Starting phenix.real_space_refine (version: dev) on Mon Feb 27 09:08:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/02_2023/6ee8_9039_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/02_2023/6ee8_9039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/02_2023/6ee8_9039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/02_2023/6ee8_9039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/02_2023/6ee8_9039_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/02_2023/6ee8_9039_neut.pdb" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.065 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 Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 760": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 866": "NH1" <-> "NH2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29784 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1228 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain breaks: 1 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} 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 19125 SG CYS D 891 109.432 60.877 82.960 1.00169.12 S ATOM 19692 SG CYS D 968 106.034 61.770 84.984 1.00174.51 S ATOM 19734 SG CYS D 975 106.982 63.228 81.798 1.00161.34 S ATOM 19752 SG CYS D 978 106.509 59.787 80.902 1.00164.55 S ATOM 12567 SG CYS D 60 80.575 107.049 123.762 1.00178.81 S ATOM 12585 SG CYS D 62 79.844 107.368 127.301 1.00173.66 S ATOM 12720 SG CYS D 78 82.010 104.201 126.479 1.00175.82 S Time building chain proxies: 17.41, per 1000 atoms: 0.58 Number of scatterers: 29784 At special positions: 0 Unit cell: (135.2, 180.7, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 125 15.00 Mg 1 11.99 O 5964 8.00 N 5323 7.00 C 18270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.64 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 44 sheets defined 42.7% alpha, 15.1% beta 56 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 8.83 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.785A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.910A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.318A 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 203 through 224 removed outlier: 3.540A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.443A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.570A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.720A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.954A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.511A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.644A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.558A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 922 through 926 removed outlier: 3.540A pdb=" N MET C 926 " --> pdb=" O PRO C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.627A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.285A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.600A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.388A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 186 removed outlier: 5.485A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.700A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.727A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.299A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.080A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.321A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 419 removed outlier: 3.584A pdb=" N GLY D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.553A 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 469 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.044A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (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 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 removed outlier: 4.100A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.592A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.859A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.517A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.579A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.921A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.102A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.757A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.667A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.529A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.661A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 4.184A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.595A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.512A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 223 removed outlier: 4.249A pdb=" N GLU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.185A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.626A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.820A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.885A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 84 through 99 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 158 removed outlier: 3.742A pdb=" N GLU M 156 " --> pdb=" O THR M 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.075A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.934A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 13 removed outlier: 3.573A pdb=" N SER B 19 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.652A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.206A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.966A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 189 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.130A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.756A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 700 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 668 removed outlier: 6.840A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.896A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.623A pdb=" N GLY C 765 " --> pdb=" O THR C 762 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.582A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.532A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.605A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.942A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.195A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 236 removed outlier: 4.054A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.219A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.636A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.163A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 3.964A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1182 removed outlier: 6.540A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.913A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 14.55 Time building geometry restraints manager: 13.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8051 1.33 - 1.45: 5583 1.45 - 1.57: 16486 1.57 - 1.69: 247 1.69 - 1.81: 175 Bond restraints: 30542 Sorted by residual: bond pdb=" C ARG C 421 " pdb=" N PRO C 422 " ideal model delta sigma weight residual 1.336 1.396 -0.061 1.23e-02 6.61e+03 2.42e+01 bond pdb=" CA ILE C 773 " pdb=" C ILE C 773 " ideal model delta sigma weight residual 1.524 1.480 0.045 1.05e-02 9.07e+03 1.80e+01 bond pdb=" C VAL C 922 " pdb=" N PRO C 923 " ideal model delta sigma weight residual 1.336 1.378 -0.043 1.23e-02 6.61e+03 1.21e+01 bond pdb=" CA ALA A 222 " pdb=" C ALA A 222 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.15e+01 bond pdb=" CA ALA C 634 " pdb=" C ALA C 634 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.35e-02 5.49e+03 1.10e+01 ... (remaining 30537 not shown) Histogram of bond angle deviations from ideal: 97.20 - 106.38: 1660 106.38 - 115.57: 19026 115.57 - 124.75: 20319 124.75 - 133.94: 894 133.94 - 143.13: 7 Bond angle restraints: 41906 Sorted by residual: angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.99 103.99 16.00 1.08e+00 8.57e-01 2.20e+02 angle pdb=" N LEU A 225 " pdb=" CA LEU A 225 " pdb=" C LEU A 225 " ideal model delta sigma weight residual 113.37 99.17 14.20 1.38e+00 5.25e-01 1.06e+02 angle pdb=" C ILE C 773 " pdb=" N PRO C 774 " pdb=" CA PRO C 774 " ideal model delta sigma weight residual 119.84 129.19 -9.35 1.25e+00 6.40e-01 5.59e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 142.39 -15.39 2.40e+00 1.74e-01 4.11e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 106.71 13.89 2.20e+00 2.07e-01 3.98e+01 ... (remaining 41901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 17495 35.43 - 70.86: 712 70.86 - 106.29: 11 106.29 - 141.72: 0 141.72 - 177.15: 5 Dihedral angle restraints: 18223 sinusoidal: 8175 harmonic: 10048 Sorted by residual: dihedral pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual 122.80 138.78 -15.98 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C GLU A 224 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual -122.60 -137.99 15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" CA VAL D 4 " pdb=" C VAL D 4 " pdb=" N ASN D 5 " pdb=" CA ASN D 5 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 18220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4704 0.150 - 0.300: 65 0.300 - 0.450: 3 0.450 - 0.600: 1 0.600 - 0.750: 2 Chirality restraints: 4775 Sorted by residual: chirality pdb=" CA GLU A 224 " pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CB GLU A 224 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CG LEU A 221 " pdb=" CB LEU A 221 " pdb=" CD1 LEU A 221 " pdb=" CD2 LEU A 221 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ARG A 223 " pdb=" N ARG A 223 " pdb=" C ARG A 223 " pdb=" CB ARG A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 4772 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG M 75 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C ARG M 75 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG M 75 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA M 76 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 56 " -0.031 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR E 56 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR E 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR E 56 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 56 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 21 " 0.039 2.00e-02 2.50e+03 1.65e-02 8.19e+00 pdb=" N9 DG O 21 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 21 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DG O 21 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG O 21 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG O 21 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG O 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG O 21 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG O 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG O 21 " -0.004 2.00e-02 2.50e+03 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 571 2.65 - 3.21: 26564 3.21 - 3.77: 50049 3.77 - 4.34: 63859 4.34 - 4.90: 99898 Nonbonded interactions: 240941 Sorted by model distance: nonbonded pdb=" NH2 ARG F 502 " pdb=" OP2 DT O 23 " model vdw 2.082 2.520 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.099 2.170 nonbonded pdb=" O GLY D 408 " pdb=" NH1 ARG D 414 " model vdw 2.120 2.520 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.126 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.129 2.170 ... (remaining 240936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18270 2.51 5 N 5323 2.21 5 O 5964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.750 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: 0.020 Extract box with map and model: 6.260 Check model and map are aligned: 0.470 Process input model: 91.030 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.300 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.007 0.074 30542 Z= 0.431 Angle : 1.044 18.126 41906 Z= 0.608 Chirality : 0.058 0.750 4775 Planarity : 0.007 0.060 5070 Dihedral : 15.738 177.146 11759 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.38 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -3.18 (0.12), residues: 3488 helix: -1.64 (0.11), residues: 1366 sheet: -2.12 (0.25), residues: 349 loop : -2.50 (0.13), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 3.504 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 outliers start: 19 outliers final: 7 residues processed: 237 average time/residue: 0.4767 time to fit residues: 175.4158 Evaluate side-chains 121 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 3.424 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4975 time to fit residues: 9.9406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 325 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 61 HIS B 124 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 81 ASN C 141 ASN C 143 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 388 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN C 729 HIS C 875 GLN C 920 HIS C1062 GLN C1066 GLN D 239 ASN D 307 ASN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 564 ASN D 687 GLN D 693 GLN D 771 ASN D 797 ASN D1139 GLN D1145 GLN D1190 ASN E 65 ASN E 69 ASN E 88 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS M 14 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 30542 Z= 0.244 Angle : 0.656 13.144 41906 Z= 0.349 Chirality : 0.042 0.161 4775 Planarity : 0.005 0.054 5070 Dihedral : 19.068 175.316 5096 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -1.60 (0.14), residues: 3488 helix: 0.11 (0.13), residues: 1396 sheet: -1.46 (0.28), residues: 323 loop : -1.99 (0.14), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 3.783 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 outliers start: 48 outliers final: 11 residues processed: 169 average time/residue: 0.4149 time to fit residues: 117.2289 Evaluate side-chains 120 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 3.541 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2581 time to fit residues: 10.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 351 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 261 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN ** M 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 30542 Z= 0.277 Angle : 0.651 11.792 41906 Z= 0.341 Chirality : 0.042 0.223 4775 Planarity : 0.005 0.055 5070 Dihedral : 18.925 175.719 5096 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -1.03 (0.14), residues: 3488 helix: 0.71 (0.14), residues: 1409 sheet: -1.33 (0.27), residues: 340 loop : -1.77 (0.14), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 3.787 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 outliers start: 45 outliers final: 22 residues processed: 153 average time/residue: 0.4406 time to fit residues: 112.6456 Evaluate side-chains 129 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 3.532 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3337 time to fit residues: 17.6898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 346 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 151 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 30542 Z= 0.310 Angle : 0.661 10.690 41906 Z= 0.345 Chirality : 0.042 0.225 4775 Planarity : 0.004 0.056 5070 Dihedral : 18.852 175.972 5096 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.76 (0.14), residues: 3488 helix: 1.00 (0.14), residues: 1411 sheet: -1.35 (0.27), residues: 352 loop : -1.65 (0.15), residues: 1725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 112 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 142 average time/residue: 0.4121 time to fit residues: 100.1993 Evaluate side-chains 115 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 3.527 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2685 time to fit residues: 11.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 257 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30542 Z= 0.201 Angle : 0.608 10.146 41906 Z= 0.312 Chirality : 0.041 0.222 4775 Planarity : 0.004 0.051 5070 Dihedral : 18.723 175.681 5096 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3488 helix: 1.36 (0.14), residues: 1405 sheet: -0.85 (0.29), residues: 315 loop : -1.53 (0.15), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 3.579 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 outliers start: 29 outliers final: 14 residues processed: 141 average time/residue: 0.4196 time to fit residues: 100.8541 Evaluate side-chains 122 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 3.933 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2949 time to fit residues: 12.9497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 85 optimal weight: 0.0020 chunk 346 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 160 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 181 optimal weight: 20.0000 overall best weight: 2.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 325 ASN F 516 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30542 Z= 0.209 Angle : 0.614 12.907 41906 Z= 0.313 Chirality : 0.041 0.193 4775 Planarity : 0.004 0.058 5070 Dihedral : 18.655 175.643 5096 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.23 (0.15), residues: 3488 helix: 1.52 (0.14), residues: 1404 sheet: -0.85 (0.29), residues: 327 loop : -1.47 (0.15), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 3.903 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 outliers start: 25 outliers final: 9 residues processed: 134 average time/residue: 0.4600 time to fit residues: 104.4079 Evaluate side-chains 115 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 3.957 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3722 time to fit residues: 10.3660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 291 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 345 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 30542 Z= 0.291 Angle : 0.652 11.033 41906 Z= 0.335 Chirality : 0.042 0.230 4775 Planarity : 0.004 0.063 5070 Dihedral : 18.667 176.317 5096 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.22 (0.15), residues: 3488 helix: 1.50 (0.14), residues: 1409 sheet: -0.92 (0.27), residues: 358 loop : -1.42 (0.15), residues: 1721 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 127 average time/residue: 0.4688 time to fit residues: 99.8676 Evaluate side-chains 114 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 3.606 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3114 time to fit residues: 10.2596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 HIS D 416 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 30542 Z= 0.259 Angle : 0.647 11.503 41906 Z= 0.328 Chirality : 0.041 0.170 4775 Planarity : 0.004 0.060 5070 Dihedral : 18.659 176.384 5096 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.07 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.14 (0.15), residues: 3488 helix: 1.54 (0.14), residues: 1407 sheet: -0.72 (0.29), residues: 325 loop : -1.38 (0.15), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 3.612 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 outliers start: 12 outliers final: 4 residues processed: 118 average time/residue: 0.4310 time to fit residues: 86.7063 Evaluate side-chains 108 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 3.828 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4660 time to fit residues: 7.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 0.9980 chunk 330 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 321 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 304 optimal weight: 7.9990 chunk 320 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 30542 Z= 0.215 Angle : 0.628 10.825 41906 Z= 0.319 Chirality : 0.041 0.198 4775 Planarity : 0.004 0.058 5070 Dihedral : 18.641 176.296 5096 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.05 (0.15), residues: 3488 helix: 1.61 (0.14), residues: 1405 sheet: -0.63 (0.29), residues: 329 loop : -1.33 (0.15), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 121 average time/residue: 0.4613 time to fit residues: 92.5200 Evaluate side-chains 110 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3137 time to fit residues: 7.3875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS C 352 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 30542 Z= 0.437 Angle : 0.768 14.132 41906 Z= 0.395 Chirality : 0.043 0.197 4775 Planarity : 0.005 0.080 5070 Dihedral : 18.760 178.140 5096 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.02 % Favored : 92.95 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.45 (0.14), residues: 3488 helix: 1.17 (0.14), residues: 1414 sheet: -0.93 (0.28), residues: 356 loop : -1.44 (0.15), residues: 1718 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 114 average time/residue: 0.4517 time to fit residues: 86.5451 Evaluate side-chains 106 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5729 time to fit residues: 7.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.5980 chunk 302 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 292 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.035795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.026426 restraints weight = 259139.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.027265 restraints weight = 142378.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027830 restraints weight = 95403.157| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 30542 Z= 0.276 Angle : 0.677 13.026 41906 Z= 0.345 Chirality : 0.042 0.238 4775 Planarity : 0.004 0.065 5070 Dihedral : 18.750 177.604 5096 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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 (0.14), residues: 3488 helix: 1.36 (0.14), residues: 1414 sheet: -0.68 (0.29), residues: 327 loop : -1.40 (0.15), residues: 1747 =============================================================================== Job complete usr+sys time: 4124.96 seconds wall clock time: 77 minutes 54.65 seconds (4674.65 seconds total)