Starting phenix.real_space_refine on Fri Sep 27 02:32:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znn_14812/09_2024/7znn_14812.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znn_14812/09_2024/7znn_14812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znn_14812/09_2024/7znn_14812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znn_14812/09_2024/7znn_14812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znn_14812/09_2024/7znn_14812.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znn_14812/09_2024/7znn_14812.cif" } resolution = 4.8 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= 0.036 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 Zn 1 6.06 5 S 83 5.16 5 C 9301 2.51 5 N 2528 2.21 5 O 2693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14606 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6179 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 757} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4605 Classifications: {'peptide': 559} Link IDs: {'PTRANS': 22, 'TRANS': 536} Chain breaks: 5 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3821 Classifications: {'peptide': 472} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 450} Chain breaks: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8098 SG CYS B 273 33.777 77.640 117.518 1.00332.18 S ATOM 8112 SG CYS B 275 30.980 75.131 118.149 1.00311.40 S ATOM 8136 SG CYS B 278 33.890 73.152 118.333 1.00284.24 S Time building chain proxies: 8.10, per 1000 atoms: 0.55 Number of scatterers: 14606 At special positions: 0 Unit cell: (106.25, 105, 176.25, 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) Zn 1 29.99 S 83 16.00 O 2693 8.00 N 2528 7.00 C 9301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 332 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 273 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 278 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 275 " Number of angles added : 3 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 24 sheets defined 32.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.648A pdb=" N LYS A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 987 through 991 Processing helix chain 'A' and resid 1044 through 1060 removed outlier: 3.806A pdb=" N ASN A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A1051 " --> pdb=" O TRP A1047 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1105 through 1110 removed outlier: 3.528A pdb=" N ALA A1110 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.884A pdb=" N LYS A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.955A pdb=" N LYS B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.510A pdb=" N ALA B 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG B 66 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.623A pdb=" N VAL B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.547A pdb=" N GLU B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.753A pdb=" N TYR B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 213 removed outlier: 3.549A pdb=" N LEU B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.447A pdb=" N ILE B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.700A pdb=" N ILE B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 235' Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.909A pdb=" N LEU B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 271 removed outlier: 3.964A pdb=" N ASP B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 264 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.663A pdb=" N MET B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.946A pdb=" N LEU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 437 removed outlier: 3.730A pdb=" N LEU B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.221A pdb=" N LEU B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 469 removed outlier: 3.979A pdb=" N GLU B 469 " --> pdb=" O SER B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 466 through 469' Processing helix chain 'B' and resid 485 through 493 removed outlier: 3.853A pdb=" N ALA B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.728A pdb=" N ASP B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 519 removed outlier: 3.771A pdb=" N ALA B 510 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.810A pdb=" N TYR B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 545 removed outlier: 4.138A pdb=" N TYR B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.887A pdb=" N VAL B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 559 " --> pdb=" O VAL B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 removed outlier: 4.042A pdb=" N VAL B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.952A pdb=" N LEU B 583 " --> pdb=" O MET B 579 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.821A pdb=" N ILE B 592 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.539A pdb=" N GLU B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 175 removed outlier: 4.089A pdb=" N THR D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 210 removed outlier: 3.702A pdb=" N THR D 201 " --> pdb=" O GLN D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.895A pdb=" N LEU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 227 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 284 removed outlier: 3.790A pdb=" N ALA D 265 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 276 " --> pdb=" O HIS D 272 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 279 " --> pdb=" O GLN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 removed outlier: 3.711A pdb=" N VAL D 298 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP D 299 " --> pdb=" O GLY D 295 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 300 " --> pdb=" O GLN D 296 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN D 301 " --> pdb=" O GLY D 297 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN D 314 " --> pdb=" O GLN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 393 removed outlier: 3.751A pdb=" N ARG D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.884A pdb=" N GLU D 427 " --> pdb=" O VAL D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.613A pdb=" N SER D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 476 removed outlier: 4.341A pdb=" N LEU D 475 " --> pdb=" O TRP D 471 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 476' Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.783A pdb=" N LEU D 496 " --> pdb=" O PRO D 492 " (cutoff:3.500A) Proline residue: D 498 - end of helix removed outlier: 3.667A pdb=" N SER D 501 " --> pdb=" O GLY D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.680A pdb=" N SER D 506 " --> pdb=" O TRP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.537A pdb=" N GLY D 518 " --> pdb=" O PRO D 514 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.048A pdb=" N SER D 542 " --> pdb=" O TRP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 564 Processing helix chain 'D' and resid 582 through 590 removed outlier: 4.021A pdb=" N ARG D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 590 " --> pdb=" O GLU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 639 removed outlier: 3.761A pdb=" N LEU D 636 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 639 " --> pdb=" O VAL D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 647 removed outlier: 4.005A pdb=" N ILE D 644 " --> pdb=" O PRO D 640 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 674 removed outlier: 3.778A pdb=" N PHE D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 670 through 674' Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.563A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1029 " --> pdb=" O CYS A1008 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1028 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A1038 " --> pdb=" O PHE A1030 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.644A pdb=" N ARG A 38 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU A 39 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 54 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE A 41 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.794A pdb=" N PHE A 67 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 79 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 87 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 5.459A pdb=" N ARG A 134 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LYS A 141 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 136 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 142 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 155 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.776A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 193 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.941A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.941A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 313 through 316 removed outlier: 3.700A pdb=" N CYS A 313 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 324 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 332 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 365 removed outlier: 3.995A pdb=" N VAL A 365 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 374 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 721 through 727 removed outlier: 5.971A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 741 through 742 Processing sheet with id=AB4, first strand: chain 'A' and resid 816 through 817 removed outlier: 3.634A pdb=" N ASP A 824 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 821 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 816 through 817 removed outlier: 6.788A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 833 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 880 through 881 removed outlier: 3.647A pdb=" N ARG A 900 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 913 through 917 removed outlier: 3.705A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.686A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.955A pdb=" N SER B 615 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N ILE B 33 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 95 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 321 through 324 removed outlier: 3.666A pdb=" N THR D 321 " --> pdb=" O ARG D 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 344 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR D 342 " --> pdb=" O PRO D 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 334 through 336 Processing sheet with id=AC3, first strand: chain 'D' and resid 383 through 386 removed outlier: 3.525A pdb=" N ALA D 360 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 386 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS D 359 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU D 436 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 361 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC5, first strand: chain 'D' and resid 545 through 546 removed outlier: 3.632A pdb=" N ILE D 551 " --> pdb=" O SER D 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 611 through 614 411 hydrogen bonds defined for protein. 1137 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: 4.93 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4780 1.34 - 1.46: 1747 1.46 - 1.57: 8217 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 14876 Sorted by residual: bond pdb=" C VAL A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.25e-02 6.40e+03 7.65e+00 bond pdb=" C VAL B 539 " pdb=" N PRO B 540 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.23e-02 6.61e+03 7.27e+00 bond pdb=" CA VAL B 194 " pdb=" C VAL B 194 " ideal model delta sigma weight residual 1.524 1.550 -0.025 1.05e-02 9.07e+03 5.85e+00 bond pdb=" CA THR B 42 " pdb=" CB THR B 42 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.86e-02 2.89e+03 4.85e+00 bond pdb=" C ARG A 50 " pdb=" O ARG A 50 " ideal model delta sigma weight residual 1.249 1.230 0.018 8.50e-03 1.38e+04 4.64e+00 ... (remaining 14871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 19439 2.14 - 4.27: 588 4.27 - 6.41: 45 6.41 - 8.54: 7 8.54 - 10.68: 3 Bond angle restraints: 20082 Sorted by residual: angle pdb=" C THR B 42 " pdb=" CA THR B 42 " pdb=" CB THR B 42 " ideal model delta sigma weight residual 116.54 109.79 6.75 1.15e+00 7.56e-01 3.44e+01 angle pdb=" C VAL A 222 " pdb=" N PRO A 223 " pdb=" CA PRO A 223 " ideal model delta sigma weight residual 120.21 115.16 5.05 9.60e-01 1.09e+00 2.77e+01 angle pdb=" N THR B 42 " pdb=" CA THR B 42 " pdb=" C THR B 42 " ideal model delta sigma weight residual 108.31 115.98 -7.67 1.52e+00 4.33e-01 2.55e+01 angle pdb=" C VAL B 539 " pdb=" N PRO B 540 " pdb=" CA PRO B 540 " ideal model delta sigma weight residual 119.19 114.25 4.94 1.06e+00 8.90e-01 2.17e+01 angle pdb=" C SER A 929 " pdb=" CA SER A 929 " pdb=" CB SER A 929 " ideal model delta sigma weight residual 116.54 111.56 4.98 1.15e+00 7.56e-01 1.87e+01 ... (remaining 20077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8128 17.97 - 35.94: 702 35.94 - 53.91: 158 53.91 - 71.88: 22 71.88 - 89.85: 17 Dihedral angle restraints: 9027 sinusoidal: 3750 harmonic: 5277 Sorted by residual: dihedral pdb=" CA TYR D 665 " pdb=" C TYR D 665 " pdb=" N PRO D 666 " pdb=" CA PRO D 666 " ideal model delta harmonic sigma weight residual 0.00 -19.35 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CB GLU D 604 " pdb=" CG GLU D 604 " pdb=" CD GLU D 604 " pdb=" OE1 GLU D 604 " ideal model delta sinusoidal sigma weight residual 0.00 -89.85 89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 728 " pdb=" CG GLU A 728 " pdb=" CD GLU A 728 " pdb=" OE1 GLU A 728 " ideal model delta sinusoidal sigma weight residual 0.00 -84.91 84.91 1 3.00e+01 1.11e-03 9.72e+00 ... (remaining 9024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1919 0.056 - 0.113: 306 0.113 - 0.169: 24 0.169 - 0.226: 2 0.226 - 0.282: 1 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CG LEU B 88 " pdb=" CB LEU B 88 " pdb=" CD1 LEU B 88 " pdb=" CD2 LEU B 88 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE B 86 " pdb=" N ILE B 86 " pdb=" C ILE B 86 " pdb=" CB ILE B 86 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 2249 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 665 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 666 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 666 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 666 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 664 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C LEU D 664 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU D 664 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR D 665 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 176 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.020 5.00e-02 4.00e+02 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4350 2.83 - 3.35: 12395 3.35 - 3.87: 24382 3.87 - 4.38: 28801 4.38 - 4.90: 47334 Nonbonded interactions: 117262 Sorted by model distance: nonbonded pdb=" O CYS A 903 " pdb=" OD1 ASN A 904 " model vdw 2.316 3.040 nonbonded pdb=" O LYS D 523 " pdb=" OG SER D 546 " model vdw 2.337 3.040 nonbonded pdb=" O SER A 818 " pdb=" OG SER A 818 " model vdw 2.346 3.040 nonbonded pdb=" OG SER D 613 " pdb=" O TYR D 626 " model vdw 2.351 3.040 nonbonded pdb=" O GLN D 200 " pdb=" ND2 ASN D 204 " model vdw 2.352 3.120 ... (remaining 117257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 0.790 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14876 Z= 0.213 Angle : 0.796 10.677 20082 Z= 0.522 Chirality : 0.042 0.282 2252 Planarity : 0.003 0.040 2576 Dihedral : 14.159 89.846 5611 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 0.93 % Allowed : 10.50 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -4.19 (0.16), residues: 1774 helix: -3.75 (0.15), residues: 429 sheet: -2.85 (0.26), residues: 295 loop : -2.36 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1073 HIS 0.012 0.001 HIS B 332 PHE 0.009 0.001 PHE D 341 TYR 0.009 0.001 TYR A 182 ARG 0.006 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.837 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: A 63 VAL cc_start: 0.9186 (t) cc_final: 0.8975 (p) REVERT: A 80 LEU cc_start: 0.9218 (tp) cc_final: 0.8832 (tp) REVERT: A 220 ILE cc_start: 0.8812 (mp) cc_final: 0.8456 (mp) REVERT: A 258 ILE cc_start: 0.7793 (mm) cc_final: 0.7149 (mm) REVERT: A 1105 MET cc_start: 0.9225 (mtt) cc_final: 0.8702 (mtt) REVERT: B 88 LEU cc_start: 0.1204 (OUTLIER) cc_final: 0.0945 (mm) REVERT: B 99 MET cc_start: 0.6434 (mmm) cc_final: 0.6148 (tpt) REVERT: B 280 MET cc_start: 0.7729 (tpp) cc_final: 0.7261 (tpp) REVERT: B 352 ASP cc_start: 0.7792 (m-30) cc_final: 0.7532 (p0) REVERT: B 369 LEU cc_start: 0.9358 (mt) cc_final: 0.9103 (tp) REVERT: B 517 HIS cc_start: 0.8512 (t70) cc_final: 0.8072 (m-70) REVERT: B 524 MET cc_start: 0.5270 (tpt) cc_final: 0.5017 (ttt) REVERT: D 444 MET cc_start: 0.5332 (ttm) cc_final: 0.4989 (mtp) REVERT: D 519 MET cc_start: 0.1746 (ppp) cc_final: 0.0630 (ptm) outliers start: 15 outliers final: 1 residues processed: 166 average time/residue: 0.3103 time to fit residues: 74.7406 Evaluate side-chains 96 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 0.0060 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN A 149 ASN A 156 ASN A 163 HIS A 189 HIS A 234 GLN A 241 ASN A 261 HIS A 337 ASN A 370 GLN A 950 ASN A 999 HIS A1025 GLN B 141 ASN B 209 GLN B 242 GLN B 338 GLN B 365 GLN B 375 GLN D 304 GLN D 392 GLN D 573 ASN D 659 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14876 Z= 0.210 Angle : 0.588 8.476 20082 Z= 0.301 Chirality : 0.042 0.182 2252 Planarity : 0.005 0.103 2576 Dihedral : 3.352 18.178 1990 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -3.05 (0.18), residues: 1774 helix: -2.08 (0.20), residues: 467 sheet: -2.21 (0.25), residues: 353 loop : -1.87 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1073 HIS 0.004 0.001 HIS A 261 PHE 0.019 0.002 PHE A1072 TYR 0.024 0.002 TYR B 197 ARG 0.006 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.839 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: A 1 MET cc_start: 0.6066 (mmm) cc_final: 0.5546 (tpt) REVERT: A 350 MET cc_start: 0.7875 (mmm) cc_final: 0.7635 (mmm) REVERT: A 953 TRP cc_start: 0.9108 (m100) cc_final: 0.8566 (m100) REVERT: B 99 MET cc_start: 0.6984 (mmm) cc_final: 0.6719 (tpt) REVERT: B 280 MET cc_start: 0.8128 (tpp) cc_final: 0.7438 (tpp) REVERT: B 352 ASP cc_start: 0.8000 (m-30) cc_final: 0.7788 (p0) REVERT: B 394 MET cc_start: 0.9543 (ttt) cc_final: 0.9188 (ttt) REVERT: B 517 HIS cc_start: 0.8464 (t70) cc_final: 0.7905 (m90) REVERT: B 524 MET cc_start: 0.4918 (tpt) cc_final: 0.4521 (ttt) REVERT: D 519 MET cc_start: 0.1740 (ppp) cc_final: 0.1013 (ptm) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2676 time to fit residues: 45.1127 Evaluate side-chains 80 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 50.0000 chunk 50 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 176 optimal weight: 50.0000 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 ASN A1059 ASN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS B 602 GLN D 170 GLN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14876 Z= 0.312 Angle : 0.703 10.691 20082 Z= 0.362 Chirality : 0.044 0.199 2252 Planarity : 0.005 0.068 2576 Dihedral : 4.104 17.046 1990 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.58 % Favored : 94.36 % Rotamer: Outliers : 0.31 % Allowed : 5.34 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.40 (0.19), residues: 1774 helix: -1.12 (0.21), residues: 484 sheet: -2.00 (0.27), residues: 344 loop : -1.64 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1073 HIS 0.019 0.002 HIS D 272 PHE 0.022 0.002 PHE A 281 TYR 0.019 0.002 TYR A 935 ARG 0.008 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.757 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: A 1 MET cc_start: 0.6428 (mmm) cc_final: 0.6019 (tpp) REVERT: A 64 MET cc_start: 0.9084 (ppp) cc_final: 0.8644 (tmm) REVERT: A 350 MET cc_start: 0.8379 (mmm) cc_final: 0.8121 (mmm) REVERT: A 953 TRP cc_start: 0.9244 (m100) cc_final: 0.8878 (m100) REVERT: B 99 MET cc_start: 0.7332 (mmm) cc_final: 0.7021 (tpt) REVERT: B 268 MET cc_start: 0.9595 (ptt) cc_final: 0.9169 (tmm) REVERT: B 394 MET cc_start: 0.9571 (ttt) cc_final: 0.9208 (ttt) REVERT: B 517 HIS cc_start: 0.8473 (t70) cc_final: 0.7973 (m90) REVERT: B 524 MET cc_start: 0.4565 (tpt) cc_final: 0.4265 (ttm) REVERT: D 444 MET cc_start: 0.6016 (mtp) cc_final: 0.5374 (mtp) REVERT: D 519 MET cc_start: 0.2448 (ppp) cc_final: 0.1882 (ptm) outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.2779 time to fit residues: 41.4981 Evaluate side-chains 70 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 40.0000 chunk 46 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 711 HIS A 845 GLN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN B 508 HIS D 153 GLN D 200 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14876 Z= 0.302 Angle : 0.696 9.191 20082 Z= 0.361 Chirality : 0.044 0.212 2252 Planarity : 0.005 0.064 2576 Dihedral : 4.598 19.500 1990 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.34 (0.19), residues: 1774 helix: -1.06 (0.21), residues: 527 sheet: -2.00 (0.26), residues: 340 loop : -1.60 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1073 HIS 0.012 0.002 HIS B 332 PHE 0.030 0.002 PHE A 140 TYR 0.028 0.002 TYR A 271 ARG 0.007 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9058 (ppp) cc_final: 0.8834 (ppp) REVERT: A 130 MET cc_start: 0.9371 (tpt) cc_final: 0.8621 (mmm) REVERT: A 350 MET cc_start: 0.8595 (mmm) cc_final: 0.8357 (mmm) REVERT: A 953 TRP cc_start: 0.9294 (m100) cc_final: 0.8685 (m100) REVERT: B 268 MET cc_start: 0.9625 (ptt) cc_final: 0.9224 (tmm) REVERT: B 280 MET cc_start: 0.8392 (mmp) cc_final: 0.8137 (tpp) REVERT: B 379 MET cc_start: 0.7313 (tpp) cc_final: 0.7038 (tpp) REVERT: B 517 HIS cc_start: 0.8357 (t70) cc_final: 0.7862 (m90) REVERT: B 524 MET cc_start: 0.4154 (tpt) cc_final: 0.3841 (ttm) REVERT: D 444 MET cc_start: 0.6235 (mtp) cc_final: 0.5765 (mtp) REVERT: D 519 MET cc_start: 0.3707 (ppp) cc_final: 0.3096 (ptm) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2678 time to fit residues: 36.2935 Evaluate side-chains 67 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 71 optimal weight: 0.4980 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 43 optimal weight: 0.1980 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 ASN A1077 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN D 279 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14876 Z= 0.197 Angle : 0.571 8.376 20082 Z= 0.292 Chirality : 0.042 0.168 2252 Planarity : 0.004 0.043 2576 Dihedral : 4.315 18.446 1990 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.06 (0.19), residues: 1774 helix: -0.64 (0.22), residues: 521 sheet: -2.01 (0.26), residues: 340 loop : -1.47 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1073 HIS 0.007 0.001 HIS A 999 PHE 0.012 0.001 PHE B 607 TYR 0.023 0.002 TYR B 197 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.872 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: A 1 MET cc_start: 0.6066 (tpp) cc_final: 0.5706 (tpp) REVERT: A 64 MET cc_start: 0.8650 (ppp) cc_final: 0.8403 (tmm) REVERT: A 130 MET cc_start: 0.9373 (tpt) cc_final: 0.8639 (mmm) REVERT: A 350 MET cc_start: 0.8573 (mmm) cc_final: 0.8347 (mmm) REVERT: A 910 MET cc_start: 0.8142 (pmm) cc_final: 0.7399 (pmm) REVERT: A 953 TRP cc_start: 0.9308 (m100) cc_final: 0.8802 (m100) REVERT: A 1105 MET cc_start: 0.9605 (mtm) cc_final: 0.9208 (mtt) REVERT: B 42 THR cc_start: 0.8172 (t) cc_final: 0.7955 (t) REVERT: B 280 MET cc_start: 0.8520 (mmp) cc_final: 0.8051 (tpp) REVERT: B 517 HIS cc_start: 0.8306 (t70) cc_final: 0.7526 (m-70) REVERT: B 524 MET cc_start: 0.3980 (tpt) cc_final: 0.3553 (ttm) REVERT: D 444 MET cc_start: 0.6003 (mtp) cc_final: 0.5510 (mtp) REVERT: D 519 MET cc_start: 0.3959 (ppp) cc_final: 0.3248 (ptm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2661 time to fit residues: 35.5048 Evaluate side-chains 70 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 20.0000 chunk 156 optimal weight: 50.0000 chunk 34 optimal weight: 0.2980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 174 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 343 GLN A 374 GLN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 HIS A1106 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14876 Z= 0.257 Angle : 0.633 9.293 20082 Z= 0.326 Chirality : 0.043 0.214 2252 Planarity : 0.004 0.041 2576 Dihedral : 4.584 18.445 1990 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.01 (0.19), residues: 1774 helix: -0.61 (0.22), residues: 518 sheet: -1.93 (0.26), residues: 333 loop : -1.47 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1073 HIS 0.008 0.002 HIS A 999 PHE 0.016 0.002 PHE A 140 TYR 0.017 0.002 TYR B 197 ARG 0.005 0.001 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6577 (tpp) cc_final: 0.6292 (tpp) REVERT: A 130 MET cc_start: 0.9352 (tpt) cc_final: 0.8574 (mmm) REVERT: A 350 MET cc_start: 0.8608 (mmm) cc_final: 0.8392 (mmm) REVERT: A 927 MET cc_start: 0.9419 (mpp) cc_final: 0.8906 (tpt) REVERT: A 953 TRP cc_start: 0.9446 (m100) cc_final: 0.8875 (m100) REVERT: B 280 MET cc_start: 0.8698 (mmp) cc_final: 0.8140 (tpp) REVERT: B 341 MET cc_start: 0.8816 (ptp) cc_final: 0.8247 (ptp) REVERT: B 524 MET cc_start: 0.4331 (tpt) cc_final: 0.3964 (ttm) REVERT: D 444 MET cc_start: 0.5905 (mtp) cc_final: 0.5456 (mtp) REVERT: D 519 MET cc_start: 0.4023 (ppp) cc_final: 0.3748 (ppp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2727 time to fit residues: 33.4187 Evaluate side-chains 66 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 40.0000 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 50.0000 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 HIS A1140 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14876 Z= 0.207 Angle : 0.588 7.523 20082 Z= 0.301 Chirality : 0.042 0.200 2252 Planarity : 0.004 0.039 2576 Dihedral : 4.510 24.629 1990 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.90 (0.20), residues: 1774 helix: -0.51 (0.22), residues: 529 sheet: -1.92 (0.26), residues: 345 loop : -1.37 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1073 HIS 0.009 0.001 HIS B 332 PHE 0.011 0.001 PHE D 341 TYR 0.015 0.002 TYR B 197 ARG 0.003 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9374 (tpt) cc_final: 0.8614 (mmm) REVERT: A 927 MET cc_start: 0.9413 (mpp) cc_final: 0.8896 (tpt) REVERT: A 953 TRP cc_start: 0.9432 (m100) cc_final: 0.8837 (m100) REVERT: B 280 MET cc_start: 0.8583 (mmp) cc_final: 0.8200 (tpp) REVERT: B 341 MET cc_start: 0.8731 (ptp) cc_final: 0.8210 (ptm) REVERT: B 524 MET cc_start: 0.3863 (tpt) cc_final: 0.3453 (ttm) REVERT: D 444 MET cc_start: 0.5651 (mtp) cc_final: 0.5199 (mtp) REVERT: D 519 MET cc_start: 0.4074 (ppp) cc_final: 0.3701 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2794 time to fit residues: 34.3416 Evaluate side-chains 66 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14876 Z= 0.222 Angle : 0.611 9.695 20082 Z= 0.313 Chirality : 0.043 0.187 2252 Planarity : 0.004 0.037 2576 Dihedral : 4.599 22.318 1990 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.81 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.87 (0.19), residues: 1774 helix: -0.43 (0.22), residues: 523 sheet: -1.87 (0.27), residues: 330 loop : -1.42 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1073 HIS 0.007 0.001 HIS A 999 PHE 0.011 0.002 PHE B 472 TYR 0.016 0.002 TYR B 257 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8924 (mmp) cc_final: 0.8633 (tpp) REVERT: A 130 MET cc_start: 0.9389 (tpt) cc_final: 0.8612 (mmm) REVERT: A 927 MET cc_start: 0.9414 (mpp) cc_final: 0.8921 (tpt) REVERT: A 953 TRP cc_start: 0.9425 (m100) cc_final: 0.8838 (m100) REVERT: A 1054 MET cc_start: 0.9438 (tpt) cc_final: 0.9217 (mmm) REVERT: A 1102 ARG cc_start: 0.9819 (tmm160) cc_final: 0.9538 (tpm170) REVERT: A 1105 MET cc_start: 0.9536 (mtm) cc_final: 0.9101 (mtt) REVERT: B 280 MET cc_start: 0.8646 (mmp) cc_final: 0.8133 (tpp) REVERT: B 341 MET cc_start: 0.8751 (ptp) cc_final: 0.8102 (ptp) REVERT: B 524 MET cc_start: 0.3819 (tpt) cc_final: 0.3479 (ttm) REVERT: D 444 MET cc_start: 0.5769 (mtp) cc_final: 0.5335 (mtp) REVERT: D 519 MET cc_start: 0.4013 (ppp) cc_final: 0.3577 (ppp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2704 time to fit residues: 32.4361 Evaluate side-chains 67 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 97 optimal weight: 0.0870 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 ASN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14876 Z= 0.193 Angle : 0.580 12.142 20082 Z= 0.296 Chirality : 0.043 0.295 2252 Planarity : 0.003 0.037 2576 Dihedral : 4.568 24.409 1990 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.77 (0.20), residues: 1774 helix: -0.32 (0.22), residues: 522 sheet: -1.78 (0.27), residues: 330 loop : -1.39 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1073 HIS 0.007 0.001 HIS A 999 PHE 0.010 0.001 PHE A 949 TYR 0.016 0.001 TYR A 239 ARG 0.003 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4682 (tpt) cc_final: 0.4331 (tpt) REVERT: A 57 MET cc_start: 0.8960 (mmp) cc_final: 0.8695 (tpp) REVERT: A 130 MET cc_start: 0.9384 (tpt) cc_final: 0.8654 (mmm) REVERT: A 218 MET cc_start: 0.7197 (mtp) cc_final: 0.6605 (mtp) REVERT: A 927 MET cc_start: 0.9408 (mpp) cc_final: 0.8905 (tpt) REVERT: A 953 TRP cc_start: 0.9454 (m100) cc_final: 0.8846 (m100) REVERT: A 1102 ARG cc_start: 0.9820 (tmm160) cc_final: 0.9536 (tpm170) REVERT: A 1105 MET cc_start: 0.9529 (mtm) cc_final: 0.9135 (mtt) REVERT: B 280 MET cc_start: 0.8415 (mmp) cc_final: 0.7932 (tpp) REVERT: B 341 MET cc_start: 0.8731 (ptp) cc_final: 0.8200 (ptm) REVERT: B 524 MET cc_start: 0.3899 (tpt) cc_final: 0.3505 (ttm) REVERT: D 444 MET cc_start: 0.5729 (mtp) cc_final: 0.5283 (mtp) REVERT: D 519 MET cc_start: 0.4027 (ppp) cc_final: 0.3594 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2716 time to fit residues: 33.7191 Evaluate side-chains 67 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 30.0000 chunk 104 optimal weight: 0.0020 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 0.0000 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14876 Z= 0.165 Angle : 0.559 11.377 20082 Z= 0.282 Chirality : 0.042 0.190 2252 Planarity : 0.003 0.036 2576 Dihedral : 4.457 22.764 1990 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.66 (0.20), residues: 1774 helix: -0.16 (0.22), residues: 526 sheet: -1.79 (0.27), residues: 329 loop : -1.34 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1073 HIS 0.006 0.001 HIS A 999 PHE 0.013 0.001 PHE B 607 TYR 0.015 0.001 TYR A 239 ARG 0.003 0.000 ARG B 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5040 (tpt) cc_final: 0.4363 (tpt) REVERT: A 57 MET cc_start: 0.9028 (mmp) cc_final: 0.8748 (tpp) REVERT: A 218 MET cc_start: 0.7482 (mtp) cc_final: 0.7086 (mtp) REVERT: A 927 MET cc_start: 0.9386 (mpp) cc_final: 0.8887 (tpt) REVERT: A 953 TRP cc_start: 0.9466 (m100) cc_final: 0.8842 (m100) REVERT: A 1014 MET cc_start: 0.8068 (tpt) cc_final: 0.7787 (tpp) REVERT: A 1102 ARG cc_start: 0.9819 (tmm160) cc_final: 0.9516 (tpm170) REVERT: A 1105 MET cc_start: 0.9517 (mtm) cc_final: 0.9139 (mtt) REVERT: B 280 MET cc_start: 0.8256 (mmp) cc_final: 0.7679 (tpp) REVERT: B 341 MET cc_start: 0.8689 (ptp) cc_final: 0.8166 (ptm) REVERT: B 524 MET cc_start: 0.3900 (tpt) cc_final: 0.3562 (ttm) REVERT: D 444 MET cc_start: 0.5872 (mtp) cc_final: 0.5503 (mtp) REVERT: D 519 MET cc_start: 0.4050 (ppp) cc_final: 0.3637 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2703 time to fit residues: 33.5546 Evaluate side-chains 68 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 125 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.049435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.033650 restraints weight = 213782.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033871 restraints weight = 185229.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034167 restraints weight = 155507.028| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.7255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14876 Z= 0.246 Angle : 0.646 20.305 20082 Z= 0.326 Chirality : 0.043 0.184 2252 Planarity : 0.004 0.046 2576 Dihedral : 4.774 38.583 1990 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.74 (0.20), residues: 1774 helix: -0.33 (0.22), residues: 526 sheet: -1.73 (0.28), residues: 321 loop : -1.37 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1073 HIS 0.009 0.001 HIS A 999 PHE 0.028 0.002 PHE B 85 TYR 0.018 0.002 TYR B 269 ARG 0.004 0.001 ARG B 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.90 seconds wall clock time: 46 minutes 10.32 seconds (2770.32 seconds total)