955 (tt) REVERT: c 1103 TYR cc_start: 0.8859 (t80) cc_final: 0.8652 (t80) REVERT: d 148 LEU cc_start: 0.7287 (mt) cc_final: 0.6246 (pp) REVERT: d 152 GLU cc_start: 0.7684 (pp20) cc_final: 0.7296 (pp20) REVERT: d 244 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8339 (mm) REVERT: d 256 MET cc_start: 0.8390 (ptm) cc_final: 0.7838 (mtp) REVERT: d 312 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8396 (mtm) REVERT: d 493 GLU cc_start: 0.7785 (mp0) cc_final: 0.7545 (mp0) REVERT: d 554 GLU cc_start: 0.8873 (tp30) cc_final: 0.8135 (tp30) REVERT: d 614 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9058 (m) REVERT: d 688 MET cc_start: 0.8399 (tpp) cc_final: 0.8136 (tpp) REVERT: d 757 GLU cc_start: 0.8738 (tp30) cc_final: 0.8384 (tp30) REVERT: d 820 MET cc_start: 0.8673 (mmm) cc_final: 0.8223 (mmm) REVERT: d 1112 MET cc_start: 0.5834 (tpt) cc_final: 0.5631 (tpp) REVERT: d 1208 MET cc_start: 0.8938 (pmm) cc_final: 0.8428 (pmm) REVERT: e 30 ASP cc_start: 0.8916 (t0) cc_final: 0.8595 (t0) REVERT: e 33 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8885 (pp) REVERT: e 41 ASP cc_start: 0.8436 (p0) cc_final: 0.7761 (p0) REVERT: e 42 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: f 25 ASP cc_start: 0.8438 (t0) cc_final: 0.7897 (t0) REVERT: f 28 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7407 (mmp80) REVERT: f 92 GLU cc_start: 0.8418 (tp30) cc_final: 0.7656 (tm-30) outliers start: 67 outliers final: 51 residues processed: 277 average time/residue: 0.1573 time to fit residues: 70.6021 Evaluate side-chains 277 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain b residue 95 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 296 LEU Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 490 GLU Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 582 SER Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 758 ASP Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 952 VAL Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1091 ILE Chi-restraints excluded: chain c residue 1102 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 733 MET Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 937 ILE Chi-restraints excluded: chain d residue 960 VAL Chi-restraints excluded: chain d residue 974 VAL Chi-restraints excluded: chain d residue 1008 THR Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain d residue 1125 GLN Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1264 ILE Chi-restraints excluded: chain d residue 1272 VAL Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 42 GLU Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 135 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 282 optimal weight: 0.1980 chunk 245 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 693 GLN ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069212 restraints weight = 67164.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071363 restraints weight = 37877.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072800 restraints weight = 26121.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073759 restraints weight = 20562.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074368 restraints weight = 17566.383| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24227 Z= 0.126 Angle : 0.594 10.790 32811 Z= 0.298 Chirality : 0.042 0.183 3723 Planarity : 0.004 0.052 4332 Dihedral : 4.121 20.857 3363 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.41 % Allowed : 16.82 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3045 helix: 1.19 (0.16), residues: 1146 sheet: -0.95 (0.28), residues: 338 loop : -1.04 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 218 TYR 0.019 0.001 TYR e 29 PHE 0.018 0.001 PHE c 252 TRP 0.011 0.001 TRP c 938 HIS 0.003 0.001 HIS d 94 Details of bonding type rmsd covalent geometry : bond 0.00289 (24219) covalent geometry : angle 0.59265 (32799) hydrogen bonds : bond 0.04152 ( 988) hydrogen bonds : angle 4.60438 ( 2847) metal coordination : bond 0.00286 ( 8) metal coordination : angle 1.91558 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8545 (pp) REVERT: c 122 CYS cc_start: 0.8665 (m) cc_final: 0.8025 (m) REVERT: c 157 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: c 165 THR cc_start: 0.9059 (p) cc_final: 0.8842 (t) REVERT: c 188 ASP cc_start: 0.7678 (m-30) cc_final: 0.7393 (p0) REVERT: c 383 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7327 (mm-30) REVERT: c 393 MET cc_start: 0.7881 (tpp) cc_final: 0.7594 (tpp) REVERT: c 396 MET cc_start: 0.8275 (tmm) cc_final: 0.7599 (tmm) REVERT: c 661 MET cc_start: 0.8475 (tpp) cc_final: 0.7966 (mmt) REVERT: c 689 ILE cc_start: 0.9468 (pt) cc_final: 0.9126 (tp) REVERT: c 724 MET cc_start: 0.8649 (ptm) cc_final: 0.8369 (ppp) REVERT: c 891 ASN cc_start: 0.9444 (OUTLIER) cc_final: 0.8932 (p0) REVERT: c 1091 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8918 (tt) REVERT: d 108 LYS cc_start: 0.8378 (tptt) cc_final: 0.8131 (tptt) REVERT: d 148 LEU cc_start: 0.7176 (mt) cc_final: 0.6158 (pp) REVERT: d 152 GLU cc_start: 0.7552 (pp20) cc_final: 0.7276 (pp20) REVERT: d 244 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8319 (mm) REVERT: d 256 MET cc_start: 0.8454 (ptm) cc_final: 0.7974 (mtp) REVERT: d 312 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8243 (mmm) REVERT: d 493 GLU cc_start: 0.7744 (mp0) cc_final: 0.7477 (mp0) REVERT: d 554 GLU cc_start: 0.8758 (tp30) cc_final: 0.7969 (tp30) REVERT: d 614 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8941 (m) REVERT: d 688 MET cc_start: 0.8255 (tpp) cc_final: 0.8027 (tpp) REVERT: d 729 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9056 (p) REVERT: d 757 GLU cc_start: 0.8698 (tp30) cc_final: 0.8382 (tp30) REVERT: d 1112 MET cc_start: 0.5842 (tpt) cc_final: 0.5638 (tpp) REVERT: d 1208 MET cc_start: 0.8995 (pmm) cc_final: 0.8436 (pmm) REVERT: e 30 ASP cc_start: 0.8893 (t0) cc_final: 0.8571 (t0) REVERT: f 48 LEU cc_start: 0.7327 (tp) cc_final: 0.7036 (mt) REVERT: f 92 GLU cc_start: 0.8458 (tp30) cc_final: 0.7460 (tm-30) outliers start: 62 outliers final: 45 residues processed: 284 average time/residue: 0.1566 time to fit residues: 71.9929 Evaluate side-chains 277 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain b residue 95 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 582 SER Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 952 VAL Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1091 ILE Chi-restraints excluded: chain c residue 1102 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 693 GLN Chi-restraints excluded: chain d residue 729 VAL Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 937 ILE Chi-restraints excluded: chain d residue 974 VAL Chi-restraints excluded: chain d residue 1008 THR Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1264 ILE Chi-restraints excluded: chain e residue 42 GLU Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 189 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.067869 restraints weight = 67244.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069919 restraints weight = 37974.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071377 restraints weight = 26336.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072302 restraints weight = 20714.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072928 restraints weight = 17707.589| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24227 Z= 0.192 Angle : 0.623 10.637 32811 Z= 0.316 Chirality : 0.043 0.262 3723 Planarity : 0.004 0.051 4332 Dihedral : 4.233 20.559 3363 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.45 % Allowed : 16.78 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3045 helix: 1.08 (0.15), residues: 1152 sheet: -0.96 (0.28), residues: 342 loop : -1.10 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 218 TYR 0.039 0.002 TYR f 105 PHE 0.016 0.002 PHE c 107 TRP 0.008 0.001 TRP d 105 HIS 0.005 0.001 HIS d 94 Details of bonding type rmsd covalent geometry : bond 0.00442 (24219) covalent geometry : angle 0.62148 (32799) hydrogen bonds : bond 0.04559 ( 988) hydrogen bonds : angle 4.73427 ( 2847) metal coordination : bond 0.00677 ( 8) metal coordination : angle 2.35371 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 172 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8536 (pp) REVERT: c 122 CYS cc_start: 0.8597 (m) cc_final: 0.8027 (m) REVERT: c 157 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: c 165 THR cc_start: 0.9083 (p) cc_final: 0.8877 (t) REVERT: c 188 ASP cc_start: 0.7637 (m-30) cc_final: 0.7345 (p0) REVERT: c 393 MET cc_start: 0.7817 (tpp) cc_final: 0.7511 (tpp) REVERT: c 396 MET cc_start: 0.8289 (tmm) cc_final: 0.7616 (tmm) REVERT: c 661 MET cc_start: 0.8513 (tpp) cc_final: 0.8047 (mmt) REVERT: c 689 ILE cc_start: 0.9484 (pt) cc_final: 0.9171 (tp) REVERT: c 724 MET cc_start: 0.8616 (ptm) cc_final: 0.8324 (ppp) REVERT: c 891 ASN cc_start: 0.9500 (OUTLIER) cc_final: 0.9007 (p0) REVERT: c 1091 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8957 (tt) REVERT: d 92 MET cc_start: 0.8696 (ptp) cc_final: 0.8488 (mtm) REVERT: d 108 LYS cc_start: 0.8475 (tptt) cc_final: 0.8198 (tptt) REVERT: d 148 LEU cc_start: 0.7300 (mt) cc_final: 0.6265 (pp) REVERT: d 152 GLU cc_start: 0.7696 (pp20) cc_final: 0.7361 (pp20) REVERT: d 244 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8344 (mm) REVERT: d 256 MET cc_start: 0.8426 (ptm) cc_final: 0.7858 (mtp) REVERT: d 312 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: d 493 GLU cc_start: 0.7798 (mp0) cc_final: 0.7539 (mp0) REVERT: d 554 GLU cc_start: 0.8867 (tp30) cc_final: 0.8125 (tp30) REVERT: d 614 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.9060 (m) REVERT: d 757 GLU cc_start: 0.8704 (tp30) cc_final: 0.8358 (tp30) REVERT: d 1208 MET cc_start: 0.8999 (pmm) cc_final: 0.8520 (pmm) REVERT: e 30 ASP cc_start: 0.8915 (t0) cc_final: 0.8563 (t0) REVERT: f 48 LEU cc_start: 0.7370 (tp) cc_final: 0.7072 (mt) REVERT: f 92 GLU cc_start: 0.8469 (tp30) cc_final: 0.7439 (tm-30) REVERT: f 127 MET cc_start: 0.8584 (tpp) cc_final: 0.8360 (mmp) outliers start: 63 outliers final: 48 residues processed: 271 average time/residue: 0.1552 time to fit residues: 68.0736 Evaluate side-chains 274 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 95 MET Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain b residue 172 LEU Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 139 PHE Chi-restraints excluded: chain c residue 157 PHE Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 185 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 270 THR Chi-restraints excluded: chain c residue 472 VAL Chi-restraints excluded: chain c residue 490 GLU Chi-restraints excluded: chain c residue 581 VAL Chi-restraints excluded: chain c residue 582 SER Chi-restraints excluded: chain c residue 649 VAL Chi-restraints excluded: chain c residue 758 ASP Chi-restraints excluded: chain c residue 891 ASN Chi-restraints excluded: chain c residue 952 VAL Chi-restraints excluded: chain c residue 989 LEU Chi-restraints excluded: chain c residue 1091 ILE Chi-restraints excluded: chain c residue 1102 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 244 LEU Chi-restraints excluded: chain d residue 261 ILE Chi-restraints excluded: chain d residue 312 MET Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 418 LEU Chi-restraints excluded: chain d residue 441 CYS Chi-restraints excluded: chain d residue 451 LEU Chi-restraints excluded: chain d residue 574 LEU Chi-restraints excluded: chain d residue 614 SER Chi-restraints excluded: chain d residue 733 MET Chi-restraints excluded: chain d residue 777 ILE Chi-restraints excluded: chain d residue 824 VAL Chi-restraints excluded: chain d residue 846 VAL Chi-restraints excluded: chain d residue 910 LEU Chi-restraints excluded: chain d residue 937 ILE Chi-restraints excluded: chain d residue 974 VAL Chi-restraints excluded: chain d residue 1008 THR Chi-restraints excluded: chain d residue 1122 LEU Chi-restraints excluded: chain d residue 1125 GLN Chi-restraints excluded: chain d residue 1229 THR Chi-restraints excluded: chain d residue 1264 ILE Chi-restraints excluded: chain f residue 75 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 209 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 285 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069874 restraints weight = 66331.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072049 restraints weight = 37209.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073524 restraints weight = 25638.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074504 restraints weight = 20095.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.075080 restraints weight = 17142.559| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24227 Z= 0.117 Angle : 0.595 10.852 32811 Z= 0.298 Chirality : 0.042 0.231 3723 Planarity : 0.004 0.052 4332 Dihedral : 4.042 23.045 3363 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.18 % Allowed : 17.02 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3045 helix: 1.25 (0.16), residues: 1145 sheet: -0.84 (0.28), residues: 340 loop : -1.00 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG d1123 TYR 0.019 0.001 TYR e 29 PHE 0.018 0.001 PHE d1061 TRP 0.012 0.001 TRP c 938 HIS 0.003 0.000 HIS d 94 Details of bonding type rmsd covalent geometry : bond 0.00265 (24219) covalent geometry : angle 0.59445 (32799) hydrogen bonds : bond 0.03952 ( 988) hydrogen bonds : angle 4.51311 ( 2847) metal coordination : bond 0.00224 ( 8) metal coordination : angle 1.76530 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3887.34 seconds wall clock time: 67 minutes 56.81 seconds (4076.81 seconds total)