Starting phenix.real_space_refine on Wed Apr 17 14:59:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x89_22090/04_2024/6x89_22090_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x89_22090/04_2024/6x89_22090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x89_22090/04_2024/6x89_22090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x89_22090/04_2024/6x89_22090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x89_22090/04_2024/6x89_22090_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x89_22090/04_2024/6x89_22090_updated.pdb" } resolution = 3.9 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= 1.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 2 6.06 5 P 10 5.49 5 S 297 5.16 5 C 28847 2.51 5 N 7646 2.21 5 O 8187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A2 ARG 15": "NH1" <-> "NH2" Residue "A2 GLU 57": "OE1" <-> "OE2" Residue "A5 GLU 24": "OE1" <-> "OE2" Residue "A6 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A7 ARG 43": "NH1" <-> "NH2" Residue "A7 ASP 73": "OD1" <-> "OD2" Residue "A7 GLU 97": "OE1" <-> "OE2" Residue "A9 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 94": "NH1" <-> "NH2" Residue "A9 GLU 97": "OE1" <-> "OE2" Residue "A9 GLU 152": "OE1" <-> "OE2" Residue "A9 GLU 159": "OE1" <-> "OE2" Residue "A9 ARG 192": "NH1" <-> "NH2" Residue "A9 GLU 199": "OE1" <-> "OE2" Residue "A9 ASP 221": "OD1" <-> "OD2" Residue "A9 ASP 254": "OD1" <-> "OD2" Residue "A9 ASP 286": "OD1" <-> "OD2" Residue "A9 GLU 297": "OE1" <-> "OE2" Residue "A9 ARG 300": "NH1" <-> "NH2" Residue "A9 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 GLU 317": "OE1" <-> "OE2" Residue "A9 PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ASP 336": "OD1" <-> "OD2" Residue "AL ASP 35": "OD1" <-> "OD2" Res Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS2M 325 " - pdb=" SG CYS2M 409 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 29 " - pdb=" SG CYSA8 59 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 39 " - pdb=" SG CYSA8 49 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 71 " - pdb=" SG CYSA8 103 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 81 " - pdb=" SG CYSA8 92 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 14 " - pdb=" SG CYSS5 44 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 24 " - pdb=" SG CYSS5 34 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.71 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 118 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 107 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 135 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 121 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 167 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 126 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 171 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 131 " pdb=" SF4S1 801 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 171 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 174 " pdb="FE2 SF4S1 801 " - pdb=" NE2 HISS1 167 " pdb="FE3 SF4S1 801 " - pdb=" SG CYSS1 180 " pdb=" SF4S1 802 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 222 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 219 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 269 " pdb=" SF4S7 301 " pdb="FE4 SF4S7 301 " - pdb=" SG CYSS7 88 " pdb=" SF4S8 301 " pdb="FE2 SF4S8 301 " - pdb=" SG CYSS8 168 " pdb="FE1 SF4S8 301 " - pdb=" SG CYSS8 162 " pdb="FE4 SF4S8 301 " - pdb=" SG CYSS8 133 " pdb="FE3 SF4S8 301 " - pdb=" SG CYSS8 165 " pdb=" SF4S8 302 " pdb="FE4 SF4S8 302 " - pdb=" SG CYSS8 172 " pdb="FE3 SF4S8 302 " - pdb=" SG CYSS8 126 " pdb="FE2 SF4S8 302 " - pdb=" SG CYSS8 129 " pdb="FE1 SF4S8 302 " - pdb=" SG CYSS8 123 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 413 " Number of angles added : 60 Zn2+ tetrahedral coordination pdb=" ZNG1 703 " pdb="ZN ZNG1 703 " - pdb=" NE2 HISG2 135 " pdb="ZN ZNG1 703 " - pdb=" NE2 HISG1 130 " pdb="ZN ZNG1 703 " - pdb=" ND1 HISG2 107 " pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 75 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 65 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 90 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 93 " Number of angles added : 3 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 207 helices and 36 sheets defined 46.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.18 Creating SS restraints... Processing helix chain 'A2' and resid 28 through 42 Processing helix chain 'A2' and resid 79 through 90 Processing helix chain 'A5' and resid 29 through 46 Processing helix chain 'A5' and resid 52 through 71 Processing helix chain 'A5' and resid 74 through 81 Processing helix chain 'A5' and resid 86 through 105 Processing helix chain 'A6' and resid 122 through 127 Processing helix chain 'A7' and resid 26 through 28 No H-bonds generated for 'chain 'A7' and resid 26 through 28' Processing helix chain 'A7' and resid 39 through 42 No H-bonds generated for 'chain 'A7' and resid 39 through 42' Processing helix chain 'A7' and resid 61 through 65 Processing helix chain 'A7' and resid 69 through 72 No H-bonds generated for 'chain 'A7' and resid 69 through 72' Processing helix chain 'A7' and resid 88 through 97 Processing helix chain 'A7' and resid 121 through 125 Processing helix chain 'A9' and resid 73 through 85 Processing helix chain 'A9' and resid 100 through 104 Processing helix chain 'A9' and resid 122 through 128 Processing helix chain 'A9' and resid 150 through 167 Processing helix chain 'A9' and resid 190 through 204 Processing helix chain 'A9' and resid 224 through 233 Processing helix chain 'A9' and resid 252 through 264 Processing helix chain 'A9' and resid 284 through 295 Processing helix chain 'A9' and resid 305 through 321 Proline residue: A9 315 - end of helix removed outlier: 3.704A pdb=" N ILEA9 318 " --> pdb=" O THRA9 314 " (cutoff:3.500A) Processing helix chain 'A9' and resid 335 through 342 Processing helix chain 'A9' and resid 354 through 357 No H-bonds generated for 'chain 'A9' and resid 354 through 357' Processing helix chain 'A9' and resid 370 through 374 removed outlier: 3.711A pdb=" N SERA9 374 " --> pdb=" O PHEA9 371 " (cutoff:3.500A) Processing helix chain 'AL' and resid 22 through 28 Processing helix chain 'AL' and resid 30 through 35 Proline residue: AL 34 - end of helix Processing helix chain 'AL' and resid 37 through 46 Processing helix chain 'AL' and resid 90 through 97 Processing helix chain 'AL' and resid 104 through 110 Processing helix chain 'AL' and resid 127 through 130 No H-bonds generated for 'chain 'AL' and resid 127 through 130' Processing helix chain 'S1' and resid 92 through 99 Processing helix chain 'S1' and resid 150 through 165 Processing helix chain 'S1' and resid 181 through 189 Processing helix chain 'S1' and resid 216 through 218 No H-bonds generated for 'chain 'S1' and resid 216 through 218' Processing helix chain 'S1' and resid 224 through 231 Processing helix chain 'S1' and resid 262 through 268 Processing helix chain 'S1' and resid 277 through 279 No H-bonds generated for 'chain 'S1' and resid 277 through 279' Processing helix chain 'S1' and resid 331 through 334 No H-bonds generated for 'chain 'S1' and resid 331 through 334' Processing helix chain 'S1' and resid 337 through 342 Processing helix chain 'S1' and resid 362 through 375 Processing helix chain 'S1' and resid 391 through 404 Processing helix chain 'S1' and resid 423 through 426 No H-bonds generated for 'chain 'S1' and resid 423 through 426' Processing helix chain 'S1' and resid 433 through 437 Processing helix chain 'S1' and resid 453 through 465 Processing helix chain 'S1' and resid 490 through 497 Processing helix chain 'S1' and resid 502 through 508 Processing helix chain 'S1' and resid 519 through 522 Processing helix chain 'S1' and resid 527 through 541 Processing helix chain 'S1' and resid 560 through 566 Processing helix chain 'S1' and resid 575 through 578 No H-bonds generated for 'chain 'S1' and resid 575 through 578' Processing helix chain 'S1' and resid 589 through 593 Processing helix chain 'S1' and resid 612 through 614 No H-bonds generated for 'chain 'S1' and resid 612 through 614' Processing helix chain 'S1' and resid 654 through 664 Processing helix chain 'S1' and resid 674 through 684 Processing helix chain 'S1' and resid 728 through 732 Processing helix chain 'S1' and resid 735 through 742 Processing helix chain 'S2' and resid 51 through 56 Processing helix chain 'S2' and resid 64 through 69 Processing helix chain 'S2' and resid 77 through 90 Processing helix chain 'S2' and resid 96 through 125 Processing helix chain 'S2' and resid 129 through 148 Processing helix chain 'S2' and resid 171 through 193 Processing helix chain 'S2' and resid 197 through 203 Processing helix chain 'S2' and resid 211 through 217 Processing helix chain 'S2' and resid 221 through 226 Processing helix chain 'S2' and resid 233 through 236 No H-bonds generated for 'chain 'S2' and resid 233 through 236' Processing helix chain 'S2' and resid 241 through 243 No H-bonds generated for 'chain 'S2' and resid 241 through 243' Processing helix chain 'S2' and resid 257 through 281 Proline residue: S2 279 - end of helix Processing helix chain 'S2' and resid 299 through 304 Processing helix chain 'S2' and resid 307 through 317 Processing helix chain 'S2' and resid 359 through 369 Processing helix chain 'S2' and resid 375 through 385 Processing helix chain 'S2' and resid 389 through 393 Processing helix chain 'S3' and resid 4 through 13 Processing helix chain 'S3' and resid 16 through 18 No H-bonds generated for 'chain 'S3' and resid 16 through 18' Processing helix chain 'S3' and resid 38 through 44 Processing helix chain 'S3' and resid 109 through 117 Processing helix chain 'S4' and resid 92 through 94 No H-bonds generated for 'chain 'S4' and resid 92 through 94' Processing helix chain 'S4' and resid 102 through 112 Processing helix chain 'S4' and resid 131 through 134 No H-bonds generated for 'chain 'S4' and resid 131 through 134' Processing helix chain 'S6' and resid 33 through 37 Processing helix chain 'S6' and resid 46 through 52 Processing helix chain 'S7' and resid 58 through 77 Processing helix chain 'S7' and resid 88 through 97 Processing helix chain 'S7' and resid 104 through 106 No H-bonds generated for 'chain 'S7' and resid 104 through 106' Processing helix chain 'S7' and resid 131 through 139 Processing helix chain 'S7' and resid 160 through 162 No H-bonds generated for 'chain 'S7' and resid 160 through 162' Processing helix chain 'S7' and resid 170 through 172 No H-bonds generated for 'chain 'S7' and resid 170 through 172' Processing helix chain 'S7' and resid 187 through 202 Processing helix chain 'S7' and resid 207 through 212 Processing helix chain 'S8' and resid 43 through 56 removed outlier: 3.665A pdb=" N ILES8 56 " --> pdb=" O LEUS8 52 " (cutoff:3.500A) Processing helix chain 'S8' and resid 60 through 72 Processing helix chain 'S8' and resid 74 through 88 Processing helix chain 'S8' and resid 96 through 98 No H-bonds generated for 'chain 'S8' and resid 96 through 98' Processing helix chain 'S8' and resid 128 through 132 Processing helix chain 'S8' and resid 167 through 171 Processing helix chain 'S8' and resid 190 through 193 No H-bonds generated for 'chain 'S8' and resid 190 through 193' Processing helix chain 'S8' and resid 199 through 219 removed outlier: 4.528A pdb=" N ASPS8 205 " --> pdb=" O LEUS8 201 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARGS8 206 " --> pdb=" O GLUS8 202 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TRPS8 207 " --> pdb=" O ASNS8 203 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLUS8 208 " --> pdb=" O GLYS8 204 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THRS8 209 " --> pdb=" O ASPS8 205 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLUS8 210 " --> pdb=" O ARGS8 206 " (cutoff:3.500A) Processing helix chain 'V1' and resid 93 through 98 Processing helix chain 'V1' and resid 101 through 111 Processing helix chain 'V1' and resid 123 through 128 Processing helix chain 'V1' and resid 155 through 161 Processing helix chain 'V1' and resid 163 through 176 Processing helix chain 'V1' and resid 191 through 206 Processing helix chain 'V1' and resid 233 through 235 No H-bonds generated for 'chain 'V1' and resid 233 through 235' Processing helix chain 'V1' and resid 237 through 245 Processing helix chain 'V1' and resid 273 through 284 Proline residue: V1 280 - end of helix Processing helix chain 'V1' and resid 287 through 291 Processing helix chain 'V1' and resid 324 through 330 Processing helix chain 'V1' and resid 369 through 373 Processing helix chain 'V1' and resid 391 through 405 Processing helix chain 'V1' and resid 411 through 429 Processing helix chain 'V1' and resid 434 through 449 Processing helix chain 'V1' and resid 455 through 469 Proline residue: V1 462 - end of helix Processing helix chain 'V1' and resid 471 through 489 Processing helix chain 'V2' and resid 47 through 59 removed outlier: 4.526A pdb=" N HISV2 59 " --> pdb=" O GLUV2 55 " (cutoff:3.500A) Processing helix chain 'V2' and resid 66 through 80 Proline residue: V2 71 - end of helix Processing helix chain 'V2' and resid 86 through 95 Processing helix chain 'V2' and resid 100 through 109 Processing helix chain 'V2' and resid 129 through 132 No H-bonds generated for 'chain 'V2' and resid 129 through 132' Processing helix chain 'V2' and resid 136 through 146 Processing helix chain 'V2' and resid 199 through 210 Processing helix chain '1M' and resid 4 through 34 Proline residue: 1M 15 - end of helix Processing helix chain '1M' and resid 50 through 60 Processing helix chain '1M' and resid 77 through 89 Processing helix chain '1M' and resid 106 through 126 Processing helix chain '1M' and resid 132 through 160 Processing helix chain '1M' and resid 167 through 176 Processing helix chain '1M' and resid 179 through 182 No H-bonds generated for 'chain '1M' and resid 179 through 182' Processing helix chain '1M' and resid 184 through 197 Processing helix chain '1M' and resid 205 through 210 Processing helix chain '1M' and resid 222 through 246 Processing helix chain '1M' and resid 260 through 262 No H-bonds generated for 'chain '1M' and resid 260 through 262' Processing helix chain '1M' and resid 266 through 286 removed outlier: 3.702A pdb=" N ALA1M 286 " --> pdb=" O TRP1M 282 " (cutoff:3.500A) Processing helix chain '1M' and resid 293 through 301 Processing helix chain '1M' and resid 303 through 320 Processing helix chain '2M' and resid 5 through 7 No H-bonds generated for 'chain '2M' and resid 5 through 7' Processing helix chain '2M' and resid 9 through 29 Processing helix chain '2M' and resid 40 through 65 Proline residue: 2M 63 - end of helix Processing helix chain '2M' and resid 69 through 73 Processing helix chain '2M' and resid 80 through 107 removed outlier: 4.945A pdb=" N ASP2M 102 " --> pdb=" O SER2M 98 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE2M 103 " --> pdb=" O MET2M 99 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE2M 104 " --> pdb=" O CYS2M 100 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU2M 105 " --> pdb=" O PHE2M 101 " (cutoff:3.500A) Processing helix chain '2M' and resid 112 through 129 removed outlier: 3.922A pdb=" N LEU2M 117 " --> pdb=" O PHE2M 114 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE2M 118 " --> pdb=" O ILE2M 115 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU2M 119 " --> pdb=" O VAL2M 116 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER2M 121 " --> pdb=" O ILE2M 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE2M 129 " --> pdb=" O LEU2M 126 " (cutoff:3.500A) Processing helix chain '2M' and resid 134 through 152 Processing helix chain '2M' and resid 160 through 190 Processing helix chain '2M' and resid 195 through 202 Processing helix chain '2M' and resid 213 through 230 removed outlier: 4.102A pdb=" N MET2M 217 " --> pdb=" O SER2M 213 " (cutoff:3.500A) Processing helix chain '2M' and resid 233 through 235 No H-bonds generated for 'chain '2M' and resid 233 through 235' Processing helix chain '2M' and resid 239 through 245 Processing helix chain '2M' and resid 248 through 272 Proline residue: 2M 258 - end of helix removed outlier: 3.834A pdb=" N TYR2M 272 " --> pdb=" O ARG2M 268 " (cutoff:3.500A) Processing helix chain '2M' and resid 278 through 298 removed outlier: 4.085A pdb=" N CYS2M 286 " --> pdb=" O ILE2M 282 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE2M 288 " --> pdb=" O CYS2M 284 " (cutoff:3.500A) Processing helix chain '2M' and resid 304 through 322 removed outlier: 3.803A pdb=" N LEU2M 308 " --> pdb=" O VAL2M 304 " (cutoff:3.500A) Processing helix chain '2M' and resid 328 through 354 Processing helix chain '2M' and resid 357 through 359 No H-bonds generated for 'chain '2M' and resid 357 through 359' Processing helix chain '2M' and resid 369 through 372 No H-bonds generated for 'chain '2M' and resid 369 through 372' Processing helix chain '2M' and resid 374 through 388 Processing helix chain '2M' and resid 394 through 409 Processing helix chain '2M' and resid 414 through 436 removed outlier: 3.626A pdb=" N MET2M 436 " --> pdb=" O LEU2M 432 " (cutoff:3.500A) Processing helix chain '2M' and resid 453 through 471 removed outlier: 3.597A pdb=" N THR2M 466 " --> pdb=" O SER2M 462 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE2M 469 " --> pdb=" O ILE2M 465 " (cutoff:3.500A) Proline residue: 2M 470 - end of helix Processing helix chain '2M' and resid 473 through 487 removed outlier: 4.406A pdb=" N TYR2M 487 " --> pdb=" O ALA2M 483 " (cutoff:3.500A) Processing helix chain '3M' and resid 4 through 23 Processing helix chain '3M' and resid 58 through 82 Proline residue: 3M 72 - end of helix Proline residue: 3M 79 - end of helix Processing helix chain '3M' and resid 89 through 112 Processing helix chain '4L' and resid 2 through 23 Processing helix chain '4L' and resid 28 through 52 Processing helix chain '4L' and resid 57 through 83 Processing helix chain '6M' and resid 2 through 19 Processing helix chain '6M' and resid 23 through 44 Processing helix chain '6M' and resid 47 through 55 Processing helix chain '6M' and resid 61 through 71 Processing helix chain '6M' and resid 98 through 105 Processing helix chain '6M' and resid 113 through 122 removed outlier: 4.282A pdb=" N ASN6M 118 " --> pdb=" O PRO6M 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR6M 119 " --> pdb=" O THR6M 115 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER6M 121 " --> pdb=" O ILE6M 117 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU6M 122 " --> pdb=" O ASN6M 118 " (cutoff:3.500A) Processing helix chain '6M' and resid 136 through 146 Processing helix chain '6M' and resid 150 through 170 Proline residue: 6M 155 - end of helix Processing helix chain 'A1' and resid 4 through 34 removed outlier: 3.758A pdb=" N VALA1 9 " --> pdb=" O META1 6 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEUA1 10 " --> pdb=" O GLUA1 7 " (cutoff:3.500A) Proline residue: A1 11 - end of helix removed outlier: 4.284A pdb=" N HISA1 34 " --> pdb=" O LYSA1 31 " (cutoff:3.500A) Processing helix chain 'A1' and resid 44 through 62 Processing helix chain 'A3' and resid 3 through 13 Processing helix chain 'A3' and resid 15 through 44 Proline residue: A3 31 - end of helix Proline residue: A3 36 - end of helix Processing helix chain 'A8' and resid 16 through 27 removed outlier: 4.558A pdb=" N HISA8 24 " --> pdb=" O ALAA8 20 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLYA8 26 " --> pdb=" O SERA8 22 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILEA8 27 " --> pdb=" O LYSA8 23 " (cutoff:3.500A) Processing helix chain 'A8' and resid 30 through 42 removed outlier: 3.769A pdb=" N PHEA8 36 " --> pdb=" O GLUA8 32 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUA8 37 " --> pdb=" O ASNA8 33 " (cutoff:3.500A) Processing helix chain 'A8' and resid 51 through 69 removed outlier: 3.596A pdb=" N GLNA8 69 " --> pdb=" O LYSA8 65 " (cutoff:3.500A) Processing helix chain 'A8' and resid 72 through 81 Processing helix chain 'A8' and resid 93 through 100 Processing helix chain 'AM' and resid 4 through 8 Processing helix chain 'AM' and resid 47 through 111 Proline residue: AM 87 - end of helix Processing helix chain 'B' and resid 24 through 27 No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.895A pdb=" N UNK C 10 " --> pdb=" O UNK C 6 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N UNK C 11 " --> pdb=" O UNK C 7 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N UNK C 16 " --> pdb=" O UNK C 12 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N UNK C 19 " --> pdb=" O UNK C 15 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N UNK C 20 " --> pdb=" O UNK C 16 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N UNK C 23 " --> pdb=" O UNK C 19 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK C 24 " --> pdb=" O UNK C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 40 through 43 No H-bonds generated for 'chain 'C' and resid 40 through 43' Processing helix chain 'C2' and resid 5 through 23 Processing helix chain 'C2' and resid 35 through 72 removed outlier: 3.665A pdb=" N ALAC2 69 " --> pdb=" O GLUC2 65 " (cutoff:3.500A) Processing helix chain 'P2' and resid 83 through 105 Processing helix chain 'S5' and resid 16 through 27 Processing helix chain 'S5' and resid 35 through 46 removed outlier: 3.808A pdb=" N GLUS5 39 " --> pdb=" O LEUS5 36 " (cutoff:3.500A) Processing helix chain 'S5' and resid 48 through 65 removed outlier: 3.596A pdb=" N ILES5 65 " --> pdb=" O GLUS5 61 " (cutoff:3.500A) Processing helix chain 'X1' and resid 22 through 27 Processing helix chain 'X1' and resid 31 through 55 Proline residue: X1 55 - end of helix Processing helix chain 'X1' and resid 58 through 86 Processing helix chain 'X1' and resid 93 through 98 Processing helix chain 'G1' and resid 4 through 30 Processing helix chain 'G1' and resid 194 through 218 Processing helix chain 'G1' and resid 224 through 232 Processing helix chain 'G2' and resid 3 through 29 Processing helix chain 'G2' and resid 194 through 218 Processing helix chain 'G2' and resid 222 through 236 Processing helix chain 'L2' and resid 211 through 235 Proline residue: L2 218 - end of helix Processing helix chain 'L2' and resid 242 through 252 Processing sheet with id= A, first strand: chain 'A2' and resid 47 through 53 Processing sheet with id= B, first strand: chain 'A9' and resid 273 through 276 removed outlier: 6.092A pdb=" N ILEA9 210 " --> pdb=" O TYRA9 274 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEUA9 276 " --> pdb=" O ILEA9 210 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYSA9 212 " --> pdb=" O LEUA9 276 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLNA9 88 " --> pdb=" O ALAA9 65 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VALA9 67 " --> pdb=" O GLNA9 88 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEUA9 90 " --> pdb=" O VALA9 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'AL' and resid 52 through 54 Processing sheet with id= D, first strand: chain 'S1' and resid 75 through 78 Processing sheet with id= E, first strand: chain 'S1' and resid 124 through 126 Processing sheet with id= F, first strand: chain 'S1' and resid 212 through 214 Processing sheet with id= G, first strand: chain 'S1' and resid 240 through 243 Processing sheet with id= H, first strand: chain 'S1' and resid 289 through 294 removed outlier: 6.176A pdb=" N ARGS1 309 " --> pdb=" O VALS1 313 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VALS1 313 " --> pdb=" O ARGS1 309 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S1' and resid 349 through 352 Processing sheet with id= J, first strand: chain 'S1' and resid 408 through 410 removed outlier: 6.323A pdb=" N PHES1 581 " --> pdb=" O VALS1 382 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VALS1 384 " --> pdb=" O PHES1 581 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYRS1 583 " --> pdb=" O VALS1 384 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHES1 600 " --> pdb=" O VALS1 582 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEUS1 584 " --> pdb=" O PHES1 600 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VALS1 602 " --> pdb=" O LEUS1 584 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VALS1 617 " --> pdb=" O TYRS1 603 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLYS1 605 " --> pdb=" O VALS1 617 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEUS1 619 " --> pdb=" O GLYS1 605 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S1' and resid 551 through 553 removed outlier: 7.463A pdb=" N ASNS1 552 " --> pdb=" O PROS1 513 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILES1 515 " --> pdb=" O ASNS1 552 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VALS1 440 " --> pdb=" O VALS1 514 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILES1 516 " --> pdb=" O VALS1 440 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEUS1 442 " --> pdb=" O ILES1 516 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYSS1 469 " --> pdb=" O PHES1 441 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEUS1 443 " --> pdb=" O LYSS1 469 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLYS1 471 " --> pdb=" O LEUS1 443 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYSS1 484 " --> pdb=" O TYRS1 472 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S1' and resid 630 through 633 Processing sheet with id= M, first strand: chain 'S2' and resid 11 through 15 removed outlier: 6.808A pdb=" N ASNS2 33 " --> pdb=" O VALS2 37 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VALS2 37 " --> pdb=" O ASNS2 33 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S2' and resid 327 through 332 Processing sheet with id= O, first strand: chain 'S3' and resid 21 through 24 removed outlier: 7.890A pdb=" N ARGS3 85 " --> pdb=" O ASNS3 29 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N PHES3 31 " --> pdb=" O ARGS3 85 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARGS3 87 " --> pdb=" O PHES3 31 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THRS3 33 " --> pdb=" O ARGS3 87 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLNS3 89 " --> pdb=" O THRS3 33 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALAS3 92 " --> pdb=" O PHES3 71 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEUS3 78 " --> pdb=" O LEUS3 56 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEUS3 56 " --> pdb=" O LEUS3 78 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'S3' and resid 155 through 158 Processing sheet with id= Q, first strand: chain 'S4' and resid 65 through 69 removed outlier: 3.742A pdb=" N ILES4 47 " --> pdb=" O SERS4 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S7' and resid 83 through 85 removed outlier: 7.643A pdb=" N PHES7 84 " --> pdb=" O CYSS7 119 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILES7 121 " --> pdb=" O PHES7 84 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRPS7 146 " --> pdb=" O METS7 120 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VALS7 122 " --> pdb=" O TRPS7 146 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILES7 148 " --> pdb=" O VALS7 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'S8' and resid 111 through 113 Processing sheet with id= T, first strand: chain 'S8' and resid 138 through 144 removed outlier: 6.535A pdb=" N GLUS8 143 " --> pdb=" O THRS8 152 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THRS8 152 " --> pdb=" O GLUS8 143 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V1' and resid 267 through 272 removed outlier: 6.309A pdb=" N ALAV1 181 " --> pdb=" O LEUV1 141 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VALV1 143 " --> pdb=" O ALAV1 181 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYRV1 183 " --> pdb=" O VALV1 143 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASPV1 222 " --> pdb=" O ALAV1 182 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILEV1 184 " --> pdb=" O ASPV1 222 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HISV1 224 " --> pdb=" O ILEV1 184 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V1' and resid 301 through 306 Processing sheet with id= W, first strand: chain 'V1' and resid 342 through 346 removed outlier: 6.640A pdb=" N METV1 385 " --> pdb=" O LEUV1 343 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VALV1 345 " --> pdb=" O ILEV1 383 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILEV1 383 " --> pdb=" O VALV1 345 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'V2' and resid 190 through 192 Processing sheet with id= Y, first strand: chain 'G1' and resid 66 through 69 removed outlier: 6.913A pdb=" N SERG1 104 " --> pdb=" O VALG1 84 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ARGG1 86 " --> pdb=" O SERG1 104 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VALG1 106 " --> pdb=" O ARGG1 86 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALAG1 132 " --> pdb=" O LEUG1 105 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N HISG1 107 " --> pdb=" O ALAG1 132 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEUG1 134 " --> pdb=" O HISG1 107 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALAG1 149 " --> pdb=" O VALG1 133 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLNG1 135 " --> pdb=" O ALAG1 149 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEUG1 151 " --> pdb=" O GLNG1 135 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALAG1 167 " --> pdb=" O THRG1 150 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G1' and resid 71 through 73 removed outlier: 6.288A pdb=" N ILEG1 92 " --> pdb=" O HISG1 72 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THRG1 120 " --> pdb=" O VALG1 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G1' and resid 98 through 100 removed outlier: 6.437A pdb=" N VALG1 126 " --> pdb=" O ASNG1 99 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALAG1 143 " --> pdb=" O THRG1 127 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALAG1 161 " --> pdb=" O PHEG1 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G1' and resid 155 through 157 removed outlier: 6.594A pdb=" N THRG1 173 " --> pdb=" O TYRG1 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G1' and resid 180 through 182 removed outlier: 3.659A pdb=" N VALG1 180 " --> pdb=" O ARGG1 190 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARGG1 190 " --> pdb=" O VALG1 180 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLYG1 182 " --> pdb=" O PHEG1 188 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N PHEG1 188 " --> pdb=" O GLYG1 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G2' and resid 66 through 69 Processing sheet with id= AE, first strand: chain 'G2' and resid 71 through 73 removed outlier: 6.991A pdb=" N ILEG2 92 " --> pdb=" O GLNG2 72 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THRG2 120 " --> pdb=" O ARGG2 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G2' and resid 144 through 146 Processing sheet with id= AG, first strand: chain 'L2' and resid 83 through 86 Processing sheet with id= AH, first strand: chain 'L2' and resid 88 through 90 removed outlier: 6.548A pdb=" N ILEL2 109 " --> pdb=" O THRL2 89 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THRL2 137 " --> pdb=" O SERL2 110 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYSL2 154 " --> pdb=" O SERL2 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'L2' and resid 149 through 151 removed outlier: 6.713A pdb=" N SERL2 166 " --> pdb=" O LEUL2 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'L2' and resid 196 through 199 removed outlier: 3.776A pdb=" N LEUL2 197 " --> pdb=" O ARGL2 207 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARGL2 207 " --> pdb=" O LEUL2 197 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALAL2 199 " --> pdb=" O PHEL2 205 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHEL2 205 " --> pdb=" O ALAL2 199 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 1890 hydrogen bonds defined for protein. 5385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.28 Time building geometry restraints manager: 14.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 19382 1.43 - 1.67: 26176 1.67 - 1.90: 423 1.90 - 2.14: 0 2.14 - 2.37: 80 Bond restraints: 46061 Sorted by residual: bond pdb=" O2B NAPA9 401 " pdb=" P2B NAPA9 401 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C4N NAPA9 401 " pdb=" C5N NAPA9 401 " ideal model delta sigma weight residual 1.384 1.482 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C3N NAPA9 401 " pdb=" C4N NAPA9 401 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C4A FMNV1 501 " pdb=" N5 FMNV1 501 " ideal model delta sigma weight residual 1.380 1.301 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O13 PC1G1 701 " pdb=" P PC1G1 701 " ideal model delta sigma weight residual 1.652 1.588 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 46056 not shown) Histogram of bond angle deviations from ideal: 56.61 - 72.12: 47 72.12 - 87.62: 25 87.62 - 103.12: 572 103.12 - 118.63: 36300 118.63 - 134.13: 25523 Bond angle restraints: 62467 Sorted by residual: angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 89.63 14.70 1.14e+00 7.69e-01 1.66e+02 angle pdb=" S3 SF4S8 302 " pdb="FE2 SF4S8 302 " pdb=" S4 SF4S8 302 " ideal model delta sigma weight residual 104.10 123.09 -18.99 1.50e+00 4.44e-01 1.60e+02 angle pdb=" S1 SF4S8 301 " pdb="FE4 SF4S8 301 " pdb=" S2 SF4S8 301 " ideal model delta sigma weight residual 104.10 123.04 -18.94 1.50e+00 4.44e-01 1.59e+02 angle pdb=" S3 SF4S8 302 " pdb="FE1 SF4S8 302 " pdb=" S4 SF4S8 302 " ideal model delta sigma weight residual 104.10 122.96 -18.86 1.50e+00 4.44e-01 1.58e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 89.50 14.83 1.20e+00 6.94e-01 1.53e+02 ... (remaining 62462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 24602 17.67 - 35.35: 2445 35.35 - 53.02: 414 53.02 - 70.70: 82 70.70 - 88.37: 40 Dihedral angle restraints: 27583 sinusoidal: 11079 harmonic: 16504 Sorted by residual: dihedral pdb=" CA ASPS1 589 " pdb=" C ASPS1 589 " pdb=" N VALS1 590 " pdb=" CA VALS1 590 " ideal model delta harmonic sigma weight residual -180.00 -128.67 -51.33 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA ASPV2 157 " pdb=" C ASPV2 157 " pdb=" N GLYV2 158 " pdb=" CA GLYV2 158 " ideal model delta harmonic sigma weight residual -180.00 -131.56 -48.44 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA PHEA7 105 " pdb=" C PHEA7 105 " pdb=" N PROA7 106 " pdb=" CA PROA7 106 " ideal model delta harmonic sigma weight residual 180.00 133.48 46.52 0 5.00e+00 4.00e-02 8.66e+01 ... (remaining 27580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 6922 4.237 - 8.473: 0 8.473 - 12.710: 0 12.710 - 16.946: 0 16.946 - 21.183: 24 Chirality restraints: 6946 Sorted by residual: chirality pdb="FE2 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S3 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S3 SF4S1 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4S8 302 " pdb=" S1 SF4S8 302 " pdb=" S2 SF4S8 302 " pdb=" S4 SF4S8 302 " both_signs ideal model delta sigma weight residual False -10.55 10.55 -21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 6943 not shown) Planarity restraints: 7931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHEA7 105 " -0.066 5.00e-02 4.00e+02 9.89e-02 1.57e+01 pdb=" N PROA7 106 " 0.171 5.00e-02 4.00e+02 pdb=" CA PROA7 106 " -0.052 5.00e-02 4.00e+02 pdb=" CD PROA7 106 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRPG1 80 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C TRPG1 80 " 0.064 2.00e-02 2.50e+03 pdb=" O TRPG1 80 " -0.024 2.00e-02 2.50e+03 pdb=" N TYRG1 81 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGS2 356 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ARGS2 356 " -0.060 2.00e-02 2.50e+03 pdb=" O ARGS2 356 " 0.023 2.00e-02 2.50e+03 pdb=" N ALAS2 357 " 0.020 2.00e-02 2.50e+03 ... (remaining 7928 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 404 2.50 - 3.10: 36443 3.10 - 3.70: 68879 3.70 - 4.30: 96157 4.30 - 4.90: 159074 Nonbonded interactions: 360957 Sorted by model distance: nonbonded pdb=" O TYRS6 92 " pdb="ZN ZNS6 300 " model vdw 1.899 2.230 nonbonded pdb=" O GLNS3 173 " pdb=" OH TYRS7 162 " model vdw 2.016 2.440 nonbonded pdb=" OE1 GLUA5 92 " pdb=" OG1 THRS3 49 " model vdw 2.077 2.440 nonbonded pdb=" OG1 THRS2 109 " pdb=" OH TYRS2 145 " model vdw 2.081 2.440 nonbonded pdb=" OG1 THRA9 219 " pdb=" OE1 GLUA9 220 " model vdw 2.107 2.440 ... (remaining 360952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.410 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: 0.050 Extract box with map and model: 32.510 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 104.150 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.220 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 46061 Z= 0.461 Angle : 0.901 18.987 62467 Z= 0.515 Chirality : 1.219 21.183 6946 Planarity : 0.005 0.099 7931 Dihedral : 14.460 88.373 16958 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.97 % Favored : 84.80 % Rotamer: Outliers : 0.23 % Allowed : 9.79 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.19 % 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: -3.80 (0.10), residues: 5572 helix: -1.10 (0.09), residues: 2675 sheet: -2.74 (0.22), residues: 428 loop : -4.24 (0.10), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPS3 18 HIS 0.023 0.001 HISS6 75 PHE 0.031 0.002 PHEA9 73 TYR 0.035 0.002 TYRS7 159 ARG 0.008 0.000 ARGS1 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 4779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1470 time to evaluate : 4.601 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: A5 88 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A5 106 TRP cc_start: 0.8187 (p90) cc_final: 0.7747 (p90) REVERT: A5 115 TYR cc_start: 0.8105 (t80) cc_final: 0.7392 (t80) REVERT: A6 124 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8513 (tmtp) REVERT: A7 52 GLU cc_start: 0.7348 (mp0) cc_final: 0.7108 (mp0) REVERT: A7 57 PRO cc_start: 0.9135 (Cg_exo) cc_final: 0.8905 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7883 (tm-30) REVERT: A7 109 TYR cc_start------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 470 optimal weight: 1.9990 chunk 422 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 436 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 324 optimal weight: 0.7980 chunk 505 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2 20 GLN A2 43 ASN A7 45 GLN A7 58 ASN A7 77 ASN A9 48 HIS A9 80 GLN A9 88 GLN A9 133 ASN AL 137 HIS S1 109 HIS S1 485 HIS ** S1 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 571 GLN ** S1 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 683 ASN S2 10 ASN S2 78 GLN S2 99 GLN ** S2 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 121 HIS ** S2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 4 GLN S3 27 HIS S3 29 ASN S4 57 GLN S4 73 GLN S6 99 GLN S6 102 HIS S7 72 ASN S7 116 GLN S8 111 HIS V1 226 HIS V1 464 GLN V2 37 ASN V2 77 GLN ** V2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 122 HIS V2 221 ASN ** 1M 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1M 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2M 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 197 GLN ** 2M 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2M 265 ASN 2M 332 GLN ** 4L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6M 22 ASN A1 2 ASN A1 34 HIS A1 39 HIS A8 10 ASN A8 24 HIS ** A8 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 90 GLN AM 102 HIS C2 35 HIS C2 71 ASN P2 86 ASN ** S5 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 212 GLN G2 218 ASN L2 107 ASN ** L2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.256 46061 Z= 0.603 Angle : 1.916 51.058 62467 Z= 1.242 Chirality : 0.373 6.548 6946 Planarity : 0.005 0.093 7931 Dihedral : 7.996 85.532 6486 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.58 % Favored : 88.32 % Rotamer: Outliers : 3.47 % Allowed : 17.94 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 5572 helix: 0.33 (0.10), residues: 2660 sheet: -1.99 (0.26), residues: 391 loop : -3.64 (0.10), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPAM 130 HIS 0.015 0.001 HISA8 24 PHE 0.037 0.002 PHEAM 30 TYR 0.031 0.002 TYR2M 149 ARG 0.009 0.000 ARGV1 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1558 residues out of total 4779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1393 time to evaluate : 5.263 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: A2 74 LEU cc_start: 0.9030 (mt) cc_final: 0.8796 (mt) REVERT: A5 88 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A5 115 TYR cc_start: 0.8019 (t80) cc_final: 0.7511 (t80) REVERT: A6 124 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8518 (tmtp) REVERT: A7 52 GLU cc_start: 0.7351 (mp0) cc_final: 0.6966 (mp0) REVERT: A7 57 PRO cc_start: 0.9111 (Cg_exo) cc_final: 0.8874 (Cg_endo) REVERT: A7 92 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7946 (tm-30) REVERT: A7 109 TYR cc_start: 0.8996 (t80) cc_final: 0.8342 (t80) REVERT: A7 115 GLU cc_start: 0.7972 (tt0) cc_final: 0.7769 (tm-30) REVERT: A9 199 GLU cc_start: 0.8943 (tp30) cc_final: 0.7937 (tt0) REVERT: A9 222 ARG cc_start: 0.8481 (mpp80) cc_final: 0.8123 (mtt180) REVERT: A9 306 PHE cc_start: 0.7603 (p90) cc_final: 0.7109 (m-10) REVERT: AL 22 ARG cc_start: 0.6803 (mtm180) cc_final: 0.6565 (mpp-170) REVERT: S1 124 GLU cc_start: 0.7963 (pt0) cc_final: 0.7592 (pt0) REVERT: S1 144 LYS cc_start: 0.7535 (mttp) cc_final: 0.7312 (mtpt) REVERT: S1 151 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8132 (p) REVERT: S1 165 MET cc_start: 0.8974 (tmm) cc_final: 0.8684 (ttp) REVERT: S1 505 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7463 (mttm) REVERT: S1 594 LYS cc_start: 0.8713 (tppt) cc_final: 0.8342 (mmtp) REVERT: S1 604 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8447 (tm-30) REVERT: S1 656 LYS cc_start: 0.9054 (mttt) cc_final: 0.8603 (mttt) REVERT: S1 690 ASN cc_start: 0.8869 (t0) cc_final: 0.8240 (t0) REVERT: S1 707 PHE cc_start: 0.7936 (m-80) cc_final: 0.7645 (m-80) REVERT: S2 166 ASP cc_start: 0.8581 (t0) cc_final: 0.8122 (t0) REVERT: S2 205 ASP cc_start: 0.8449 (t0) cc_final: 0.8063 (t0) REVERT: S2 212 GLN cc_start: 0.8715 (tp40) cc_final: 0.8176 (tp40) REVERT: S3 1 MET cc_start: 0.7529 (tmm) cc_final: 0.6933 (tmm) REVERT: S3 63 ASP cc_start: 0.9314 (t70) cc_final: 0.9099 (t0) REVERT: S3 84 SER cc_start: 0.9144 (m) cc_final: 0.8914 (t) REVERT: S3 94 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6983 (mt-10) REVERT: S3 167 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7076 (mt-10) REVERT: S4 111 LYS cc_start: 0.8851 (ttpp) cc_final: 0.8574 (tttt) REVERT: S4 129 LYS cc_start: 0.8674 (mttt) cc_final: 0.8461 (mttm) REVERT: S8 46 ASP cc_start: 0.9075 (m-30) cc_final: 0.8745 (m-30) REVERT: S8 49 ARG cc_start: 0.8653 (ttm170) cc_final: 0.7150 (tpt170) REVERT: S8 51 GLN cc_start: 0.9239 (tt0) cc_final: 0.8989 (tp40) REVERT: S8 85 LYS cc_start: 0.9007 (tmmt) cc_final: 0.8622 (tttt) REVERT: S8 208 GLU cc_start: 0.8979 (tp30) cc_final: 0.8731 (tp30) REVERT: V1 78 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7968 (p0) REVERT: V1 266 CYS cc_start: 0.8838 (m) cc_final: 0.8438 (m) REVERT: V1 297 ASN cc_start: 0.8752 (m110) cc_final: 0.8195 (t0) REVERT: V1 367 TYR cc_start: 0.8146 (m-80) cc_final: 0.7780 (m-80) REVERT: V1 435 GLU cc_start: 0.8921 (mp0) cc_final: 0.8372 (mp0) REVERT: V2 53 VAL cc_start: 0.9613 (t) cc_final: 0.9327 (p) REVERT: V2 165 MET cc_start: 0.8503 (ttt) cc_final: 0.8268 (ttp) REVERT: V2 168 MET cc_start: 0.7820 (mtp) cc_final: 0.7617 (mtm) REVERT: V2 176 MET cc_start: 0.8607 (ppp) cc_final: 0.8287 (ppp) REVERT: V2 195 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7062 (mt-10) REVERT: 1M 82 PHE cc_start: 0.9177 (t80) cc_final: 0.8794 (t80) REVERT: 1M 262 ARG cc_start: 0.8267 (tpt170) cc_final: 0.7951 (mtt180) REVERT: 2M 32 LYS cc_start: 0.9076 (tttt) cc_final: 0.8862 (ttmt) REVERT: 2M 113 GLU cc_start: 0.8034 (mp0) cc_final: 0.7462 (mp0) REVERT: 2M 179 LEU cc_start: 0.9570 (tp) cc_final: 0.9341 (tt) REVERT: 2M 243 TYR cc_start: 0.7618 (m-10) cc_final: 0.7305 (m-80) REVERT: 2M 244 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8451 (tm-30) REVERT: 2M 293 LEU cc_start: 0.8245 (tp) cc_final: 0.8037 (tp) REVERT: 2M 301 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8714 (mm-40) REVERT: 2M 303 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8122 (mmtt) REVERT: 2M 347 ASP cc_start: 0.8540 (t70) cc_final: 0.8305 (t0) REVERT: 2M 434 LYS cc_start: 0.7477 (mmtm) cc_final: 0.6980 (tmtt) REVERT: 2M 436 MET cc_start: 0.8001 (mmm) cc_final: 0.6641 (tmm) REVERT: 2M 439 ASP cc_start: 0.8223 (t70) cc_final: 0.7968 (t0) REVERT: 3M 96 MET cc_start: 0.8900 (mmp) cc_final: 0.8516 (mmt) REVERT: 4L 6 TYR cc_start: 0.8874 (m-80) cc_final: 0.8589 (m-80) REVERT: 4L 77 LEU cc_start: 0.9100 (tp) cc_final: 0.8775 (tp) REVERT: 4L 82 ILE cc_start: 0.8974 (tp) cc_final: 0.8745 (tp) REVERT: 6M 70 MET cc_start: 0.9124 (mmp) cc_final: 0.8619 (mmt) REVERT: 6M 116 GLN cc_start: 0.8806 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A1 4 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8250 (tpp-160) REVERT: A1 49 MET cc_start: 0.8505 (mmp) cc_final: 0.8148 (mmm) REVERT: A1 54 LYS cc_start: 0.9293 (tmtt) cc_final: 0.9024 (tttp) REVERT: A1 58 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A8 39 CYS cc_start: 0.6907 (t) cc_final: 0.6603 (t) REVERT: A8 45 ASN cc_start: 0.8894 (t0) cc_final: 0.8325 (t0) REVERT: A8 75 MET cc_start: 0.9117 (ttt) cc_final: 0.8786 (tpp) REVERT: A8 87 ASN cc_start: 0.8998 (m-40) cc_final: 0.8795 (m-40) REVERT: C2 62 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8868 (ttmm) REVERT: C2 63 MET cc_start: 0.8823 (tpp) cc_final: 0.8538 (tpp) REVERT: P2 105 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8244 (mmmm) REVERT: X1 10 LYS cc_start: 0.8884 (mttt) cc_final: 0.8571 (mttp) REVERT: G1 16 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8746 (ttp-170) REVERT: G1 80 TRP cc_start: 0.9248 (m100) cc_final: 0.8824 (m100) REVERT: G1 181 TRP cc_start: 0.7986 (m100) cc_final: 0.7204 (m100) REVERT: G1 206 ASN cc_start: 0.8459 (m-40) cc_final: 0.8163 (m110) REVERT: G1 209 ASN cc_start: 0.8305 (m-40) cc_final: 0.8004 (m-40) REVERT: G1 226 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7707 (mm-30) REVERT: G2 36 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: G2 70 ASP cc_start: 0.8532 (p0) cc_final: 0.8318 (p0) REVERT: G2 212 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8577 (tm-30) REVERT: L2 165 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8041 (m170) REVERT: L2 235 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8140 (t80) outliers start: 165 outliers final: 101 residues processed: 1481 average time/residue: 0.5450 time to fit residues: 1320.9363 Evaluate side-chains 1366 residues out of total 4779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1260 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 21 SER Chi-restraints excluded: chain A2 residue 32 VAL Chi-restraints excluded: chain A5 residue 26 VAL Chi-restraints excluded: chain A5 residue 62 LYS Chi-restraints excluded: chain A5 residue 68 CYS Chi-restraints excluded: chain A5 residue 111 VAL Chi-restraints excluded: chain A6 residue 128 SER Chi-restraints excluded: chain A7 residue 50 THR Chi-restraints excluded: chain A9 residue 71 THR Chi-restraints excluded: chain A9 residue 153 VAL Chi-restraints excluded: chain A9 residue 190 MET Chi-restraints excluded: chain A9 residue 202 LEU Chi-restraints excluded: chain A9 residue 344 ASP Chi-restraints excluded: chain A9 residue 353 THR Chi-restraints excluded: chain A9 residue 369 VAL Chi-restraints excluded: chain AL residue 53 VAL Chi-restraints excluded: chain AL residue 100 THR Chi-restraints excluded: chain AL residue 134 SER Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 101 VAL Chi-restraints excluded: chain S1 residue 114 ILE Chi-restraints excluded: chain S1 residue 149 THR Chi-restraints excluded: chain S1 residue 151 VAL Chi-restraints excluded: chain S1 residue 214 THR Chi-restraints excluded: chain S1 residue 265 VAL Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 470 VAL Chi-restraints excluded: chain S1 residue 588 ASP Chi-restraints excluded: chain S1 residue 638 THR Chi-restraints excluded: chain S1 residue 698 THR Chi-restraints excluded: chain S2 residue 210 THR Chi-restraints excluded: chain S2 residue 220 SER Chi-restraints excluded: chain S2 residue 230 CYS Chi-restraints excluded: chain S2 residue 251 VAL Chi-restraints excluded: chain S2 residue 317 THR Chi-restraints excluded: chain S3 residue 102 VAL Chi-restraints excluded: chain S3 residue 150 SER Chi-restraints excluded: chain S3 residue 172 THR Chi-restraints excluded: chain S3 residue 184 TRP Chi-restraints excluded: chain S4 residue 49 SER Chi-restraints excluded: chain S4 residue 72 THR Chi-restraints excluded: chain S4 residue 126 LEU Chi-restraints excluded: chain S7 residue 137 VAL Chi-restraints excluded: chain S8 residue 124 ILE Chi-restraints excluded: chain S8 residue 187 THR Chi-restraints excluded: chain V1 residue 78 ASP Chi-restraints excluded: chain V1 residue 81 LEU Chi-restraints excluded: chain V1 residue 142 VAL Chi-restraints excluded: chain V1 residue 155 ASP Chi-restraints excluded: chain V1 residue 191 VAL Chi-restraints excluded: chain V1 residue 390 ASP Chi-restraints excluded: chain V1 residue 429 VAL Chi-restraints excluded: chain V1 residue 437 ILE Chi-restraints excluded: chain V2 residue 126 CYS Chi-restraints excluded: chain V2 residue 129 THR Chi-restraints excluded: chain V2 residue 149 VAL Chi-restraints excluded: chain V2 residue 177 ILE Chi-restraints excluded: chain V2 residue 202 VAL Chi-restraints excluded: chain 1M residue 118 VAL Chi-restraints excluded: chain 1M residue 157 THR Chi-restraints excluded: chain 1M residue 240 SER Chi-restraints excluded: chain 2M residue 3 ASN Chi-restraints excluded: chain 2M residue 87 ILE Chi-restraints excluded: chain 2M residue 101 PHE Chi-restraints excluded: chain 2M residue 162 THR Chi-restraints excluded: chain 2M residue 260 ILE Chi-restraints excluded: chain 2M residue 327 THR Chi-restraints excluded: chain 2M residue 349 PHE Chi-restraints excluded: chain 2M residue 446 LEU Chi-restraints excluded: chain 2M residue 479 THR Chi-restraints excluded: chain 3M residue 21 LEU Chi-restraints excluded: chain 3M residue 68 ILE Chi-restraints excluded: chain 3M residue 82 VAL Chi-restraints excluded: chain 3M residue 103 THR Chi-restraints excluded: chain 4L residue 65 VAL Chi-restraints excluded: chain 6M residue 8 SER Chi-restraints excluded: chain 6M residue 33 VAL Chi-restraints excluded: chain 6M residue 146 THR Chi-restraints excluded: chain 6M residue 150 VAL Chi-restraints excluded: chain 6M residue 163 MET Chi-restraints excluded: chain A1 residue 24 ASN Chi-restraints excluded: chain A1 residue 40 ILE Chi-restraints excluded: chain A8 residue 91 LEU Chi-restraints excluded: chain AM residue 49 ILE Chi-restraints excluded: chain C2 residue 6 THR Chi-restraints excluded: chain C2 residue 20 SER Chi-restraints excluded: chain P2 residue 94 ILE Chi-restraints excluded: chain X1 residue 53 ILE Chi-restraints excluded: chain X1 residue 93 ASP Chi-restraints excluded: chain G1 residue 13 PHE Chi-restraints excluded: chain G1 residue 39 LEU Chi-restraints excluded: chain G1 residue 45 LEU Chi-restraints excluded: chain G1 residue 197 MET Chi-restraints excluded: chain G2 residue 36 GLN Chi-restraints excluded: chain G2 residue 73 VAL Chi-restraints excluded: chain G2 residue 102 ASP Chi-restraints excluded: chain G2 residue 128 VAL Chi-restraints excluded: chain G2 residue 141 ASP Chi-restraints excluded: chain G2 residue 156 VAL Chi-restraints excluded: chain G2 residue 162 MET Chi-restraints excluded: chain G2 residue 188 PHE Chi-restraints excluded: chain L2 residue 46 THR Chi-restraints excluded: chain L2 residue 74 VAL Chi-restraints excluded: chain L2 residue 122 VAL Chi-restraints excluded: chain L2 residue 165 HIS Chi-restraints excluded: chain L2 residue 235 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 420 optimal weight: 9.9990 chunk 344 optimal weight: 0.5980 chunk 139 optimal weight: 6.9990 chunk 506 optimal weight: 4.9990 chunk 547 optimal weight: 4.9990 chunk 451 optimal weight: 2.9990 chunk 502 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 406 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: