Starting phenix.real_space_refine (version: dev) on Thu Dec 22 05:05:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/12_2022/7q59_13829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/12_2022/7q59_13829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/12_2022/7q59_13829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/12_2022/7q59_13829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/12_2022/7q59_13829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/12_2022/7q59_13829.pdb" } resolution = 4.36 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47632 Number of models: 1 Model: "" Number of chains: 14 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: "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} 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 53.397 85.968 100.003 1.00 41.50 S ATOM 19719 SG CYS D 968 56.396 86.346 97.285 1.00 46.68 S ATOM 19761 SG CYS D 975 54.732 83.066 98.359 1.00 39.55 S ATOM 19779 SG CYS D 978 52.811 85.325 96.303 1.00 42.32 S ATOM 12565 SG CYS D 60 121.759 74.692 96.248 1.00112.36 S ATOM 12583 SG CYS D 62 124.353 75.719 97.287 1.00113.61 S ATOM 12692 SG CYS D 75 122.442 76.373 100.120 1.00114.67 S ATOM 12718 SG CYS D 78 121.320 78.015 97.724 1.00112.81 S ATOM 42958 SG CYS d 891 203.963 104.340 121.915 1.00 41.50 S ATOM 43532 SG CYS d 968 201.924 103.437 118.516 1.00 46.68 S ATOM 43574 SG CYS d 975 203.265 106.893 119.485 1.00 39.55 S ATOM 43592 SG CYS d 978 205.663 104.377 118.516 1.00 42.32 S ATOM 36378 SG CYS d 60 140.294 113.005 95.725 1.00112.36 S ATOM 36396 SG CYS d 62 137.482 112.096 96.081 1.00113.61 S ATOM 36505 SG CYS d 75 138.423 111.971 99.429 1.00114.67 S ATOM 36531 SG CYS d 78 140.178 109.985 97.796 1.00112.81 S Time building chain proxies: 25.20, per 1000 atoms: 0.53 Number of scatterers: 47632 At special positions: 0 Unit cell: (265.1, 188.1, 146.3, 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 4 29.99 S 174 16.00 Mg 2 11.99 O 9130 8.00 N 8466 7.00 C 29856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.28 Conformation dependent library (CDL) restraints added in 6.9 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 " 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 : 24 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11240 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 88 sheets defined 41.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.914A 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: 3.532A 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: 3.963A 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: 3.828A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.659A pdb=" N LEU C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.939A 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: 3.594A 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 816 through 825 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: 3.551A 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: 3.562A 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: 3.541A 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: 4.142A 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: 3.561A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.937A 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: 3.622A 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: 3.522A pdb=" N ASN D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.910A 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: 3.701A 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: 4.075A 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: 4.024A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.592A 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: 4.552A 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: 4.072A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.886A 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: 4.057A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.691A 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: 3.559A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.317A 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 removed outlier: 3.574A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 94 removed outlier: 3.927A pdb=" N ASN F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.750A pdb=" N GLU F 128 " --> pdb=" O ILE F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 158 Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.914A 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: 3.532A pdb=" N ALA a 207 " --> pdb=" O SER a 203 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 5.089A 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: 3.982A 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: 3.568A 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: 4.116A 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: 3.659A 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: 3.776A 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 816 through 825 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: 3.551A 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: 4.213A pdb=" N ARG d 91 " --> pdb=" O ARG d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 108 removed outlier: 3.791A 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: 4.144A 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: 3.560A pdb=" N TYR d 241 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 257 through 268 removed outlier: 3.733A 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: 3.769A 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: 3.608A 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: 3.911A 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: 3.531A 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: 4.075A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) removed outlier: 3.514A 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: 4.594A pdb=" N ARG d 726 " --> pdb=" O TYR d 722 " (cutoff:3.500A) Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.673A 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: 3.742A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.552A 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: 4.061A 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: 3.884A 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: 3.854A 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: 3.667A 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: 3.691A pdb=" N ASN d1269 " --> pdb=" O ASN d1265 " (cutoff:3.500A) Processing helix chain 'd' and resid 1275 through 1283 removed outlier: 4.486A 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: 4.136A 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 removed outlier: 3.574A pdb=" N ILE f 52 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 94 removed outlier: 3.927A pdb=" N ASN f 94 " --> pdb=" O LEU f 90 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 105 removed outlier: 3.501A pdb=" N TYR f 105 " --> pdb=" O LEU f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 128 removed outlier: 3.751A pdb=" N GLU f 128 " --> pdb=" O ILE f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 158 removed outlier: 3.533A pdb=" N TRP f 144 " --> pdb=" O THR f 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.689A 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: 4.489A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.235A 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: 3.577A 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: 3.556A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 128 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.563A 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: 6.713A 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: 6.713A 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: 6.203A 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: 6.887A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.655A 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: 4.769A 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: 3.745A 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: 6.151A 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 357 removed outlier: 7.191A pdb=" N MET C 355 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU C 362 " --> pdb=" O MET C 355 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 357 " --> pdb=" O GLY C 360 " (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: 3.601A 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: 6.951A 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: 3.549A 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: 3.522A 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: 4.171A 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: 8.805A 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: 3.836A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.673A 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: 4.171A 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: 3.858A 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: 3.628A 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: 6.658A 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 74 through 75 removed outlier: 3.523A pdb=" N VAL D 80 " --> pdb=" O CYS D 75 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AD9, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.650A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 235 " --> pdb=" O TYR D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.383A 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: 3.537A 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: 3.537A 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: 3.929A 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: 3.587A 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 Processing sheet with id=AE9, 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: 3.816A 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: 3.672A pdb=" N LYS a 173 " --> pdb=" O GLU a 197 " (cutoff:3.500A) Processing sheet with id=AF1, 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: 6.235A 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: 4.411A pdb=" N ALA a 49 " --> pdb=" O GLY a 143 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 85 through 87 removed outlier: 3.577A 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=AF2 Processing sheet with id=AF3, 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: 3.612A 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=AF4, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.715A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 9 through 10 removed outlier: 6.715A 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=AF6, first strand: chain 'b' and resid 93 through 97 removed outlier: 6.203A 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=AF7, first strand: chain 'b' and resid 93 through 97 removed outlier: 3.892A pdb=" N VAL b 147 " --> pdb=" O SER b 166 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AF9, 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=AG1, 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: 5.281A pdb=" N ASP c 109 " --> pdb=" O THR c 136 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR c 136 " --> pdb=" O ASP c 109 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 4.771A 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: 3.745A pdb=" N GLU c 146 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 166 through 168 Processing sheet with id=AG3, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.587A 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=AG4, first strand: chain 'c' and resid 184 through 191 Processing sheet with id=AG5, first strand: chain 'c' and resid 223 through 224 Processing sheet with id=AG6, first strand: chain 'c' and resid 354 through 357 removed outlier: 7.192A pdb=" N MET c 355 " --> pdb=" O GLU c 362 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU c 362 " --> pdb=" O MET c 355 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL c 357 " --> pdb=" O GLY c 360 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 529 through 531 Processing sheet with id=AG8, first strand: chain 'c' and resid 558 through 559 removed outlier: 3.601A 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=AG8 Processing sheet with id=AG9, 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=AH1, 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: 3.556A pdb=" N ALA c 684 " --> pdb=" O ALA c 676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'c' and resid 687 through 688 removed outlier: 3.522A pdb=" N ASP c 704 " --> pdb=" O CYS c 687 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.171A 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: 6.196A pdb=" N LEU c 720 " --> pdb=" O ILE c 915 " (cutoff:3.500A) removed outlier: 7.569A 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: 3.836A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 6.936A 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: 6.674A pdb=" N LEU c 737 " --> pdb=" O ILE c 898 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 885 through 886 removed outlier: 4.171A pdb=" N ALA c 886 " --> pdb=" O MET c1031 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 748 through 752 removed outlier: 6.711A 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: 3.856A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'c' and resid 748 through 752 removed outlier: 4.029A 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: 5.425A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AH7, 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=AH8, first strand: chain 'c' and resid 806 through 808 Processing sheet with id=AH9, 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=AI1, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.790A 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=AI2, 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: 6.658A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'c' and resid 1133 through 1135 Processing sheet with id=AI4, first strand: chain 'd' and resid 9 through 10 Processing sheet with id=AI5, first strand: chain 'd' and resid 74 through 75 removed outlier: 3.523A pdb=" N VAL d 80 " --> pdb=" O CYS d 75 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'd' and resid 93 through 94 Processing sheet with id=AI7, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AI8, first strand: chain 'd' and resid 134 through 135 removed outlier: 3.747A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE d 235 " --> pdb=" O TYR d 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'd' and resid 443 through 444 removed outlier: 5.383A pdb=" N LEU d 443 " --> pdb=" O VAL d 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, 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=AJ2, 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=AJ3, 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=AJ4, first strand: chain 'd' and resid 902 through 903 Processing sheet with id=AJ5, first strand: chain 'd' and resid 1075 through 1080 removed outlier: 4.243A 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: 3.890A 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=AJ6, 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=AJ7, first strand: chain 'd' and resid 1272 through 1274 2022 hydrogen bonds defined for protein. 5706 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: 21.82 Time building geometry restraints manager: 20.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8351 1.32 - 1.44: 11549 1.44 - 1.56: 28232 1.56 - 1.69: 0 1.69 - 1.81: 306 Bond restraints: 48438 Sorted by residual: bond pdb=" C GLU D 376 " pdb=" O GLU D 376 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.19e-02 7.06e+03 1.43e+01 bond pdb=" C LEU F 39 " pdb=" N LEU F 40 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.34e-02 5.57e+03 1.29e+01 bond pdb=" C LEU f 39 " pdb=" N LEU f 40 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.34e-02 5.57e+03 1.26e+01 bond pdb=" C SER F 139 " pdb=" O SER F 139 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.17e-02 7.31e+03 1.14e+01 bond pdb=" N ILE D 73 " pdb=" CA ILE D 73 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 ... (remaining 48433 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.98: 974 104.98 - 112.26: 24479 112.26 - 119.55: 17010 119.55 - 126.83: 22576 126.83 - 134.12: 559 Bond angle restraints: 65598 Sorted by residual: angle pdb=" N ASP f 82 " pdb=" CA ASP f 82 " pdb=" C ASP f 82 " ideal model delta sigma weight residual 111.28 104.63 6.65 1.09e+00 8.42e-01 3.73e+01 angle pdb=" N ASP F 82 " pdb=" CA ASP F 82 " pdb=" C ASP F 82 " ideal model delta sigma weight residual 111.28 104.66 6.62 1.09e+00 8.42e-01 3.68e+01 angle pdb=" N LEU F 76 " pdb=" CA LEU F 76 " pdb=" C LEU F 76 " ideal model delta sigma weight residual 111.28 104.72 6.56 1.09e+00 8.42e-01 3.62e+01 angle pdb=" N LEU f 76 " pdb=" CA LEU f 76 " pdb=" C LEU f 76 " ideal model delta sigma weight residual 111.28 104.76 6.52 1.09e+00 8.42e-01 3.58e+01 angle pdb=" CA GLY f 69 " pdb=" C GLY f 69 " pdb=" N GLU f 70 " ideal model delta sigma weight residual 115.89 121.94 -6.05 1.04e+00 9.25e-01 3.39e+01 ... (remaining 65593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 28277 17.80 - 35.61: 1192 35.61 - 53.41: 165 53.41 - 71.21: 56 71.21 - 89.01: 14 Dihedral angle restraints: 29704 sinusoidal: 12206 harmonic: 17498 Sorted by residual: dihedral pdb=" C ILE d 74 " pdb=" N ILE d 74 " pdb=" CA ILE d 74 " pdb=" CB ILE d 74 " ideal model delta harmonic sigma weight residual -122.00 -130.52 8.52 0 2.50e+00 1.60e-01 1.16e+01 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 -163.23 -16.77 0 5.00e+00 4.00e-02 1.13e+01 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 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 29701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 5971 0.046 - 0.093: 914 0.093 - 0.139: 503 0.139 - 0.186: 47 0.186 - 0.232: 11 Chirality restraints: 7446 Sorted by residual: chirality pdb=" CA GLU c 811 " pdb=" N GLU c 811 " pdb=" C GLU c 811 " pdb=" CB GLU c 811 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLU C 811 " pdb=" N GLU C 811 " pdb=" C GLU C 811 " pdb=" CB GLU C 811 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL f 80 " pdb=" N VAL f 80 " pdb=" C VAL f 80 " pdb=" CB VAL f 80 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 7443 not shown) Planarity restraints: 8664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR d 130 " 0.023 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C TYR d 130 " -0.077 2.00e-02 2.50e+03 pdb=" O TYR d 130 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE d 131 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 254 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C GLY D 254 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY D 254 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA D 255 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 255 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ALA d 255 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA d 255 " -0.021 2.00e-02 2.50e+03 pdb=" N MET d 256 " -0.019 2.00e-02 2.50e+03 ... (remaining 8661 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 328 2.52 - 3.12: 38876 3.12 - 3.71: 70301 3.71 - 4.31: 94867 4.31 - 4.90: 160457 Nonbonded interactions: 364829 Sorted by model distance: nonbonded pdb=" O PRO D 326 " pdb=" OG1 THR D 337 " model vdw 1.925 2.440 nonbonded pdb=" O PRO d 326 " pdb=" OG1 THR d 337 " model vdw 1.926 2.440 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 2.036 2.440 nonbonded pdb=" OG1 THR C 356 " pdb=" OE1 GLU C 362 " model vdw 2.036 2.440 nonbonded pdb=" OG SER d1170 " pdb=" O PHE d1175 " model vdw 2.063 2.440 ... (remaining 364824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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) selection = (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) } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 Mg 2 5.21 5 S 174 5.16 5 C 29856 2.51 5 N 8466 2.21 5 O 9130 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 24.200 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.390 Process input model: 127.200 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 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 0.048 48438 Z= 0.228 Angle : 0.627 9.396 65598 Z= 0.407 Chirality : 0.044 0.232 7446 Planarity : 0.004 0.099 8664 Dihedral : 10.223 89.015 18464 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 6090 helix: 1.49 (0.11), residues: 2258 sheet: -1.51 (0.20), residues: 706 loop : -0.97 (0.11), residues: 3126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 780 time to evaluate : 5.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 37 outliers final: 5 residues processed: 804 average time/residue: 0.6566 time to fit residues: 840.1900 Evaluate side-chains 359 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 354 time to evaluate : 6.113 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5070 time to fit residues: 13.1060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 7.9990 chunk 460 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 310 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 476 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 354 optimal weight: 30.0000 chunk 552 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1153 HIS F 60 HIS a 79 ASN a 185 GLN a 226 ASN c 443 ASN c 493 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 494 HIS ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 510 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 48438 Z= 0.388 Angle : 0.765 19.197 65598 Z= 0.392 Chirality : 0.046 0.233 7446 Planarity : 0.006 0.110 8664 Dihedral : 4.420 23.980 6726 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 6090 helix: 0.77 (0.11), residues: 2360 sheet: -1.55 (0.19), residues: 726 loop : -1.03 (0.11), residues: 3004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 363 time to evaluate : 5.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 369 average time/residue: 0.6133 time to fit residues: 368.2256 Evaluate side-chains 262 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 5.387 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4105 time to fit residues: 9.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 459 optimal weight: 4.9990 chunk 375 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 553 optimal weight: 9.9990 chunk 597 optimal weight: 0.9980 chunk 492 optimal weight: 4.9990 chunk 548 optimal weight: 0.0980 chunk 188 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN a 226 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 48438 Z= 0.211 Angle : 0.581 11.928 65598 Z= 0.299 Chirality : 0.043 0.222 7446 Planarity : 0.004 0.078 8664 Dihedral : 4.122 21.794 6726 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6090 helix: 1.08 (0.11), residues: 2324 sheet: -1.29 (0.19), residues: 724 loop : -0.93 (0.11), residues: 3042 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 346 time to evaluate : 5.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 3 outliers final: 1 residues processed: 348 average time/residue: 0.6137 time to fit residues: 357.4071 Evaluate side-chains 253 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 5.620 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4905 time to fit residues: 8.5734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 20.0000 chunk 415 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 61 optimal weight: 40.0000 chunk 263 optimal weight: 0.8980 chunk 371 optimal weight: 9.9990 chunk 555 optimal weight: 7.9990 chunk 587 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 526 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 941 HIS ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 48438 Z= 0.367 Angle : 0.730 18.516 65598 Z= 0.375 Chirality : 0.045 0.224 7446 Planarity : 0.005 0.083 8664 Dihedral : 4.704 21.775 6726 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 6090 helix: 0.71 (0.10), residues: 2340 sheet: -1.31 (0.19), residues: 712 loop : -1.07 (0.11), residues: 3038 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 294 time to evaluate : 5.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 297 average time/residue: 0.6002 time to fit residues: 300.4248 Evaluate side-chains 226 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 5.685 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3862 time to fit residues: 8.8976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 0.7980 chunk 333 optimal weight: 7.9990 chunk 8 optimal weight: 0.0060 chunk 437 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 501 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 527 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN F 120 ASN a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1034 HIS ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 687 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 48438 Z= 0.201 Angle : 0.585 22.719 65598 Z= 0.299 Chirality : 0.043 0.243 7446 Planarity : 0.004 0.078 8664 Dihedral : 4.331 22.371 6726 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 6090 helix: 0.98 (0.11), residues: 2364 sheet: -1.12 (0.19), residues: 684 loop : -0.91 (0.11), residues: 3042 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 5.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.6183 time to fit residues: 315.2433 Evaluate side-chains 226 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 5.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.3574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 7.9990 chunk 529 optimal weight: 0.0670 chunk 116 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 588 optimal weight: 5.9990 chunk 488 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 308 optimal weight: 5.9990 overall best weight: 2.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 510 GLN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1227 GLN f 89 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 48438 Z= 0.240 Angle : 0.596 11.128 65598 Z= 0.305 Chirality : 0.043 0.282 7446 Planarity : 0.004 0.075 8664 Dihedral : 4.327 20.610 6726 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.42 % Favored : 95.57 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 6090 helix: 0.99 (0.11), residues: 2372 sheet: -1.15 (0.19), residues: 700 loop : -0.90 (0.11), residues: 3018 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.6018 time to fit residues: 282.1122 Evaluate side-chains 219 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 6.090 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4980 time to fit residues: 9.2466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 495 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 586 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 270 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.127 48438 Z= 0.363 Angle : 0.697 13.439 65598 Z= 0.361 Chirality : 0.044 0.232 7446 Planarity : 0.005 0.072 8664 Dihedral : 4.762 24.077 6726 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 6090 helix: 0.72 (0.11), residues: 2354 sheet: -1.46 (0.19), residues: 664 loop : -1.02 (0.11), residues: 3072 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.6276 time to fit residues: 277.2605 Evaluate side-chains 210 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 5.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 349 optimal weight: 0.0020 chunk 176 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 372 optimal weight: 20.0000 chunk 399 optimal weight: 9.9990 chunk 289 optimal weight: 0.2980 chunk 54 optimal weight: 9.9990 chunk 460 optimal weight: 8.9990 overall best weight: 2.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 185 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 HIS ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN D1239 ASN E 69 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 ASN ** c 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 866 ASN ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 415 GLN ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 48438 Z= 0.229 Angle : 0.611 13.594 65598 Z= 0.314 Chirality : 0.043 0.247 7446 Planarity : 0.004 0.065 8664 Dihedral : 4.528 22.589 6726 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.35 % Favored : 95.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6090 helix: 0.92 (0.11), residues: 2358 sheet: -1.32 (0.20), residues: 656 loop : -0.97 (0.11), residues: 3076 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 5.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.6314 time to fit residues: 286.0329 Evaluate side-chains 214 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 5.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 0.8980 chunk 561 optimal weight: 9.9990 chunk 512 optimal weight: 4.9990 chunk 546 optimal weight: 20.0000 chunk 328 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 493 optimal weight: 10.0000 chunk 516 optimal weight: 6.9990 chunk 544 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN E 100 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** c 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 866 ASN ** c 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 563 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1269 ASN e 69 ASN f 89 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 48438 Z= 0.380 Angle : 0.733 9.872 65598 Z= 0.380 Chirality : 0.045 0.264 7446 Planarity : 0.005 0.076 8664 Dihedral : 4.984 29.548 6726 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 6090 helix: 0.54 (0.11), residues: 2350 sheet: -1.54 (0.19), residues: 676 loop : -1.12 (0.11), residues: 3064 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.6007 time to fit residues: 253.0541 Evaluate side-chains 202 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 0.9980 chunk 577 optimal weight: 5.9990 chunk 352 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 chunk 605 optimal weight: 0.0270 chunk 557 optimal weight: 7.9990 chunk 482 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 372 optimal weight: 8.9990 chunk 295 optimal weight: 3.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN E 100 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** c 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 48438 Z= 0.176 Angle : 0.595 12.617 65598 Z= 0.303 Chirality : 0.043 0.270 7446 Planarity : 0.004 0.060 8664 Dihedral : 4.461 25.427 6726 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6090 helix: 0.94 (0.11), residues: 2370 sheet: -1.35 (0.19), residues: 710 loop : -0.90 (0.12), residues: 3010 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.5905 time to fit residues: 276.5745 Evaluate side-chains 215 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 5.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.6034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 10.0000 chunk 513 optimal weight: 8.9990 chunk 147 optimal weight: 0.0770 chunk 444 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 483 optimal weight: 7.9990 chunk 202 optimal weight: 0.7980 chunk 496 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN E 100 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** c 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 751 HIS ** c 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.047934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034822 restraints weight = 429610.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035754 restraints weight = 266751.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.036401 restraints weight = 193858.422| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 48438 Z= 0.239 Angle : 0.609 9.359 65598 Z= 0.313 Chirality : 0.043 0.290 7446 Planarity : 0.004 0.051 8664 Dihedral : 4.472 27.058 6726 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 6090 helix: 0.97 (0.11), residues: 2364 sheet: -1.38 (0.19), residues: 700 loop : -0.88 (0.12), residues: 3026 =============================================================================== Job complete usr+sys time: 8165.41 seconds wall clock time: 150 minutes 34.84 seconds (9034.84 seconds total)