Starting phenix.real_space_refine on Mon Apr 15 15:48:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7beg_12157/04_2024/7beg_12157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7beg_12157/04_2024/7beg_12157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7beg_12157/04_2024/7beg_12157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7beg_12157/04_2024/7beg_12157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7beg_12157/04_2024/7beg_12157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7beg_12157/04_2024/7beg_12157.pdb" } resolution = 4.2 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= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 188 5.49 5 S 131 5.16 5 C 21529 2.51 5 N 6235 2.21 5 O 7163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 821": "NH1" <-> "NH2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C ARG 1331": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35246 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2350 Classifications: {'peptide': 302} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10570 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 10548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10548 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1306} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 708 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3996 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1934 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "T" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1920 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "G" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 848 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 18.32, per 1000 atoms: 0.52 Number of scatterers: 35246 At special positions: 0 Unit cell: (192.045, 190.96, 235.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 188 15.00 O 7163 8.00 N 6235 7.00 C 21529 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: 14.44 Conformation dependent library (CDL) restraints added in 5.4 seconds 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 41 sheets defined 43.1% alpha, 8.7% beta 62 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 12.73 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.829A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.608A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.816A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.534A pdb=" N ASP A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.254A pdb=" N GLU A 273 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 274 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.646A pdb=" N ARG A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.011A pdb=" N ARG B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.656A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 154 through 161 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.624A pdb=" N ALA B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.555A pdb=" N SER B 266 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA B 267 " --> pdb=" O VAL B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 267' Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.599A pdb=" N ALA B 272 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 273 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 274' Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.302A pdb=" N GLU B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.543A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.665A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 removed outlier: 4.161A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.552A pdb=" N ILE C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.640A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.241A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.748A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.764A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 4.138A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.652A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.593A pdb=" N ASP C 491 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 492' Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.646A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.638A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 628 removed outlier: 3.812A pdb=" N GLY C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS C 628 " --> pdb=" O GLU C 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 624 through 628' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.661A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.950A pdb=" N ALA C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 709 removed outlier: 3.765A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 704 through 709' Processing helix chain 'C' and resid 820 through 825 removed outlier: 4.259A pdb=" N GLN C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 820 through 825' Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 945 through 955 Processing helix chain 'C' and resid 957 through 983 removed outlier: 3.635A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1039 removed outlier: 3.868A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.770A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 4.085A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.728A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.523A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.954A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.527A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.553A 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 113 through 118 removed outlier: 3.861A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 118' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 170 removed outlier: 3.695A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.796A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 3.798A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.168A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.802A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.802A pdb=" N GLY D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.743A pdb=" N ALA D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 387 removed outlier: 4.259A pdb=" N LEU D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.772A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.504A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.738A pdb=" N GLY D 433 " --> pdb=" O HIS D 430 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 434' Processing helix chain 'D' and resid 450 through 454 removed outlier: 3.674A pdb=" N CYS D 454 " --> pdb=" O PRO D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 482 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.730A pdb=" N GLY D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.507A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 4.394A pdb=" N VAL D 592 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.684A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.726A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 669 removed outlier: 4.289A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 768 through 803 removed outlier: 3.555A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.588A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.590A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 934 removed outlier: 3.530A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 4.975A pdb=" N MET D 932 " --> pdb=" O THR D 928 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 934 " --> pdb=" O LEU D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1146 Proline residue: D1139 - end of helix Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.784A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.791A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.304A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 3.693A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1309 through 1314' Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.775A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1353 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 removed outlier: 3.666A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 33 removed outlier: 4.201A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.755A pdb=" N ALA E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.357A pdb=" N THR E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.590A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.589A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 136 removed outlier: 3.998A pdb=" N ILE F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.932A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 164' Processing helix chain 'F' and resid 213 through 233 removed outlier: 5.017A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 Processing helix chain 'F' and resid 262 through 295 Processing helix chain 'F' and resid 299 through 309 removed outlier: 4.198A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.681A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS F 329 " --> pdb=" O TRP F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.131A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN F 342 " --> pdb=" O HIS F 338 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 3.608A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 417 removed outlier: 4.020A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 444 removed outlier: 4.018A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.903A pdb=" N LEU F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 530 through 551 removed outlier: 3.501A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 removed outlier: 4.069A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 584 through 599 Processing helix chain 'F' and resid 608 through 612 removed outlier: 4.152A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.633A pdb=" N VAL G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 30 removed outlier: 3.849A pdb=" N ARG G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 46 removed outlier: 3.689A pdb=" N ARG G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU G 42 " --> pdb=" O HIS G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 67 removed outlier: 3.520A pdb=" N ARG G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.551A pdb=" N ILE G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 73 through 78' Processing helix chain 'G' and resid 85 through 90 removed outlier: 3.567A pdb=" N PHE G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 100 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.853A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 28 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 206 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 104 removed outlier: 4.100A pdb=" N VAL A 98 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 146 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 102 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.795A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.429A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.640A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 104 removed outlier: 3.532A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.364A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.566A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.549A pdb=" N ILE C 138 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 148 through 151 removed outlier: 3.747A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 4.334A pdb=" N PHE C 156 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C 175 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 158 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.611A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 529 through 530 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.634A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.501A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 615 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 636 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 722 through 723 Processing sheet with id=AC2, first strand: chain 'C' and resid 731 through 732 removed outlier: 3.849A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 798 through 801 removed outlier: 3.725A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1075 through 1076 Processing sheet with id=AC5, first strand: chain 'C' and resid 833 through 836 removed outlier: 3.596A pdb=" N GLN C 834 " --> pdb=" O LEU C1054 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C1052 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 876 through 877 removed outlier: 3.941A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 889 removed outlier: 3.662A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1336 through 1337 Processing sheet with id=AC9, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.004A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.750A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.518A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 350 through 352 Processing sheet with id=AD4, first strand: chain 'D' and resid 355 through 357 removed outlier: 6.446A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.347A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.687A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 826 through 827 removed outlier: 3.786A pdb=" N GLU D 827 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 956 through 957 removed outlier: 4.347A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 960 through 961 removed outlier: 4.138A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.677A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.636A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE4, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.591A pdb=" N VAL D1176 " --> pdb=" O SER D1164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.567A pdb=" N THR D1265 " --> pdb=" O SER D1303 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 21.46 Time building geometry restraints manager: 15.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9851 1.34 - 1.46: 9319 1.46 - 1.59: 16424 1.59 - 1.71: 351 1.71 - 1.84: 232 Bond restraints: 36177 Sorted by residual: bond pdb=" O3' DA N -15 " pdb=" P DT N -14 " ideal model delta sigma weight residual 1.607 1.410 0.197 1.50e-02 4.44e+03 1.72e+02 bond pdb=" O3' DC N 1 " pdb=" P DC N 2 " ideal model delta sigma weight residual 1.607 1.417 0.190 1.50e-02 4.44e+03 1.61e+02 bond pdb=" O3' DT N -40 " pdb=" P DA N -39 " ideal model delta sigma weight residual 1.607 1.440 0.167 1.50e-02 4.44e+03 1.24e+02 bond pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 1.525 1.664 -0.138 1.25e-02 6.40e+03 1.23e+02 bond pdb=" C4' DT N 7 " pdb=" O4' DT N 7 " ideal model delta sigma weight residual 1.450 1.654 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 36172 not shown) Histogram of bond angle deviations from ideal: 81.23 - 92.40: 5 92.40 - 103.57: 770 103.57 - 114.74: 22599 114.74 - 125.91: 25340 125.91 - 137.08: 966 Bond angle restraints: 49680 Sorted by residual: angle pdb=" O3' DA N -19 " pdb=" C3' DA N -19 " pdb=" C2' DA N -19 " ideal model delta sigma weight residual 111.50 81.23 30.27 1.50e+00 4.44e-01 4.07e+02 angle pdb=" N ASP A 199 " pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 108.24 128.37 -20.13 1.32e+00 5.74e-01 2.32e+02 angle pdb=" O3' DT N -63 " pdb=" P DA N -62 " pdb=" O5' DA N -62 " ideal model delta sigma weight residual 104.00 125.76 -21.76 1.50e+00 4.44e-01 2.10e+02 angle pdb=" O3' DA N -5 " pdb=" C3' DA N -5 " pdb=" C2' DA N -5 " ideal model delta sigma weight residual 111.50 90.54 20.96 1.50e+00 4.44e-01 1.95e+02 angle pdb=" O3' DA N 5 " pdb=" C3' DA N 5 " pdb=" C2' DA N 5 " ideal model delta sigma weight residual 111.50 90.98 20.52 1.50e+00 4.44e-01 1.87e+02 ... (remaining 49675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 20842 33.68 - 67.35: 926 67.35 - 101.03: 30 101.03 - 134.71: 2 134.71 - 168.38: 3 Dihedral angle restraints: 21803 sinusoidal: 10279 harmonic: 11524 Sorted by residual: dihedral pdb=" CA ARG D1242 " pdb=" C ARG D1242 " pdb=" N LEU D1243 " pdb=" CA LEU D1243 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 0.00 -28.58 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE D 381 " pdb=" C ILE D 381 " pdb=" N TYR D 382 " pdb=" CA TYR D 382 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 21800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 5592 0.213 - 0.426: 59 0.426 - 0.640: 12 0.640 - 0.853: 2 0.853 - 1.066: 1 Chirality restraints: 5666 Sorted by residual: chirality pdb=" C4' DT N -63 " pdb=" C5' DT N -63 " pdb=" O4' DT N -63 " pdb=" C3' DT N -63 " both_signs ideal model delta sigma weight residual False -2.53 -1.46 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" C4' DC N 1 " pdb=" C5' DC N 1 " pdb=" O4' DC N 1 " pdb=" C3' DC N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.76 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C4' DA N -15 " pdb=" C5' DA N -15 " pdb=" O4' DA N -15 " pdb=" C3' DA N -15 " both_signs ideal model delta sigma weight residual False -2.53 -1.82 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 5663 not shown) Planarity restraints: 5826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T -2 " 0.016 2.00e-02 2.50e+03 6.60e-02 1.31e+02 pdb=" N9 DG T -2 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG T -2 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DG T -2 " 0.108 2.00e-02 2.50e+03 pdb=" C5 DG T -2 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG T -2 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DG T -2 " -0.002 2.00e-02 2.50e+03 pdb=" N1 DG T -2 " -0.078 2.00e-02 2.50e+03 pdb=" C2 DG T -2 " 0.117 2.00e-02 2.50e+03 pdb=" N2 DG T -2 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG T -2 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DG T -2 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -54 " -0.114 2.00e-02 2.50e+03 4.94e-02 7.31e+01 pdb=" N9 DG N -54 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG N -54 " 0.055 2.00e-02 2.50e+03 pdb=" N7 DG N -54 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG N -54 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG N -54 " -0.081 2.00e-02 2.50e+03 pdb=" O6 DG N -54 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG N -54 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG N -54 " 0.022 2.00e-02 2.50e+03 pdb=" N2 DG N -54 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG N -54 " 0.029 2.00e-02 2.50e+03 pdb=" C4 DG N -54 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 4 " -0.125 2.00e-02 2.50e+03 5.35e-02 7.17e+01 pdb=" N1 DT N 4 " 0.066 2.00e-02 2.50e+03 pdb=" C2 DT N 4 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DT N 4 " 0.036 2.00e-02 2.50e+03 pdb=" N3 DT N 4 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT N 4 " -0.020 2.00e-02 2.50e+03 pdb=" O4 DT N 4 " -0.054 2.00e-02 2.50e+03 pdb=" C5 DT N 4 " 0.015 2.00e-02 2.50e+03 pdb=" C7 DT N 4 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT N 4 " 0.053 2.00e-02 2.50e+03 ... (remaining 5823 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3931 2.76 - 3.29: 31199 3.29 - 3.83: 56061 3.83 - 4.36: 62081 4.36 - 4.90: 103795 Nonbonded interactions: 257067 Sorted by model distance: nonbonded pdb=" N1 DG N -17 " pdb=" O2 DC T 17 " model vdw 2.222 2.520 nonbonded pdb=" OP2 DT N -55 " pdb=" O2 DT N -55 " model vdw 2.235 3.040 nonbonded pdb=" N6 DA N 6 " pdb=" N3 DT T -6 " model vdw 2.251 3.200 nonbonded pdb=" NZ LYS C 163 " pdb=" OP1 DA N 5 " model vdw 2.278 2.520 nonbonded pdb=" O4 DT N 7 " pdb=" N1 DA T -7 " model vdw 2.280 2.496 ... (remaining 257062 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 233 or resid 249 through 322)) selection = (chain 'B' and (resid 6 through 297 or (resid 298 and (name N or name CA or name \ C or name O or name CB )) or resid 299 through 322)) } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.100 Check model and map are aligned: 0.520 Set scattering table: 0.370 Process input model: 106.120 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 : 0.006 0.204 36177 Z= 0.330 Angle : 1.103 30.273 49680 Z= 0.675 Chirality : 0.066 1.066 5666 Planarity : 0.006 0.070 5826 Dihedral : 15.611 168.383 14371 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.09 % Favored : 92.59 % Rotamer: Outliers : 0.53 % Allowed : 4.99 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.10), residues: 3979 helix: -2.65 (0.09), residues: 1516 sheet: -1.58 (0.30), residues: 285 loop : -2.81 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 33 HIS 0.019 0.001 HIS F 338 PHE 0.030 0.001 PHE C 804 TYR 0.026 0.001 TYR D 382 ARG 0.009 0.000 ARG D1355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 574 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.6251 (p90) cc_final: 0.5745 (p90) REVERT: B 32 GLU cc_start: 0.6600 (mm-30) cc_final: 0.5116 (mp0) REVERT: B 142 MET cc_start: 0.8974 (pmm) cc_final: 0.8730 (pmm) REVERT: B 316 MET cc_start: 0.8824 (tmm) cc_final: 0.8483 (pmm) REVERT: C 503 LYS cc_start: 0.8977 (pttt) cc_final: 0.8618 (tmtt) REVERT: C 805 MET cc_start: 0.7369 (pp-130) cc_final: 0.7129 (ppp) REVERT: C 1238 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7782 (mm) REVERT: D 361 LEU cc_start: 0.5416 (mt) cc_final: 0.5133 (mt) REVERT: D 429 LEU cc_start: 0.8727 (pp) cc_final: 0.8411 (pp) REVERT: D 626 TYR cc_start: 0.7252 (m-10) cc_final: 0.6685 (m-10) REVERT: D 686 TRP cc_start: 0.9469 (m100) cc_final: 0.8393 (m100) REVERT: D 698 MET cc_start: 0.9371 (tpp) cc_final: 0.9086 (tmm) REVERT: D 724 MET cc_start: 0.7529 (mmt) cc_final: 0.7010 (tpp) REVERT: D 725 MET cc_start: 0.8116 (tmm) cc_final: 0.7903 (tmm) REVERT: D 738 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8658 (mmm160) REVERT: D 743 MET cc_start: 0.5886 (mmt) cc_final: 0.5222 (tpp) REVERT: D 792 ASN cc_start: 0.8948 (m-40) cc_final: 0.8506 (t0) REVERT: D 796 LEU cc_start: 0.9213 (tp) cc_final: 0.8944 (tt) REVERT: D 929 GLN cc_start: 0.1997 (OUTLIER) cc_final: 0.0604 (mm110) REVERT: D 981 GLU cc_start: 0.9717 (mt-10) cc_final: 0.9502 (tm-30) REVERT: D 1040 MET cc_start: 0.4428 (mtp) cc_final: 0.4031 (ttt) REVERT: E 45 LYS cc_start: 0.3584 (pttt) cc_final: 0.3277 (pttt) REVERT: E 48 VAL cc_start: 0.6998 (t) cc_final: 0.6784 (m) REVERT: E 49 ILE cc_start: 0.6783 (mt) cc_final: 0.6562 (pt) REVERT: E 54 ILE cc_start: 0.8182 (mt) cc_final: 0.7850 (pt) REVERT: F 100 MET cc_start: 0.8832 (mtp) cc_final: 0.8366 (mtt) REVERT: F 143 TYR cc_start: 0.9476 (m-80) cc_final: 0.8945 (t80) REVERT: F 297 MET cc_start: 0.4344 (ttm) cc_final: 0.4032 (ttt) REVERT: F 533 ASP cc_start: 0.9127 (m-30) cc_final: 0.8534 (t0) REVERT: G 39 LEU cc_start: 0.8960 (mt) cc_final: 0.8661 (pp) REVERT: G 62 LEU cc_start: 0.5360 (tp) cc_final: 0.4466 (pp) REVERT: G 68 ARG cc_start: 0.5697 (mtt90) cc_final: 0.5302 (mmt180) outliers start: 18 outliers final: 3 residues processed: 590 average time/residue: 0.5682 time to fit residues: 516.9111 Evaluate side-chains 306 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 301 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 40.0000 chunk 315 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 242 optimal weight: 0.5980 chunk 377 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 103 ASN C 36 GLN C 120 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 343 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C1023 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1244 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN D 153 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 419 HIS D 700 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN D1227 HIS ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1268 ASN D1350 ASN E 15 ASN E 31 GLN F 242 HIS F 301 ASN F 309 ASN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 36177 Z= 0.205 Angle : 0.617 11.139 49680 Z= 0.329 Chirality : 0.041 0.246 5666 Planarity : 0.005 0.106 5826 Dihedral : 19.327 178.693 6504 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.36 % Favored : 93.52 % Rotamer: Outliers : 0.21 % Allowed : 2.08 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.12), residues: 3979 helix: -0.68 (0.12), residues: 1557 sheet: -1.07 (0.29), residues: 304 loop : -2.33 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 33 HIS 0.010 0.001 HIS C1023 PHE 0.023 0.001 PHE C 972 TYR 0.015 0.001 TYR F 421 ARG 0.017 0.001 ARG C 996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 340 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.8724 (tmm) cc_final: 0.8393 (pmm) REVERT: C 503 LYS cc_start: 0.9081 (pttt) cc_final: 0.8763 (tmtt) REVERT: C 741 MET cc_start: 0.8110 (tpp) cc_final: 0.7734 (tpp) REVERT: C 951 MET cc_start: 0.8558 (tpt) cc_final: 0.8263 (tpp) REVERT: D 135 ILE cc_start: 0.9378 (mt) cc_final: 0.8902 (mt) REVERT: D 180 MET cc_start: 0.7875 (tpp) cc_final: 0.7548 (tpt) REVERT: D 273 ILE cc_start: 0.9249 (mt) cc_final: 0.9033 (mm) REVERT: D 298 MET cc_start: 0.8171 (mtm) cc_final: 0.7757 (ptp) REVERT: D 485 MET cc_start: 0.7923 (tpt) cc_final: 0.7580 (tpt) REVERT: D 686 TRP cc_start: 0.9443 (m100) cc_final: 0.8469 (m100) REVERT: D 698 MET cc_start: 0.9351 (tpp) cc_final: 0.9140 (tmm) REVERT: D 738 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8765 (tpt170) REVERT: D 792 ASN cc_start: 0.9098 (m-40) cc_final: 0.8700 (t0) REVERT: D 921 GLN cc_start: 0.8215 (tt0) cc_final: 0.7767 (mt0) REVERT: D 1040 MET cc_start: 0.5009 (mtp) cc_final: 0.4712 (ttt) REVERT: E 15 ASN cc_start: 0.2093 (OUTLIER) cc_final: 0.1829 (m-40) REVERT: F 297 MET cc_start: 0.4938 (ttm) cc_final: 0.4222 (ttt) REVERT: F 322 MET cc_start: 0.5316 (ptt) cc_final: 0.5023 (ptt) REVERT: F 533 ASP cc_start: 0.9126 (m-30) cc_final: 0.8738 (t0) REVERT: G 39 LEU cc_start: 0.8948 (mt) cc_final: 0.8717 (pp) REVERT: G 68 ARG cc_start: 0.5759 (mtt90) cc_final: 0.5269 (mmt180) outliers start: 7 outliers final: 2 residues processed: 345 average time/residue: 0.5347 time to fit residues: 291.9482 Evaluate side-chains 237 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 314 optimal weight: 0.0670 chunk 257 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 378 optimal weight: 2.9990 chunk 408 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 303 optimal weight: 40.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 75 GLN B 84 ASN C 120 GLN C 686 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN F 464 ASN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36177 Z= 0.234 Angle : 0.623 11.982 49680 Z= 0.330 Chirality : 0.041 0.187 5666 Planarity : 0.005 0.082 5826 Dihedral : 19.261 177.153 6504 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.69 % Favored : 93.14 % Rotamer: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.43 (0.13), residues: 3979 helix: 0.23 (0.13), residues: 1579 sheet: -0.56 (0.29), residues: 315 loop : -2.02 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 33 HIS 0.012 0.001 HIS B 160 PHE 0.034 0.002 PHE C 972 TYR 0.015 0.001 TYR D 631 ARG 0.013 0.001 ARG C 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8097 (tpp) cc_final: 0.7897 (tpt) REVERT: B 316 MET cc_start: 0.8891 (tmm) cc_final: 0.8549 (pmm) REVERT: C 503 LYS cc_start: 0.9223 (pttt) cc_final: 0.8939 (tmtt) REVERT: C 951 MET cc_start: 0.8644 (tpt) cc_final: 0.8226 (tpp) REVERT: C 1304 MET cc_start: 0.8398 (tmm) cc_final: 0.8084 (tmm) REVERT: C 1308 ILE cc_start: 0.8870 (mm) cc_final: 0.8504 (mm) REVERT: D 180 MET cc_start: 0.8102 (tpp) cc_final: 0.7802 (tpt) REVERT: D 273 ILE cc_start: 0.9219 (mt) cc_final: 0.8956 (mm) REVERT: D 581 MET cc_start: 0.9086 (ppp) cc_final: 0.8800 (ppp) REVERT: D 686 TRP cc_start: 0.9395 (m100) cc_final: 0.8407 (m100) REVERT: D 698 MET cc_start: 0.9336 (tpp) cc_final: 0.9134 (tmm) REVERT: D 725 MET cc_start: 0.7833 (tmm) cc_final: 0.7605 (tmm) REVERT: D 792 ASN cc_start: 0.9170 (m-40) cc_final: 0.8829 (t0) REVERT: D 1040 MET cc_start: 0.5329 (mtp) cc_final: 0.5102 (ttt) REVERT: E 45 LYS cc_start: 0.3662 (pttt) cc_final: 0.3431 (mttt) REVERT: E 46 THR cc_start: 0.7707 (p) cc_final: 0.7287 (t) REVERT: E 48 VAL cc_start: 0.6968 (m) cc_final: 0.6547 (p) REVERT: F 102 MET cc_start: 0.8296 (mtp) cc_final: 0.7981 (mtp) REVERT: F 297 MET cc_start: 0.5023 (ttm) cc_final: 0.4336 (ttt) REVERT: F 322 MET cc_start: 0.5559 (ptt) cc_final: 0.5336 (ptt) REVERT: F 470 MET cc_start: 0.7901 (tmm) cc_final: 0.7694 (tmm) REVERT: F 516 ASP cc_start: 0.7141 (t70) cc_final: 0.6717 (m-30) REVERT: F 533 ASP cc_start: 0.9002 (m-30) cc_final: 0.8792 (t0) REVERT: G 39 LEU cc_start: 0.8907 (mt) cc_final: 0.8644 (pp) REVERT: G 68 ARG cc_start: 0.5808 (mtt90) cc_final: 0.5364 (mmt180) outliers start: 2 outliers final: 1 residues processed: 272 average time/residue: 0.5274 time to fit residues: 228.9334 Evaluate side-chains 213 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 180 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 379 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 359 optimal weight: 0.6980 chunk 108 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN B 41 ASN B 75 GLN C 120 GLN C 148 GLN C 450 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1237 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 667 GLN D 805 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36177 Z= 0.211 Angle : 0.597 12.361 49680 Z= 0.315 Chirality : 0.041 0.187 5666 Planarity : 0.004 0.104 5826 Dihedral : 19.270 176.218 6504 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.10 (0.13), residues: 3979 helix: 0.54 (0.13), residues: 1592 sheet: -0.83 (0.28), residues: 337 loop : -1.80 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 33 HIS 0.010 0.001 HIS F 338 PHE 0.020 0.001 PHE D 763 TYR 0.013 0.001 TYR D 609 ARG 0.008 0.001 ARG C 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 257 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7110 (p90) cc_final: 0.6872 (p90) REVERT: B 316 MET cc_start: 0.8916 (tmm) cc_final: 0.8569 (pmm) REVERT: C 503 LYS cc_start: 0.9235 (pttt) cc_final: 0.8926 (tmtt) REVERT: C 658 GLN cc_start: 0.7968 (tt0) cc_final: 0.7723 (mp10) REVERT: C 766 ASN cc_start: 0.7477 (p0) cc_final: 0.7272 (p0) REVERT: C 951 MET cc_start: 0.8649 (tpt) cc_final: 0.8167 (tpp) REVERT: C 1304 MET cc_start: 0.8396 (tmm) cc_final: 0.8095 (tmm) REVERT: C 1308 ILE cc_start: 0.8807 (mm) cc_final: 0.8475 (mm) REVERT: D 180 MET cc_start: 0.8081 (tpp) cc_final: 0.7852 (tpp) REVERT: D 273 ILE cc_start: 0.9369 (mt) cc_final: 0.9145 (mm) REVERT: D 686 TRP cc_start: 0.9390 (m100) cc_final: 0.8435 (m100) REVERT: D 697 MET cc_start: 0.8730 (tpp) cc_final: 0.8383 (tpp) REVERT: D 725 MET cc_start: 0.7913 (tmm) cc_final: 0.7647 (tmm) REVERT: D 744 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7557 (mmp80) REVERT: D 792 ASN cc_start: 0.9143 (m-40) cc_final: 0.8887 (t0) REVERT: D 796 LEU cc_start: 0.9467 (tp) cc_final: 0.9262 (tt) REVERT: E 45 LYS cc_start: 0.3679 (pttt) cc_final: 0.3461 (mttt) REVERT: E 46 THR cc_start: 0.7860 (p) cc_final: 0.7566 (t) REVERT: F 102 MET cc_start: 0.8249 (mtp) cc_final: 0.7749 (mtm) REVERT: F 297 MET cc_start: 0.5187 (ttm) cc_final: 0.4495 (ttt) REVERT: F 322 MET cc_start: 0.5694 (ptt) cc_final: 0.5439 (ptt) REVERT: F 516 ASP cc_start: 0.7322 (t70) cc_final: 0.6770 (m-30) REVERT: G 39 LEU cc_start: 0.8894 (mt) cc_final: 0.8617 (pp) REVERT: G 68 ARG cc_start: 0.5663 (mtt90) cc_final: 0.5202 (mmt180) outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.5726 time to fit residues: 241.4743 Evaluate side-chains 202 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 299 optimal weight: 0.0170 chunk 165 optimal weight: 7.9990 chunk 343 optimal weight: 0.6980 chunk 277 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 360 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 75 GLN C 36 GLN C 120 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1197 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36177 Z= 0.150 Angle : 0.562 11.629 49680 Z= 0.293 Chirality : 0.040 0.176 5666 Planarity : 0.004 0.084 5826 Dihedral : 19.220 177.114 6504 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.46 % Favored : 93.39 % Rotamer: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 3979 helix: 0.78 (0.14), residues: 1583 sheet: -0.88 (0.26), residues: 358 loop : -1.67 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 33 HIS 0.009 0.001 HIS F 338 PHE 0.022 0.001 PHE D1274 TYR 0.015 0.001 TYR C1231 ARG 0.020 0.000 ARG C 779 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7043 (p90) cc_final: 0.6675 (p90) REVERT: B 316 MET cc_start: 0.8924 (tmm) cc_final: 0.8572 (pmm) REVERT: C 503 LYS cc_start: 0.9217 (pttt) cc_final: 0.8935 (tmtt) REVERT: C 741 MET cc_start: 0.8908 (tpp) cc_final: 0.8210 (tpp) REVERT: C 951 MET cc_start: 0.8567 (tpt) cc_final: 0.8091 (tpp) REVERT: C 1304 MET cc_start: 0.8335 (tmm) cc_final: 0.8086 (tmm) REVERT: C 1308 ILE cc_start: 0.8865 (mm) cc_final: 0.8547 (mm) REVERT: D 180 MET cc_start: 0.8111 (tpp) cc_final: 0.7898 (tpp) REVERT: D 273 ILE cc_start: 0.9357 (mt) cc_final: 0.9150 (mm) REVERT: D 298 MET cc_start: 0.8407 (mtm) cc_final: 0.8094 (ptp) REVERT: D 686 TRP cc_start: 0.9387 (m100) cc_final: 0.8444 (m100) REVERT: D 724 MET cc_start: 0.7729 (mmt) cc_final: 0.7524 (mmt) REVERT: D 725 MET cc_start: 0.7931 (tmm) cc_final: 0.7694 (tmm) REVERT: D 792 ASN cc_start: 0.9143 (m-40) cc_final: 0.8848 (t0) REVERT: D 796 LEU cc_start: 0.9419 (tp) cc_final: 0.9214 (tt) REVERT: E 46 THR cc_start: 0.7856 (p) cc_final: 0.7563 (t) REVERT: F 100 MET cc_start: 0.8545 (mtt) cc_final: 0.8042 (mpp) REVERT: F 102 MET cc_start: 0.8296 (mtp) cc_final: 0.7759 (mtp) REVERT: F 297 MET cc_start: 0.5240 (ttm) cc_final: 0.4561 (ttt) REVERT: F 322 MET cc_start: 0.5759 (ptt) cc_final: 0.5546 (ptt) REVERT: F 507 MET cc_start: 0.8242 (tpt) cc_final: 0.7984 (tpt) REVERT: F 516 ASP cc_start: 0.7273 (t70) cc_final: 0.6735 (m-30) REVERT: G 39 LEU cc_start: 0.8923 (mt) cc_final: 0.8616 (pp) REVERT: G 68 ARG cc_start: 0.5674 (mtt90) cc_final: 0.5234 (mmt180) outliers start: 4 outliers final: 2 residues processed: 249 average time/residue: 0.5152 time to fit residues: 208.1037 Evaluate side-chains 196 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 3.9990 chunk 362 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN C 120 GLN C 659 GLN C 832 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1197 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36177 Z= 0.246 Angle : 0.618 13.286 49680 Z= 0.324 Chirality : 0.041 0.197 5666 Planarity : 0.004 0.049 5826 Dihedral : 19.397 178.663 6504 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.84 (0.13), residues: 3979 helix: 0.78 (0.14), residues: 1594 sheet: -0.81 (0.26), residues: 356 loop : -1.65 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 37 HIS 0.009 0.001 HIS F 338 PHE 0.019 0.002 PHE C 804 TYR 0.018 0.001 TYR C1231 ARG 0.016 0.001 ARG C1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.8948 (tmm) cc_final: 0.8580 (pmm) REVERT: C 486 THR cc_start: 0.8608 (t) cc_final: 0.8300 (p) REVERT: C 503 LYS cc_start: 0.9237 (pttt) cc_final: 0.8945 (tmtt) REVERT: C 764 CYS cc_start: 0.8707 (t) cc_final: 0.8429 (p) REVERT: C 951 MET cc_start: 0.8670 (tpt) cc_final: 0.8173 (tpp) REVERT: C 957 LYS cc_start: 0.8553 (mttt) cc_final: 0.8162 (mttp) REVERT: C 1243 MET cc_start: 0.7778 (tmm) cc_final: 0.7558 (tmm) REVERT: C 1304 MET cc_start: 0.8488 (tmm) cc_final: 0.8167 (tmm) REVERT: C 1308 ILE cc_start: 0.8898 (mm) cc_final: 0.8535 (mm) REVERT: C 1319 MET cc_start: 0.7781 (tpt) cc_final: 0.7301 (tpt) REVERT: D 180 MET cc_start: 0.8223 (tpp) cc_final: 0.8001 (tpp) REVERT: D 686 TRP cc_start: 0.9342 (m100) cc_final: 0.8468 (m100) REVERT: D 724 MET cc_start: 0.7826 (mmt) cc_final: 0.7612 (mmt) REVERT: D 744 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7658 (mmp80) REVERT: D 792 ASN cc_start: 0.9063 (m-40) cc_final: 0.8854 (t0) REVERT: D 832 LYS cc_start: 0.8229 (tttt) cc_final: 0.7644 (pttt) REVERT: D 921 GLN cc_start: 0.9131 (mt0) cc_final: 0.8918 (mt0) REVERT: F 102 MET cc_start: 0.8364 (mtp) cc_final: 0.7896 (mtm) REVERT: F 297 MET cc_start: 0.5386 (ttm) cc_final: 0.4698 (ttt) REVERT: F 322 MET cc_start: 0.6158 (ptt) cc_final: 0.5919 (ptt) REVERT: G 39 LEU cc_start: 0.8908 (mt) cc_final: 0.8588 (pp) REVERT: G 68 ARG cc_start: 0.5734 (mtt90) cc_final: 0.5144 (mmt180) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.4889 time to fit residues: 181.6176 Evaluate side-chains 185 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 229 optimal weight: 0.7980 chunk 293 optimal weight: 40.0000 chunk 227 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 400 optimal weight: 7.9990 chunk 250 optimal weight: 0.8980 chunk 244 optimal weight: 0.0970 chunk 185 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1257 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 36177 Z= 0.142 Angle : 0.561 11.777 49680 Z= 0.291 Chirality : 0.040 0.173 5666 Planarity : 0.003 0.046 5826 Dihedral : 19.314 178.767 6504 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 1.47 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3979 helix: 0.97 (0.14), residues: 1596 sheet: -0.53 (0.27), residues: 340 loop : -1.54 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 580 HIS 0.009 0.001 HIS F 338 PHE 0.022 0.001 PHE C 804 TYR 0.014 0.001 TYR C1231 ARG 0.007 0.000 ARG C 779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7958 Ramachandran restraints generated. 3979 Oldfield, 0 Emsley, 3979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.8950 (tmm) cc_final: 0.8578 (pmm) REVERT: C 503 LYS cc_start: 0.9194 (pttt) cc_final: 0.8924 (tmtt) REVERT: C 741 MET cc_start: 0.8974 (tpp) cc_final: 0.8394 (tpp) REVERT: C 951 MET cc_start: 0.8516 (tpt) cc_final: 0.8049 (tpp) REVERT: C 957 LYS cc_start: 0.8453 (mttt) cc_final: 0.7717 (ttmm) REVERT: C 1170 MET cc_start: 0.8474 (mmp) cc_final: 0.8201 (mmp) REVERT: C 1243 MET cc_start: 0.7632 (tmm) cc_final: 0.7291 (tmm) REVERT: C 1254 VAL cc_start: 0.8521 (t) cc_final: 0.8255 (t) REVERT: C 1304 MET cc_start: 0.8392 (tmm) cc_final: 0.8104 (tmm) REVERT: C 1308 ILE cc_start: 0.8834 (mm) cc_final: 0.8532 (mm) REVERT: D 298 MET cc_start: 0.8456 (mtm) cc_final: 0.8124 (ptp) REVERT: D 686 TRP cc_start: 0.9317 (m100) cc_final: 0.8429 (m100) REVERT: D 724 MET cc_start: 0.7787 (mmt) cc_final: 0.7540 (mmt) REVERT: D 743 MET cc_start: 0.4864 (tpp) cc_final: 0.4599 (tpt) REVERT: D 792 ASN cc_start: 0.8993 (m-40) cc_final: 0.8724 (t0) REVERT: D 796 LEU cc_start: 0.9463 (tp) cc_final: 0.9227 (tt) REVERT: D 832 LYS cc_start: 0.8125 (tttt) cc_final: 0.7553 (pttt) REVERT: D 921 GLN cc_start: 0.9038 (mt0) cc_final: 0.8827 (mt0) REVERT: F 100 MET cc_start: 0.8813 (mtt) cc_final: 0.8194 (mpp) REVERT: F 102 MET cc_start: 0.8637 (mtp) cc_final: 0.8036 (mtp) REVERT: F 297 MET cc_start: 0.5281 (ttm) cc_final: 0.4614 (ttt) REVERT: F 322 MET cc_start: 0.6081 (ptt) cc_final: 0.5839 (ptt) REVERT: F 507 MET cc_start: 0.7883 (mmm) cc_final: 0.7169 (tpt) REVERT: G 39 LEU cc_start: 0.8889 (mt) cc_final: 0.8567 (pp) REVERT: G 61 LEU cc_start: 0.4713 (pp) cc_final: 0.2769 (pp) REVERT: G 65 ARG cc_start: 0.4953 (ptt180) cc_final: 0.3904 (ptt-90) REVERT: G 68 ARG cc_start: 0.5741 (mtt90) cc_final: 0.5122 (mmt180) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.5171 time to fit residues: 199.3212 Evaluate side-chains 189 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 2.9990 chunk 160 optimal weight: 0.0060 chunk 239 optimal weight: 3.9990 chunk 120 optimal weight: 0.0010 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 273 optimal weight: 10.0000 chunk 198 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: