Starting phenix.real_space_refine on Mon Sep 23 17:17:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/09_2024/7q59_13829.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/09_2024/7q59_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_13829/09_2024/7q59_13829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/09_2024/7q59_13829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/09_2024/7q59_13829.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q59_13829/09_2024/7q59_13829.cif" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 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 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. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 20.24, per 1000 atoms: 0.42 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 4.5 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: 5.04 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: 18.08 Time building geometry restraints manager: 10.23 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: 0.00 - 1.88: 64002 1.88 - 3.76: 1345 3.76 - 5.64: 217 5.64 - 7.52: 30 7.52 - 9.40: 4 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 3.040 nonbonded pdb=" O PRO d 326 " pdb=" OG1 THR d 337 " model vdw 1.926 3.040 nonbonded pdb=" OG1 THR c 356 " pdb=" OE1 GLU c 362 " model vdw 2.036 3.040 nonbonded pdb=" OG1 THR C 356 " pdb=" OE1 GLU C 362 " model vdw 2.036 3.040 nonbonded pdb=" OG SER d1170 " pdb=" O PHE d1175 " model vdw 2.063 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 210 or (resid 211 through 212 and (name N or nam \ e CA or name C or name O )) or resid 213 through 226)) selection = (chain 'B' and resid 4 through 226) 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 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.330 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 89.230 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.72 % Allowed : 4.58 % Favored : 94.70 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 223 HIS 0.011 0.001 HIS f 60 PHE 0.016 0.001 PHE D 107 TYR 0.025 0.001 TYR F 57 ARG 0.008 0.000 ARG d 242 *********************** 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 : 4.287 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 REVERT: C 827 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.5016 (mm-30) REVERT: D 104 ILE cc_start: 0.7787 (tt) cc_final: 0.6309 (tp) REVERT: D 256 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7095 (ptt) REVERT: E 78 TYR cc_start: 0.4587 (m-80) cc_final: 0.4368 (m-80) REVERT: F 52 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.8984 (tp) REVERT: d 256 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: d 368 ASN cc_start: 0.6959 (m110) cc_final: 0.5884 (m-40) REVERT: d 438 LEU cc_start: 0.7604 (tp) cc_final: 0.7372 (tp) REVERT: d 865 LEU cc_start: 0.7891 (pp) cc_final: 0.7438 (pp) REVERT: e 42 GLU cc_start: 0.6335 (mp0) cc_final: 0.6134 (mp0) REVERT: f 52 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.8975 (tp) outliers start: 37 outliers final: 5 residues processed: 804 average time/residue: 0.6031 time to fit residues: 782.4489 Evaluate side-chains 366 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 356 time to evaluate : 4.186 ------------------------------------------------------------------------------- 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: 8.9990 chunk 157 optimal weight: 0.9980 chunk 310 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 476 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 289 optimal weight: 9.9990 chunk 354 optimal weight: 30.0000 chunk 552 optimal weight: 10.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS C 323 HIS D 415 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1153 HIS F 60 HIS a 185 GLN a 226 ASN b 20 GLN c 493 ASN c 662 HIS ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 494 HIS ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 510 GLN d 523 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 48438 Z= 0.372 Angle : 0.742 18.635 65598 Z= 0.382 Chirality : 0.046 0.231 7446 Planarity : 0.006 0.220 8664 Dihedral : 4.272 27.862 6726 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.68 % 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: -0.54 (0.11), residues: 6090 helix: 0.86 (0.11), residues: 2358 sheet: -1.55 (0.19), residues: 726 loop : -1.01 (0.11), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP d 778 HIS 0.007 0.001 HIS c 941 PHE 0.021 0.002 PHE D 70 TYR 0.023 0.002 TYR c 129 ARG 0.011 0.001 ARG D 387 *********************** 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 385 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 380 time to evaluate : 4.186 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: C 715 LEU cc_start: 0.8578 (mp) cc_final: 0.8344 (mt) REVERT: D 283 ASN cc_start: 0.8194 (m-40) cc_final: 0.7982 (m-40) REVERT: b 219 PHE cc_start: 0.6002 (m-80) cc_final: 0.5699 (m-10) REVERT: c 396 MET cc_start: 0.6800 (tmm) cc_final: 0.6352 (tmm) REVERT: d 118 LEU cc_start: 0.8635 (tp) cc_final: 0.8370 (tp) REVERT: d 155 MET cc_start: 0.8236 (mtt) cc_final: 0.7771 (mtt) REVERT: d 373 MET cc_start: 0.7440 (ttt) cc_final: 0.7203 (ttt) outliers start: 5 outliers final: 1 residues processed: 384 average time/residue: 0.5101 time to fit residues: 321.2740 Evaluate side-chains 266 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 4.090 ------------------------------------------------------------------------------- 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: 0.9990 chunk 171 optimal weight: 0.9980 chunk 459 optimal weight: 2.9990 chunk 375 optimal weight: 40.0000 chunk 152 optimal weight: 4.9990 chunk 553 optimal weight: 0.8980 chunk 597 optimal weight: 3.9990 chunk 492 optimal weight: 9.9990 chunk 548 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 443 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 HIS D 687 GLN D1139 GLN a 226 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 415 GLN ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 687 GLN d1139 GLN e 100 HIS f 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 48438 Z= 0.175 Angle : 0.567 10.638 65598 Z= 0.291 Chirality : 0.043 0.172 7446 Planarity : 0.004 0.062 8664 Dihedral : 3.986 19.145 6726 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % 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: -0.25 (0.11), residues: 6090 helix: 1.07 (0.11), residues: 2338 sheet: -1.27 (0.19), residues: 672 loop : -0.85 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP d 223 HIS 0.005 0.001 HIS D 94 PHE 0.014 0.001 PHE C 153 TYR 0.025 0.001 TYR D 849 ARG 0.018 0.000 ARG D1083 *********************** 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 362 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 4.188 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: D 256 MET cc_start: 0.7646 (ptm) cc_final: 0.7113 (ppp) REVERT: D 379 ASP cc_start: 0.7626 (t70) cc_final: 0.7423 (t70) REVERT: E 51 TYR cc_start: 0.7088 (m-80) cc_final: 0.6722 (m-80) REVERT: b 219 PHE cc_start: 0.5937 (m-80) cc_final: 0.5586 (m-10) REVERT: c 396 MET cc_start: 0.6688 (tmm) cc_final: 0.6440 (tmm) REVERT: d 865 LEU cc_start: 0.8090 (pp) cc_final: 0.7447 (pp) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.4941 time to fit residues: 302.9906 Evaluate side-chains 256 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 4.159 ------------------------------------------------------------------------------- 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: 30.0000 chunk 415 optimal weight: 0.2980 chunk 287 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 555 optimal weight: 9.9990 chunk 587 optimal weight: 0.0070 chunk 290 optimal weight: 10.0000 chunk 526 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 overall best weight: 2.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS C 443 ASN C 585 GLN C 679 ASN C1034 HIS C1055 GLN a 226 ASN c 443 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 941 HIS ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 510 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 48438 Z= 0.205 Angle : 0.575 9.978 65598 Z= 0.295 Chirality : 0.043 0.231 7446 Planarity : 0.004 0.060 8664 Dihedral : 3.986 20.291 6726 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -0.18 (0.11), residues: 6090 helix: 1.07 (0.11), residues: 2342 sheet: -1.01 (0.20), residues: 658 loop : -0.82 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 223 HIS 0.005 0.001 HIS c 941 PHE 0.027 0.001 PHE D 302 TYR 0.021 0.001 TYR d 849 ARG 0.005 0.000 ARG C 421 *********************** 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 321 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 4.261 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: C 713 MET cc_start: 0.5154 (mmt) cc_final: 0.4874 (mmt) REVERT: D 155 MET cc_start: 0.6596 (mtt) cc_final: 0.5999 (mtt) REVERT: D 256 MET cc_start: 0.7732 (ptm) cc_final: 0.6694 (ppp) REVERT: D 373 MET cc_start: 0.8748 (ppp) cc_final: 0.8417 (ppp) REVERT: D 709 VAL cc_start: 0.8422 (t) cc_final: 0.8179 (t) REVERT: d 515 MET cc_start: 0.7887 (tpp) cc_final: 0.7532 (tpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.4792 time to fit residues: 263.6712 Evaluate side-chains 248 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 4.187 ------------------------------------------------------------------------------- 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: 5.9990 chunk 333 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 437 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 chunk 501 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 300 optimal weight: 1.9990 chunk 527 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN ** a 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** d 439 HIS ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 523 GLN ** 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: 0.7267 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 48438 Z= 0.338 Angle : 0.699 8.702 65598 Z= 0.361 Chirality : 0.045 0.205 7446 Planarity : 0.005 0.088 8664 Dihedral : 4.593 22.824 6726 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % 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: -0.54 (0.11), residues: 6090 helix: 0.71 (0.10), residues: 2346 sheet: -1.31 (0.18), residues: 716 loop : -0.92 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 243 HIS 0.012 0.002 HIS C1042 PHE 0.026 0.002 PHE C 554 TYR 0.022 0.002 TYR d 344 ARG 0.009 0.001 ARG c1044 *********************** 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 296 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 4.191 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: C 1071 MET cc_start: 0.8637 (mmm) cc_final: 0.7958 (mmp) REVERT: D 256 MET cc_start: 0.8018 (ptm) cc_final: 0.7812 (ptm) REVERT: D 373 MET cc_start: 0.9035 (ppp) cc_final: 0.8615 (ppp) REVERT: E 78 TYR cc_start: 0.4584 (m-80) cc_final: 0.4277 (m-80) REVERT: d 129 ILE cc_start: 0.9408 (pt) cc_final: 0.9172 (tp) REVERT: d 155 MET cc_start: 0.7674 (mtm) cc_final: 0.6453 (mtm) REVERT: d 435 GLN cc_start: 0.8253 (pm20) cc_final: 0.7683 (pp30) REVERT: d 457 MET cc_start: 0.7971 (tpp) cc_final: 0.7752 (tpp) REVERT: d 562 SER cc_start: 0.9054 (m) cc_final: 0.8463 (t) outliers start: 2 outliers final: 2 residues processed: 296 average time/residue: 0.4836 time to fit residues: 243.3836 Evaluate side-chains 234 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 4.173 ------------------------------------------------------------------------------- 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: 4.9990 chunk 529 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 345 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 588 optimal weight: 0.9980 chunk 488 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1055 GLN D 494 HIS D 552 GLN D1239 ASN E 69 ASN F 120 ASN a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 493 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1034 HIS ** d 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 48438 Z= 0.167 Angle : 0.569 14.891 65598 Z= 0.290 Chirality : 0.043 0.308 7446 Planarity : 0.004 0.060 8664 Dihedral : 4.143 19.740 6726 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.17 (0.11), residues: 6090 helix: 1.06 (0.11), residues: 2340 sheet: -1.08 (0.19), residues: 696 loop : -0.77 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 223 HIS 0.009 0.001 HIS c 479 PHE 0.016 0.001 PHE c 153 TYR 0.017 0.001 TYR D 134 ARG 0.005 0.000 ARG f 72 *********************** 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 316 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 4.195 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: C 483 MET cc_start: 0.7257 (tmm) cc_final: 0.6646 (tmm) REVERT: C 1071 MET cc_start: 0.8499 (mmm) cc_final: 0.7898 (mmp) REVERT: D 373 MET cc_start: 0.8931 (ppp) cc_final: 0.8487 (ppp) REVERT: D 706 MET cc_start: 0.7827 (tpt) cc_final: 0.7450 (tpt) REVERT: E 78 TYR cc_start: 0.3942 (m-80) cc_final: 0.3679 (m-80) REVERT: F 59 GLU cc_start: 0.8577 (pm20) cc_final: 0.8346 (pm20) REVERT: c 396 MET cc_start: 0.6784 (tmm) cc_final: 0.6514 (tmm) REVERT: d 155 MET cc_start: 0.7916 (mtm) cc_final: 0.6535 (mtm) REVERT: d 435 GLN cc_start: 0.8115 (pm20) cc_final: 0.7508 (pp30) REVERT: d 562 SER cc_start: 0.8990 (m) cc_final: 0.8364 (t) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4813 time to fit residues: 258.4111 Evaluate side-chains 242 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 4.218 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 429 optimal weight: 9.9990 chunk 332 optimal weight: 5.9990 chunk 495 optimal weight: 3.9990 chunk 328 optimal weight: 7.9990 chunk 586 optimal weight: 0.2980 chunk 366 optimal weight: 30.0000 chunk 357 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 443 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1239 ASN a 5 GLN a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** 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** f 89 HIS f 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 48438 Z= 0.348 Angle : 0.695 11.498 65598 Z= 0.358 Chirality : 0.045 0.290 7446 Planarity : 0.005 0.061 8664 Dihedral : 4.608 21.785 6726 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -0.52 (0.11), residues: 6090 helix: 0.74 (0.11), residues: 2364 sheet: -1.39 (0.19), residues: 684 loop : -0.92 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP d 223 HIS 0.011 0.001 HIS c 479 PHE 0.023 0.002 PHE D 382 TYR 0.037 0.002 TYR C1029 ARG 0.018 0.001 ARG c 38 *********************** 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 278 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 4.409 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: C 1071 MET cc_start: 0.8516 (mmm) cc_final: 0.8085 (mmp) REVERT: D 205 MET cc_start: 0.8959 (mpp) cc_final: 0.8728 (mpp) REVERT: D 373 MET cc_start: 0.9049 (ppp) cc_final: 0.8666 (ppp) REVERT: E 78 TYR cc_start: 0.4411 (m-80) cc_final: 0.4137 (m-80) REVERT: c 396 MET cc_start: 0.6710 (tmm) cc_final: 0.6415 (tmm) REVERT: d 129 ILE cc_start: 0.9402 (pt) cc_final: 0.9133 (tp) REVERT: d 155 MET cc_start: 0.7936 (mtm) cc_final: 0.7269 (mtm) REVERT: d 562 SER cc_start: 0.9069 (m) cc_final: 0.8430 (t) REVERT: d 1212 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8679 (mmtm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4955 time to fit residues: 235.2562 Evaluate side-chains 220 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 4.230 ------------------------------------------------------------------------------- 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: 2.9990 chunk 234 optimal weight: 9.9990 chunk 349 optimal weight: 0.2980 chunk 176 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 372 optimal weight: 20.0000 chunk 399 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 730 ASN ** 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** ** d 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1227 GLN e 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5495 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= 0.214 Angle : 0.591 11.740 65598 Z= 0.303 Chirality : 0.043 0.248 7446 Planarity : 0.004 0.045 8664 Dihedral : 4.376 19.818 6726 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -0.33 (0.11), residues: 6090 helix: 0.95 (0.11), residues: 2374 sheet: -1.30 (0.19), residues: 698 loop : -0.85 (0.11), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 70 HIS 0.006 0.001 HIS C 479 PHE 0.016 0.001 PHE d 70 TYR 0.025 0.002 TYR f 57 ARG 0.005 0.000 ARG D1083 *********************** 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 287 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 4.306 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: C 483 MET cc_start: 0.7397 (tmm) cc_final: 0.6746 (tmm) REVERT: C 593 MET cc_start: 0.7979 (mmm) cc_final: 0.7289 (mmm) REVERT: D 256 MET cc_start: 0.7980 (ptp) cc_final: 0.7778 (mtp) REVERT: D 373 MET cc_start: 0.8900 (ppp) cc_final: 0.8404 (ppp) REVERT: D 983 MET cc_start: 0.7699 (tpp) cc_final: 0.7131 (tpt) REVERT: c 396 MET cc_start: 0.6815 (tmm) cc_final: 0.6572 (tmm) REVERT: d 129 ILE cc_start: 0.9349 (pt) cc_final: 0.9078 (tp) REVERT: d 155 MET cc_start: 0.7975 (mtm) cc_final: 0.7468 (mtm) REVERT: d 435 GLN cc_start: 0.7862 (pm20) cc_final: 0.7591 (pp30) REVERT: d 562 SER cc_start: 0.9013 (m) cc_final: 0.8353 (t) REVERT: d 714 ASP cc_start: 0.6123 (t70) cc_final: 0.5776 (t70) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.5176 time to fit residues: 253.8499 Evaluate side-chains 221 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 4.182 ------------------------------------------------------------------------------- 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: 0.9980 chunk 561 optimal weight: 3.9990 chunk 512 optimal weight: 3.9990 chunk 546 optimal weight: 20.0000 chunk 328 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 428 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 493 optimal weight: 0.9980 chunk 516 optimal weight: 0.1980 chunk 544 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 440 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 48438 Z= 0.166 Angle : 0.583 10.219 65598 Z= 0.296 Chirality : 0.043 0.229 7446 Planarity : 0.004 0.051 8664 Dihedral : 4.168 19.742 6726 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.09 (0.11), residues: 6090 helix: 1.18 (0.11), residues: 2334 sheet: -1.15 (0.19), residues: 708 loop : -0.72 (0.12), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 70 HIS 0.008 0.001 HIS C 680 PHE 0.019 0.001 PHE d 302 TYR 0.021 0.001 TYR C1029 ARG 0.005 0.000 ARG c 181 *********************** 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 290 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 4.283 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: C 483 MET cc_start: 0.7352 (tmm) cc_final: 0.6710 (tmm) REVERT: C 593 MET cc_start: 0.7715 (mmm) cc_final: 0.7311 (mmm) REVERT: D 256 MET cc_start: 0.8017 (ptp) cc_final: 0.7656 (mtm) REVERT: D 312 MET cc_start: 0.7295 (mtp) cc_final: 0.7035 (mmm) REVERT: D 373 MET cc_start: 0.8897 (ppp) cc_final: 0.8374 (ppp) REVERT: D 983 MET cc_start: 0.7673 (tpp) cc_final: 0.7018 (tpt) REVERT: c 396 MET cc_start: 0.6771 (tmm) cc_final: 0.6548 (tmm) REVERT: c 607 MET cc_start: 0.7443 (mmm) cc_final: 0.6641 (mmm) REVERT: d 129 ILE cc_start: 0.9315 (pt) cc_final: 0.9042 (tp) REVERT: d 155 MET cc_start: 0.7891 (mtm) cc_final: 0.7535 (mtm) REVERT: d 865 LEU cc_start: 0.8273 (pp) cc_final: 0.7486 (pp) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.5203 time to fit residues: 259.4440 Evaluate side-chains 222 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 4.221 ------------------------------------------------------------------------------- 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: 0.0980 chunk 577 optimal weight: 2.9990 chunk 352 optimal weight: 0.0170 chunk 273 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 chunk 605 optimal weight: 6.9990 chunk 557 optimal weight: 10.0000 chunk 482 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 372 optimal weight: 6.9990 chunk 295 optimal weight: 8.9990 overall best weight: 3.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 443 ASN ** c 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 48438 Z= 0.266 Angle : 0.629 10.250 65598 Z= 0.322 Chirality : 0.043 0.247 7446 Planarity : 0.004 0.060 8664 Dihedral : 4.353 20.987 6726 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.11), residues: 6090 helix: 1.05 (0.11), residues: 2350 sheet: -1.16 (0.19), residues: 674 loop : -0.81 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP d 223 HIS 0.007 0.001 HIS C 680 PHE 0.020 0.002 PHE C 134 TYR 0.034 0.002 TYR D 241 ARG 0.012 0.000 ARG f 72 ********************** 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 263 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 4.307 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: C 483 MET cc_start: 0.7469 (tmm) cc_final: 0.6542 (tmm) REVERT: C 593 MET cc_start: 0.7909 (mmm) cc_final: 0.7445 (mmm) REVERT: D 256 MET cc_start: 0.8053 (ptp) cc_final: 0.6978 (ptp) REVERT: D 310 MET cc_start: 0.7503 (ppp) cc_final: 0.7246 (ppp) REVERT: D 373 MET cc_start: 0.8992 (ppp) cc_final: 0.8552 (ppp) REVERT: E 66 ASP cc_start: 0.5797 (t70) cc_final: 0.5434 (t0) REVERT: c 396 MET cc_start: 0.6862 (tmm) cc_final: 0.6639 (tmm) REVERT: d 92 MET cc_start: 0.7677 (mmm) cc_final: 0.7427 (mmm) REVERT: d 129 ILE cc_start: 0.9386 (pt) cc_final: 0.9097 (tp) REVERT: d 155 MET cc_start: 0.7952 (mtm) cc_final: 0.7518 (mtm) REVERT: d 865 LEU cc_start: 0.8265 (pp) cc_final: 0.7492 (pp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.4985 time to fit residues: 226.7863 Evaluate side-chains 216 residues out of total 5148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 4.214 ------------------------------------------------------------------------------- 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: 9.9990 chunk 513 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 chunk 444 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 0.0370 chunk 483 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 496 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 overall best weight: 2.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 ASN ** a 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 ASN c 443 ASN ** c 730 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.048605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035346 restraints weight = 419637.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036330 restraints weight = 259466.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.036989 restraints weight = 187947.200| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48438 Z= 0.194 Angle : 0.589 9.803 65598 Z= 0.300 Chirality : 0.043 0.228 7446 Planarity : 0.004 0.074 8664 Dihedral : 4.239 21.410 6726 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.11 (0.11), residues: 6090 helix: 1.12 (0.11), residues: 2348 sheet: -1.10 (0.20), residues: 674 loop : -0.73 (0.12), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP d 223 HIS 0.005 0.001 HIS C 680 PHE 0.017 0.001 PHE D 382 TYR 0.020 0.001 TYR C1029 ARG 0.005 0.000 ARG f 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7338.24 seconds wall clock time: 129 minutes 40.31 seconds (7780.31 seconds total)