Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 04:44:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/10_2023/6flq_4275_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/10_2023/6flq_4275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/10_2023/6flq_4275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/10_2023/6flq_4275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/10_2023/6flq_4275_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flq_4275/10_2023/6flq_4275_neut.pdb" } resolution = 3.6 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= 0.006 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18528 2.51 5 N 5429 2.21 5 O 6046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 905": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D ARG 1194": "NH1" <-> "NH2" Residue "D ARG 1284": "NH1" <-> "NH2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 30201 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2168 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2068 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 10573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10573 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 56, 'TRANS': 1282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10357 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 830 Chain: "N" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "R" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'RNA': 21} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain breaks: 1 Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 785 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} 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 15258 SG CYS D 70 108.278 118.706 60.781 1.00110.77 S ATOM 15272 SG CYS D 72 109.338 122.046 60.037 1.00121.27 S ATOM 15404 SG CYS D 88 111.698 119.835 57.627 1.00115.73 S ATOM 21092 SG CYS D 814 110.727 50.721 49.288 1.00 60.52 S ATOM 21657 SG CYS D 888 113.353 53.592 50.117 1.00 50.19 S ATOM 21708 SG CYS D 895 111.072 52.145 52.491 1.00 40.57 S Time building chain proxies: 16.40, per 1000 atoms: 0.54 Number of scatterers: 30201 At special positions: 0 Unit cell: (210.1, 160.6, 154, 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 105 16.00 P 90 15.00 Mg 1 11.99 O 6046 8.00 N 5429 7.00 C 18528 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: 12.84 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 52 sheets defined 38.7% alpha, 13.5% beta 37 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 10.66 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.119A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.897A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.741A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.643A pdb=" N VAL A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.620A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.656A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.760A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.536A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.986A pdb=" N ALA B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.844A pdb=" N ARG B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.621A pdb=" N THR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.523A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.857A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.036A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.588A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.831A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.641A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.579A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.641A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.524A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.804A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 4.473A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 508 removed outlier: 4.147A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.605A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.851A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.610A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 686 removed outlier: 3.819A pdb=" N GLN C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.623A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.767A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 952 " --> pdb=" O ILE C 948 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1000 removed outlier: 3.555A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 removed outlier: 3.714A pdb=" N LEU C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.082A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 removed outlier: 3.746A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1175 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.619A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.722A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1279 removed outlier: 3.743A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1291 removed outlier: 3.801A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1300 through 1309 removed outlier: 4.028A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.931A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 140 removed outlier: 4.559A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.608A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.906A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.643A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.596A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.889A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.631A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.700A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 4.027A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.362A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.871A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.784A pdb=" N GLN D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 513 removed outlier: 3.878A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 539 removed outlier: 3.903A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.676A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.709A pdb=" N ILE D 611 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.792A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 668 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.628A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.591A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 4.243A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 removed outlier: 3.878A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 4.039A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.736A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.772A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.807A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.645A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1258 removed outlier: 3.626A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1259 through 1261 No H-bonds generated for 'chain 'D' and resid 1259 through 1261' Processing helix chain 'D' and resid 1280 through 1293 removed outlier: 3.598A pdb=" N GLU D1293 " --> pdb=" O ASN D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1338 removed outlier: 3.942A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.515A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 32 removed outlier: 4.137A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.518A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.708A pdb=" N ALA F 7 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 37 Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.752A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 103 through 132 Processing helix chain 'F' and resid 201 through 213 removed outlier: 3.934A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 removed outlier: 4.233A pdb=" N GLY F 217 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 213 through 218' Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.609A pdb=" N GLY F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 258 through 267 removed outlier: 3.536A pdb=" N THR F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 287 Processing helix chain 'F' and resid 310 through 319 removed outlier: 4.217A pdb=" N GLN F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 319 " --> pdb=" O ALA F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 341 through 364 Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.670A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 removed outlier: 3.940A pdb=" N GLU F 391 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 426 Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'F' and resid 463 through 468 Processing helix chain 'F' and resid 474 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.688A pdb=" N ARG A 12 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.847A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.598A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.658A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.677A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.781A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.646A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.922A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.712A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.802A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.021A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.209A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 529 through 531 removed outlier: 3.554A pdb=" N ASN C 573 " --> pdb=" O ILE C 530 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.252A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 634 through 637 Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.744A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.501A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.706A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.706A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.413A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.659A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.922A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.652A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.767A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD9, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.560A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.641A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 548 through 559 removed outlier: 6.233A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.901A pdb=" N VAL D 894 " --> pdb=" O THR D 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 Processing sheet with id=AE7, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.570A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 3.979A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AF1, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AF2, first strand: chain 'D' and resid 1172 through 1176 Processing sheet with id=AF3, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 6.967A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 45 through 49 removed outlier: 3.798A pdb=" N GLN F 96 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 178 through 182 removed outlier: 6.918A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL F 145 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASN F 149 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL F 197 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL F 161 " --> pdb=" O VAL F 197 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 221 through 229 removed outlier: 5.289A pdb=" N ILE F 223 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS F 239 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 295 through 299 removed outlier: 4.257A pdb=" N SER F 295 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 308 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F 304 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 307 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET F 339 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL F 309 " --> pdb=" O MET F 339 " (cutoff:3.500A) 1122 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 15.19 Time building geometry restraints manager: 13.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 518 1.23 - 1.37: 11090 1.37 - 1.52: 14450 1.52 - 1.67: 4546 1.67 - 1.82: 182 Bond restraints: 30786 Sorted by residual: bond pdb=" C ASP C1084 " pdb=" N MET C1085 " ideal model delta sigma weight residual 1.329 1.078 0.251 1.60e-02 3.91e+03 2.45e+02 bond pdb=" CA VAL D 470 " pdb=" C VAL D 470 " ideal model delta sigma weight residual 1.522 1.495 0.028 7.10e-03 1.98e+04 1.52e+01 bond pdb=" CA LYS A 145 " pdb=" CB LYS A 145 " ideal model delta sigma weight residual 1.527 1.460 0.067 1.75e-02 3.27e+03 1.47e+01 bond pdb=" CA PRO D 246 " pdb=" C PRO D 246 " ideal model delta sigma weight residual 1.517 1.552 -0.035 9.30e-03 1.16e+04 1.43e+01 bond pdb=" CB TRP D 115 " pdb=" CG TRP D 115 " ideal model delta sigma weight residual 1.498 1.395 0.103 3.10e-02 1.04e+03 1.10e+01 ... (remaining 30781 not shown) Histogram of bond angle deviations from ideal: 93.94 - 103.50: 623 103.50 - 113.07: 17177 113.07 - 122.63: 20653 122.63 - 132.19: 3624 132.19 - 141.75: 37 Bond angle restraints: 42114 Sorted by residual: angle pdb=" N ILE D 135 " pdb=" CA ILE D 135 " pdb=" C ILE D 135 " ideal model delta sigma weight residual 112.96 104.36 8.60 1.00e+00 1.00e+00 7.39e+01 angle pdb=" C ASP C1084 " pdb=" N MET C1085 " pdb=" CA MET C1085 " ideal model delta sigma weight residual 120.49 130.59 -10.10 1.42e+00 4.96e-01 5.06e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 132.35 -10.65 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 132.03 -10.33 1.80e+00 3.09e-01 3.29e+01 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.59 141.75 -20.16 3.54e+00 7.98e-02 3.24e+01 ... (remaining 42109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 17876 31.01 - 62.02: 620 62.02 - 93.03: 29 93.03 - 124.04: 1 124.04 - 155.05: 3 Dihedral angle restraints: 18529 sinusoidal: 7415 harmonic: 11114 Sorted by residual: dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual 180.00 -94.66 -85.34 0 5.00e+00 4.00e-02 2.91e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta harmonic sigma weight residual 180.00 -122.17 -57.83 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ILE C 198 " pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta harmonic sigma weight residual -180.00 -126.94 -53.06 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 18526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3519 0.074 - 0.149: 1178 0.149 - 0.223: 192 0.223 - 0.297: 32 0.297 - 0.372: 10 Chirality restraints: 4931 Sorted by residual: chirality pdb=" CB THR D 514 " pdb=" CA THR D 514 " pdb=" OG1 THR D 514 " pdb=" CG2 THR D 514 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB VAL C 802 " pdb=" CA VAL C 802 " pdb=" CG1 VAL C 802 " pdb=" CG2 VAL C 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB VAL D1255 " pdb=" CA VAL D1255 " pdb=" CG1 VAL D1255 " pdb=" CG2 VAL D1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4928 not shown) Planarity restraints: 5260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 30 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.064 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO C 520 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " -0.022 2.00e-02 2.50e+03 2.62e-02 1.37e+01 pdb=" CG TYR C1229 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.004 2.00e-02 2.50e+03 ... (remaining 5257 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 133 2.50 - 3.10: 20454 3.10 - 3.70: 43657 3.70 - 4.30: 58208 4.30 - 4.90: 97171 Nonbonded interactions: 219623 Sorted by model distance: nonbonded pdb=" OD2 ASP C 393 " pdb=" NH1 ARG C 394 " model vdw 1.897 2.520 nonbonded pdb=" OD2 ASP D 129 " pdb=" NH1 ARG D 220 " model vdw 1.976 2.520 nonbonded pdb=" NH1 ARG D1341 " pdb=" OE2 GLU D1343 " model vdw 1.980 2.520 nonbonded pdb=" NH1 ARG A 33 " pdb=" OD2 ASP A 199 " model vdw 2.024 2.520 nonbonded pdb=" OH TYR D 68 " pdb=" NH1 ARG D 81 " model vdw 2.046 2.520 ... (remaining 219618 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 6 through 158 or resid 171 through 329)) selection = chain 'B' } 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: 1.150 Set stop_for_unknowns flag: 0.010 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: 6.630 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 94.620 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0214 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 : 0.016 0.251 30786 Z= 1.018 Angle : 1.332 20.164 42114 Z= 0.726 Chirality : 0.074 0.372 4931 Planarity : 0.009 0.103 5260 Dihedral : 14.726 155.052 11357 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.79 % Favored : 89.08 % Rotamer: Outliers : 1.40 % Allowed : 6.10 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.32 % 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: -4.32 (0.11), residues: 3846 helix: -2.70 (0.10), residues: 1360 sheet: -2.43 (0.20), residues: 492 loop : -3.15 (0.11), residues: 1994 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 296 time to evaluate : 3.120 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: 38 outliers final: 11 residues processed: 329 average time/residue: 0.4545 time to fit residues: 234.3479 Evaluate side-chains 208 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 3.334 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2723 time to fit residues: 10.6276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 8.9990 chunk 297 optimal weight: 0.0570 chunk 165 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 356 optimal weight: 30.0000 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 84 ASN B 147 GLN C 273 HIS C 387 ASN C 513 GLN C 526 HIS C 551 HIS C 628 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN C1116 HIS C1146 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 113 HIS D 232 ASN D 365 GLN D 424 ASN D 665 GLN ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN D1098 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN E 29 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0859 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30786 Z= 0.260 Angle : 0.729 9.984 42114 Z= 0.384 Chirality : 0.046 0.207 4931 Planarity : 0.007 0.095 5260 Dihedral : 15.381 151.121 5106 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 2.06 % Allowed : 9.71 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.08 % 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: -2.88 (0.12), residues: 3846 helix: -0.89 (0.13), residues: 1362 sheet: -2.06 (0.21), residues: 479 loop : -2.67 (0.12), residues: 2005 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 21 residues processed: 277 average time/residue: 0.4255 time to fit residues: 189.8719 Evaluate side-chains 211 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 3.069 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2653 time to fit residues: 15.0957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 450 ASN C 462 ASN C 513 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C 760 ASN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1220 GLN C1256 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 469 HIS D 594 GLN ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1327 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30786 Z= 0.273 Angle : 0.768 19.358 42114 Z= 0.399 Chirality : 0.047 0.211 4931 Planarity : 0.006 0.083 5260 Dihedral : 15.403 155.486 5106 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.32 % Favored : 91.63 % Rotamer: Outliers : 2.98 % Allowed : 12.43 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.90 % Twisted General : 0.05 % 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: -2.46 (0.13), residues: 3846 helix: -0.35 (0.14), residues: 1387 sheet: -1.75 (0.22), residues: 490 loop : -2.63 (0.12), residues: 1969 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 217 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 43 residues processed: 286 average time/residue: 0.4482 time to fit residues: 203.0814 Evaluate side-chains 247 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2881 time to fit residues: 27.0036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 30.0000 chunk 268 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 358 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 340 optimal weight: 0.0270 chunk 102 optimal weight: 4.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS C 36 GLN C 447 HIS C 462 ASN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN C1220 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D1244 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1519 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 30786 Z= 0.238 Angle : 0.692 9.898 42114 Z= 0.362 Chirality : 0.045 0.194 4931 Planarity : 0.006 0.088 5260 Dihedral : 15.173 156.578 5106 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 2.94 % Allowed : 14.49 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 3.25 % Twisted General : 0.05 % 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: -2.12 (0.13), residues: 3846 helix: -0.03 (0.14), residues: 1388 sheet: -1.37 (0.22), residues: 495 loop : -2.53 (0.13), residues: 1963 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 205 time to evaluate : 3.141 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 40 residues processed: 273 average time/residue: 0.4542 time to fit residues: 196.6754 Evaluate side-chains 226 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 3.303 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3286 time to fit residues: 29.2501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 10.0000 chunk 215 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 30.0000 chunk 324 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 0.7980 chunk 340 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 overall best weight: 2.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 673 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1279 GLN D1326 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1780 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30786 Z= 0.274 Angle : 0.784 18.579 42114 Z= 0.406 Chirality : 0.047 0.213 4931 Planarity : 0.006 0.087 5260 Dihedral : 15.332 162.445 5106 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.13 % Favored : 90.82 % Rotamer: Outliers : 3.09 % Allowed : 16.36 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.95 % Twisted General : 0.11 % 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: -2.09 (0.13), residues: 3846 helix: 0.02 (0.14), residues: 1382 sheet: -1.24 (0.22), residues: 488 loop : -2.56 (0.13), residues: 1976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 197 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 48 residues processed: 270 average time/residue: 0.4424 time to fit residues: 190.1108 Evaluate side-chains 232 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2821 time to fit residues: 29.6847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 380 optimal weight: 50.0000 chunk 315 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 31 optimal weight: 0.0870 chunk 125 optimal weight: 0.5980 chunk 199 optimal weight: 9.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 628 HIS ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1307 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 594 GLN D 792 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1773 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30786 Z= 0.223 Angle : 0.677 12.527 42114 Z= 0.352 Chirality : 0.044 0.205 4931 Planarity : 0.005 0.082 5260 Dihedral : 15.098 157.998 5106 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.77 % Favored : 92.17 % Rotamer: Outliers : 1.65 % Allowed : 17.50 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.89 (0.13), residues: 3846 helix: 0.25 (0.14), residues: 1402 sheet: -1.21 (0.22), residues: 514 loop : -2.50 (0.13), residues: 1930 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 3.033 Fit side-chains outliers start: 45 outliers final: 23 residues processed: 230 average time/residue: 0.4597 time to fit residues: 169.5268 Evaluate side-chains 210 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3078 time to fit residues: 17.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 230 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1835 moved from start: 0.8532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30786 Z= 0.218 Angle : 0.677 13.729 42114 Z= 0.352 Chirality : 0.044 0.203 4931 Planarity : 0.005 0.072 5260 Dihedral : 15.104 159.432 5106 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.92 % Favored : 91.03 % Rotamer: Outliers : 1.07 % Allowed : 19.12 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.77 (0.13), residues: 3846 helix: 0.39 (0.14), residues: 1392 sheet: -1.19 (0.21), residues: 505 loop : -2.43 (0.13), residues: 1949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 3.233 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 220 average time/residue: 0.4654 time to fit residues: 165.1758 Evaluate side-chains 201 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2606 time to fit residues: 11.5924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 297 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1653 moved from start: 0.8529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30786 Z= 0.149 Angle : 0.583 11.176 42114 Z= 0.304 Chirality : 0.042 0.195 4931 Planarity : 0.004 0.069 5260 Dihedral : 14.745 153.263 5106 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 0.37 % Allowed : 20.18 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.47 (0.13), residues: 3846 helix: 0.74 (0.15), residues: 1395 sheet: -1.12 (0.22), residues: 508 loop : -2.32 (0.13), residues: 1943 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 3.142 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 195 average time/residue: 0.4683 time to fit residues: 146.0542 Evaluate side-chains 191 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 3.034 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3409 time to fit residues: 8.6836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 40.0000 chunk 362 optimal weight: 50.0000 chunk 331 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 212 optimal weight: 0.0980 chunk 153 optimal weight: 0.0000 chunk 277 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 333 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 450 ASN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1688 moved from start: 0.8717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30786 Z= 0.153 Angle : 0.590 13.545 42114 Z= 0.306 Chirality : 0.042 0.193 4931 Planarity : 0.004 0.068 5260 Dihedral : 14.653 157.040 5106 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 0.33 % Allowed : 19.82 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.28 (0.14), residues: 3846 helix: 0.91 (0.15), residues: 1387 sheet: -0.90 (0.22), residues: 478 loop : -2.23 (0.13), residues: 1981 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 2.818 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 198 average time/residue: 0.4498 time to fit residues: 141.1944 Evaluate side-chains 188 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 2.860 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2775 time to fit residues: 5.8798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 0.9980 chunk 373 optimal weight: 50.0000 chunk 227 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 259 optimal weight: 20.0000 chunk 391 optimal weight: 5.9990 chunk 360 optimal weight: 0.0270 chunk 311 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1631 moved from start: 0.8812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30786 Z= 0.143 Angle : 0.571 11.799 42114 Z= 0.295 Chirality : 0.042 0.229 4931 Planarity : 0.004 0.067 5260 Dihedral : 14.545 155.876 5106 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 0.18 % Allowed : 20.18 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.15 (0.14), residues: 3846 helix: 1.02 (0.15), residues: 1407 sheet: -0.94 (0.22), residues: 498 loop : -2.17 (0.13), residues: 1941 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 190 average time/residue: 0.4677 time to fit residues: 142.1309 Evaluate side-chains 188 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 3.117 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2967 time to fit residues: 7.3502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 0.9980 chunk 332 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 287 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5512 r_free = 0.5512 target = 0.332944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5423 r_free = 0.5423 target = 0.322348 restraints weight = 81981.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.325013 restraints weight = 51774.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.326117 restraints weight = 33622.505| |-----------------------------------------------------------------------------| r_work (final): 0.5451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1902 moved from start: 0.9237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30786 Z= 0.180 Angle : 0.613 14.081 42114 Z= 0.317 Chirality : 0.043 0.264 4931 Planarity : 0.004 0.069 5260 Dihedral : 14.619 160.666 5106 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.65 % Rotamer: Outliers : 0.22 % Allowed : 20.04 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.08 % Twisted Proline : 1.30 % Twisted General : 0.03 % 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: -1.20 (0.14), residues: 3846 helix: 0.97 (0.15), residues: 1385 sheet: -0.73 (0.23), residues: 466 loop : -2.21 (0.13), residues: 1995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5193.42 seconds wall clock time: 104 minutes 30.74 seconds (6270.74 seconds total)