Starting phenix.real_space_refine on Wed Mar 4 16:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znn_14812/03_2026/7znn_14812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znn_14812/03_2026/7znn_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 { model { file = "/net/cci-nas-00/data/ceres_data/7znn_14812/03_2026/7znn_14812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znn_14812/03_2026/7znn_14812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7znn_14812/03_2026/7znn_14812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znn_14812/03_2026/7znn_14812.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.24, per 1000 atoms: 0.22 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: 1.08 Conformation dependent library (CDL) restraints added in 665.4 milliseconds 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: 0.71 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: 2.64 Time building geometry restraints manager: 1.48 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: 1.420 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- 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 14880 Z= 0.237 Angle : 0.855 41.499 20085 Z= 0.528 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG A 134 TYR 0.009 0.001 TYR A 182 PHE 0.009 0.001 PHE D 341 TRP 0.007 0.001 TRP A1073 HIS 0.012 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00326 (14876) covalent geometry : angle 0.79581 (20082) hydrogen bonds : bond 0.30138 ( 401) hydrogen bonds : angle 10.74249 ( 1137) metal coordination : bond 0.02915 ( 4) metal coordination : angle 25.49943 ( 3) *********************** 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 to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.562 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 63 VAL cc_start: 0.9186 (t) cc_final: 0.8975 (p) REVERT: A 80 LEU cc_start: 0.9218 (tp) cc_final: 0.8831 (tp) REVERT: A 220 ILE cc_start: 0.8812 (mp) cc_final: 0.8456 (mp) REVERT: A 258 ILE cc_start: 0.7792 (mm) cc_final: 0.7148 (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: 0.6147 (tpt) REVERT: B 280 MET cc_start: 0.7728 (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: 0.9104 (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: 0.5024 (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: 0.1309 time to fit residues: 31.6106 Evaluate side-chains 95 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- 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 189 HIS A 234 GLN A 241 ASN A 261 HIS A 727 GLN A 885 ASN A 999 HIS B 141 ASN B 209 GLN B 365 GLN B 375 GLN B 580 ASN D 392 GLN D 573 ASN D 659 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.057868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.039801 restraints weight = 186591.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.040245 restraints weight = 152821.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.040545 restraints weight = 132919.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.040779 restraints weight = 120066.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.040987 restraints weight = 111866.225| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14880 Z= 0.124 Angle : 0.539 8.962 20085 Z= 0.278 Chirality : 0.041 0.199 2252 Planarity : 0.005 0.114 2576 Dihedral : 3.075 16.357 1990 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.17), residues: 1774 helix: -2.23 (0.19), residues: 482 sheet: -2.11 (0.27), residues: 329 loop : -2.00 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 301 TYR 0.023 0.001 TYR B 197 PHE 0.021 0.001 PHE A1072 TRP 0.023 0.001 TRP A1073 HIS 0.006 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00269 (14876) covalent geometry : angle 0.53737 (20082) hydrogen bonds : bond 0.04957 ( 401) hydrogen bonds : angle 6.71026 ( 1137) metal coordination : bond 0.02795 ( 4) metal coordination : angle 3.36710 ( 3) *********************** 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 111 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.576 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: 0.6263 (mmm) cc_final: 0.5929 (tpt) REVERT: A 218 MET cc_start: 0.7527 (tpp) cc_final: 0.7282 (mtp) REVERT: A 282 MET cc_start: 0.8847 (tmm) cc_final: 0.8321 (tmm) REVERT: A 927 MET cc_start: 0.9081 (tpt) cc_final: 0.8442 (tpt) REVERT: A 953 TRP cc_start: 0.9004 (m100) cc_final: 0.8508 (m100) REVERT: A 960 LEU cc_start: 0.8614 (tp) cc_final: 0.8292 (tp) REVERT: B 99 MET cc_start: 0.6799 (mmm) cc_final: 0.6502 (tpt) REVERT: B 280 MET cc_start: 0.9134 (tpp) cc_final: 0.8387 (tpp) REVERT: B 517 HIS cc_start: 0.7905 (t70) cc_final: 0.7237 (m90) REVERT: B 524 MET cc_start: 0.5766 (tpt) cc_final: 0.5414 (ttt) REVERT: D 444 MET cc_start: 0.6320 (ttm) cc_final: 0.6071 (mtp) REVERT: D 519 MET cc_start: -0.0439 (ppp) cc_final: -0.0925 (ptm) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1093 time to fit residues: 19.1661 Evaluate side-chains 85 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 172 optimal weight: 50.0000 chunk 168 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 337 ASN A 370 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 ASN A 950 ASN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 338 GLN B 548 HIS B 602 GLN D 418 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.053132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.036278 restraints weight = 200319.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.036603 restraints weight = 165730.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.037010 restraints weight = 146278.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.037240 restraints weight = 132719.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037593 restraints weight = 121042.792| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14880 Z= 0.215 Angle : 0.662 8.307 20085 Z= 0.338 Chirality : 0.043 0.286 2252 Planarity : 0.005 0.079 2576 Dihedral : 3.763 16.846 1990 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.18), residues: 1774 helix: -1.27 (0.21), residues: 470 sheet: -2.03 (0.26), residues: 350 loop : -1.69 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.018 0.002 TYR B 205 PHE 0.022 0.002 PHE A 281 TRP 0.035 0.002 TRP A1073 HIS 0.012 0.002 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00442 (14876) covalent geometry : angle 0.66021 (20082) hydrogen bonds : bond 0.04274 ( 401) hydrogen bonds : angle 6.20825 ( 1137) metal coordination : bond 0.03414 ( 4) metal coordination : angle 4.11553 ( 3) *********************** 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 93 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9367 (mmp) cc_final: 0.9138 (mmm) REVERT: A 218 MET cc_start: 0.7217 (tpp) cc_final: 0.6850 (mtp) REVERT: B 99 MET cc_start: 0.6790 (mmm) cc_final: 0.6482 (tpt) REVERT: B 205 TYR cc_start: 0.9699 (t80) cc_final: 0.9158 (t80) REVERT: B 268 MET cc_start: 0.9319 (ptt) cc_final: 0.9052 (tmm) REVERT: B 341 MET cc_start: 0.9725 (mtm) cc_final: 0.9500 (ptp) REVERT: B 394 MET cc_start: 0.9728 (ttp) cc_final: 0.9258 (ttp) REVERT: B 517 HIS cc_start: 0.8281 (t70) cc_final: 0.7653 (m90) REVERT: B 524 MET cc_start: 0.5383 (tpt) cc_final: 0.5081 (ttm) REVERT: B 578 MET cc_start: -0.2657 (ppp) cc_final: -0.3122 (ppp) REVERT: D 444 MET cc_start: 0.6597 (ttm) cc_final: 0.5404 (ttm) REVERT: D 519 MET cc_start: -0.0094 (ppp) cc_final: -0.0642 (ptm) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1086 time to fit residues: 16.0175 Evaluate side-chains 71 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 50.0000 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 167 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS A 978 GLN A1025 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 170 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.052603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.035854 restraints weight = 199757.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036172 restraints weight = 165573.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.036416 restraints weight = 144592.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.036742 restraints weight = 130116.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.036975 restraints weight = 122441.610| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14880 Z= 0.154 Angle : 0.559 6.616 20085 Z= 0.287 Chirality : 0.041 0.227 2252 Planarity : 0.004 0.055 2576 Dihedral : 3.766 17.179 1990 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1774 helix: -0.80 (0.22), residues: 492 sheet: -1.73 (0.27), residues: 345 loop : -1.64 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 117 TYR 0.017 0.002 TYR A 271 PHE 0.013 0.001 PHE A 281 TRP 0.028 0.002 TRP A1073 HIS 0.007 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00314 (14876) covalent geometry : angle 0.55784 (20082) hydrogen bonds : bond 0.03682 ( 401) hydrogen bonds : angle 5.87275 ( 1137) metal coordination : bond 0.04971 ( 4) metal coordination : angle 3.33297 ( 3) *********************** 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 93 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4388 (tpp) cc_final: 0.3924 (tpp) REVERT: A 218 MET cc_start: 0.7241 (tpp) cc_final: 0.6851 (mtp) REVERT: B 99 MET cc_start: 0.7302 (mmm) cc_final: 0.7039 (tpt) REVERT: B 205 TYR cc_start: 0.9688 (t80) cc_final: 0.9079 (t80) REVERT: B 268 MET cc_start: 0.9498 (ptt) cc_final: 0.9226 (tmm) REVERT: B 280 MET cc_start: 0.9204 (mmp) cc_final: 0.8608 (tpp) REVERT: B 341 MET cc_start: 0.9718 (mtm) cc_final: 0.9509 (ptm) REVERT: B 394 MET cc_start: 0.9723 (ttp) cc_final: 0.9275 (ttp) REVERT: B 517 HIS cc_start: 0.8419 (t70) cc_final: 0.7675 (m90) REVERT: B 524 MET cc_start: 0.4825 (tpt) cc_final: 0.4494 (ttm) REVERT: B 578 MET cc_start: -0.2710 (ppp) cc_final: -0.2953 (ppp) REVERT: D 444 MET cc_start: 0.6712 (ttm) cc_final: 0.6265 (ttm) REVERT: D 519 MET cc_start: 0.0150 (ppp) cc_final: -0.0337 (ptm) outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.1156 time to fit residues: 16.7557 Evaluate side-chains 72 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 0.1980 chunk 168 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 161 optimal weight: 0.0060 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 overall best weight: 3.0402 ------------------------------------------------------------------------------- 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** 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 = 0.3453 r_free = 0.3453 target = 0.052191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.035495 restraints weight = 203538.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035790 restraints weight = 169307.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036020 restraints weight = 147700.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036382 restraints weight = 132620.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036469 restraints weight = 123644.906| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14880 Z= 0.146 Angle : 0.549 6.745 20085 Z= 0.282 Chirality : 0.041 0.162 2252 Planarity : 0.004 0.045 2576 Dihedral : 3.917 16.989 1990 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 1774 helix: -0.47 (0.22), residues: 514 sheet: -1.72 (0.26), residues: 354 loop : -1.51 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 117 TYR 0.019 0.002 TYR A 271 PHE 0.011 0.001 PHE D 580 TRP 0.030 0.001 TRP A1073 HIS 0.008 0.001 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00295 (14876) covalent geometry : angle 0.54859 (20082) hydrogen bonds : bond 0.03446 ( 401) hydrogen bonds : angle 5.68396 ( 1137) metal coordination : bond 0.03984 ( 4) metal coordination : angle 2.23145 ( 3) *********************** 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 89 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4915 (tpp) cc_final: 0.4694 (tpp) REVERT: A 218 MET cc_start: 0.7494 (tpp) cc_final: 0.7184 (mtp) REVERT: A 927 MET cc_start: 0.9603 (mpp) cc_final: 0.8593 (ttt) REVERT: A 953 TRP cc_start: 0.9543 (m100) cc_final: 0.8704 (m100) REVERT: B 99 MET cc_start: 0.7484 (mmm) cc_final: 0.7259 (tpt) REVERT: B 205 TYR cc_start: 0.9649 (t80) cc_final: 0.9117 (t80) REVERT: B 268 MET cc_start: 0.9545 (ptt) cc_final: 0.9259 (tmm) REVERT: B 280 MET cc_start: 0.9193 (mmp) cc_final: 0.8608 (tpp) REVERT: B 283 MET cc_start: 0.7979 (mmp) cc_final: 0.7761 (mmp) REVERT: B 341 MET cc_start: 0.9734 (mtm) cc_final: 0.9428 (ptm) REVERT: B 394 MET cc_start: 0.9715 (ttp) cc_final: 0.9248 (ttt) REVERT: B 517 HIS cc_start: 0.8474 (t70) cc_final: 0.7778 (m90) REVERT: B 524 MET cc_start: 0.4509 (tpt) cc_final: 0.4249 (ttm) REVERT: B 578 MET cc_start: -0.2811 (ppp) cc_final: -0.3056 (ppp) REVERT: D 444 MET cc_start: 0.6713 (ttm) cc_final: 0.6268 (ttm) REVERT: D 519 MET cc_start: 0.1110 (ppp) cc_final: 0.0727 (ptm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1075 time to fit residues: 15.0580 Evaluate side-chains 73 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 9 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 173 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN A1077 HIS A1106 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN D 279 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.034618 restraints weight = 209174.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034884 restraints weight = 178631.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035100 restraints weight = 153798.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035377 restraints weight = 139299.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035511 restraints weight = 129444.775| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 14880 Z= 0.181 Angle : 0.612 9.538 20085 Z= 0.314 Chirality : 0.042 0.204 2252 Planarity : 0.005 0.112 2576 Dihedral : 4.236 17.318 1990 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1774 helix: -0.51 (0.22), residues: 521 sheet: -1.71 (0.27), residues: 326 loop : -1.45 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 176 TYR 0.021 0.002 TYR A 271 PHE 0.012 0.002 PHE D 175 TRP 0.033 0.002 TRP A1073 HIS 0.011 0.002 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00364 (14876) covalent geometry : angle 0.61027 (20082) hydrogen bonds : bond 0.03704 ( 401) hydrogen bonds : angle 5.82993 ( 1137) metal coordination : bond 0.05068 ( 4) metal coordination : angle 3.72011 ( 3) *********************** 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 87 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.7539 (tpp) cc_final: 0.7152 (mtp) REVERT: A 1054 MET cc_start: 0.9404 (tpt) cc_final: 0.9126 (mmm) REVERT: B 280 MET cc_start: 0.9280 (mmp) cc_final: 0.8633 (tpp) REVERT: B 379 MET cc_start: 0.8333 (ttt) cc_final: 0.8091 (ttt) REVERT: B 394 MET cc_start: 0.9680 (ttp) cc_final: 0.9475 (ttt) REVERT: B 517 HIS cc_start: 0.8379 (t70) cc_final: 0.7682 (m90) REVERT: B 524 MET cc_start: 0.4654 (tpt) cc_final: 0.4386 (ttm) REVERT: D 444 MET cc_start: 0.6993 (ttm) cc_final: 0.6609 (ttm) REVERT: D 519 MET cc_start: 0.2215 (ppp) cc_final: 0.1673 (ptm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1006 time to fit residues: 14.0131 Evaluate side-chains 68 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS A1077 HIS B 242 GLN B 602 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034767 restraints weight = 206036.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035098 restraints weight = 175063.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035329 restraints weight = 148862.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035481 restraints weight = 135225.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.035664 restraints weight = 126493.102| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14880 Z= 0.146 Angle : 0.573 10.202 20085 Z= 0.288 Chirality : 0.042 0.245 2252 Planarity : 0.004 0.110 2576 Dihedral : 4.195 17.060 1990 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.19), residues: 1774 helix: -0.36 (0.22), residues: 522 sheet: -1.72 (0.27), residues: 332 loop : -1.37 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1102 TYR 0.018 0.001 TYR B 197 PHE 0.011 0.001 PHE B 607 TRP 0.037 0.001 TRP A1073 HIS 0.008 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00303 (14876) covalent geometry : angle 0.57209 (20082) hydrogen bonds : bond 0.03411 ( 401) hydrogen bonds : angle 5.63723 ( 1137) metal coordination : bond 0.04085 ( 4) metal coordination : angle 2.57988 ( 3) *********************** 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 85 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.7645 (tpp) cc_final: 0.7119 (mtp) REVERT: A 927 MET cc_start: 0.9691 (mpp) cc_final: 0.9049 (ttt) REVERT: B 99 MET cc_start: 0.5695 (ttt) cc_final: 0.5352 (tpt) REVERT: B 268 MET cc_start: 0.9555 (ptt) cc_final: 0.9295 (tmm) REVERT: B 280 MET cc_start: 0.9204 (mmp) cc_final: 0.8585 (tpp) REVERT: B 341 MET cc_start: 0.9788 (tpt) cc_final: 0.9535 (mtp) REVERT: B 379 MET cc_start: 0.8540 (ttt) cc_final: 0.8297 (ttt) REVERT: B 394 MET cc_start: 0.9705 (ttp) cc_final: 0.9499 (ttt) REVERT: B 517 HIS cc_start: 0.8276 (t70) cc_final: 0.7549 (m90) REVERT: B 524 MET cc_start: 0.4468 (tpt) cc_final: 0.4130 (ttm) REVERT: D 444 MET cc_start: 0.7006 (ttm) cc_final: 0.6634 (ttm) REVERT: D 519 MET cc_start: 0.2305 (ppp) cc_final: 0.1774 (ptm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1125 time to fit residues: 15.2417 Evaluate side-chains 67 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 172 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN A 374 GLN A 797 HIS A1077 HIS ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.050477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034258 restraints weight = 209115.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034664 restraints weight = 173424.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034919 restraints weight = 150553.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035124 restraints weight = 136450.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035397 restraints weight = 123682.785| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14880 Z= 0.165 Angle : 0.601 11.619 20085 Z= 0.305 Chirality : 0.042 0.224 2252 Planarity : 0.004 0.085 2576 Dihedral : 4.370 18.781 1990 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1774 helix: -0.42 (0.22), residues: 527 sheet: -1.71 (0.27), residues: 333 loop : -1.31 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.023 0.002 TYR D 507 PHE 0.013 0.002 PHE A 140 TRP 0.041 0.002 TRP A1073 HIS 0.008 0.002 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00338 (14876) covalent geometry : angle 0.59872 (20082) hydrogen bonds : bond 0.03612 ( 401) hydrogen bonds : angle 5.68041 ( 1137) metal coordination : bond 0.05035 ( 4) metal coordination : angle 4.08580 ( 3) *********************** 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 79 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5020 (mmp) cc_final: 0.4793 (tpp) REVERT: A 218 MET cc_start: 0.7840 (tpp) cc_final: 0.7180 (mtp) REVERT: A 927 MET cc_start: 0.9716 (mpp) cc_final: 0.8996 (ttt) REVERT: B 99 MET cc_start: 0.7623 (mtp) cc_final: 0.7388 (ttt) REVERT: B 268 MET cc_start: 0.9559 (ptt) cc_final: 0.9315 (tmm) REVERT: B 280 MET cc_start: 0.9281 (mmp) cc_final: 0.8626 (tpp) REVERT: B 524 MET cc_start: 0.4179 (tpt) cc_final: 0.3821 (ttm) REVERT: D 444 MET cc_start: 0.6818 (ttm) cc_final: 0.6407 (ttm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1094 time to fit residues: 13.7970 Evaluate side-chains 63 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 167 optimal weight: 0.0980 chunk 136 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 30.0000 chunk 94 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS A 905 HIS A1077 HIS B 111 ASN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.035582 restraints weight = 199109.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.035990 restraints weight = 167734.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036284 restraints weight = 140885.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.036565 restraints weight = 125352.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.036747 restraints weight = 115702.786| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14880 Z= 0.094 Angle : 0.537 11.481 20085 Z= 0.265 Chirality : 0.042 0.200 2252 Planarity : 0.004 0.097 2576 Dihedral : 4.036 17.943 1990 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.20), residues: 1774 helix: -0.09 (0.22), residues: 522 sheet: -1.51 (0.28), residues: 332 loop : -1.32 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1102 TYR 0.014 0.001 TYR B 197 PHE 0.009 0.001 PHE B 472 TRP 0.041 0.001 TRP A1073 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00211 (14876) covalent geometry : angle 0.53640 (20082) hydrogen bonds : bond 0.02927 ( 401) hydrogen bonds : angle 5.14102 ( 1137) metal coordination : bond 0.01730 ( 4) metal coordination : angle 1.86036 ( 3) *********************** 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 86 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8392 (tpp) cc_final: 0.8039 (mtp) REVERT: A 927 MET cc_start: 0.9712 (mpp) cc_final: 0.9001 (ttt) REVERT: B 99 MET cc_start: 0.7571 (mtp) cc_final: 0.7370 (ttt) REVERT: B 268 MET cc_start: 0.9496 (ptt) cc_final: 0.9219 (tmm) REVERT: B 280 MET cc_start: 0.9075 (mmp) cc_final: 0.8409 (tpp) REVERT: B 283 MET cc_start: 0.7812 (mmp) cc_final: 0.7583 (mmp) REVERT: B 340 MET cc_start: 0.9717 (ppp) cc_final: 0.9516 (ppp) REVERT: B 341 MET cc_start: 0.9790 (tpt) cc_final: 0.9522 (mtp) REVERT: B 524 MET cc_start: 0.4147 (tpt) cc_final: 0.3762 (ttm) REVERT: D 444 MET cc_start: 0.6782 (ttm) cc_final: 0.6378 (ttm) REVERT: D 519 MET cc_start: 0.2552 (ppp) cc_final: 0.2145 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1076 time to fit residues: 14.8449 Evaluate side-chains 66 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 7.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN A 905 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN A1056 ASN ** A1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.033151 restraints weight = 220200.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.033310 restraints weight = 192129.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.033602 restraints weight = 162214.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.033802 restraints weight = 143649.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033929 restraints weight = 136624.770| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.7362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 14880 Z= 0.320 Angle : 0.870 12.563 20085 Z= 0.445 Chirality : 0.049 0.492 2252 Planarity : 0.006 0.102 2576 Dihedral : 5.314 26.174 1990 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 37.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.19), residues: 1774 helix: -1.12 (0.21), residues: 518 sheet: -1.79 (0.27), residues: 337 loop : -1.42 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 68 TYR 0.025 0.003 TYR B 257 PHE 0.025 0.003 PHE A 140 TRP 0.049 0.003 TRP A1073 HIS 0.015 0.003 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00633 (14876) covalent geometry : angle 0.86379 (20082) hydrogen bonds : bond 0.05102 ( 401) hydrogen bonds : angle 6.60863 ( 1137) metal coordination : bond 0.08740 ( 4) metal coordination : angle 8.64864 ( 3) ********************** 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 78 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.609 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: 0.9664 (mmm) cc_final: 0.9460 (mmm) REVERT: A 218 MET cc_start: 0.8145 (tpp) cc_final: 0.7704 (mtp) REVERT: A 927 MET cc_start: 0.9730 (mpp) cc_final: 0.9165 (ttt) REVERT: A 1054 MET cc_start: 0.9543 (tpt) cc_final: 0.9257 (mmm) REVERT: B 99 MET cc_start: 0.7902 (mtp) cc_final: 0.7591 (ttm) REVERT: B 205 TYR cc_start: 0.9613 (t80) cc_final: 0.9254 (t80) REVERT: B 268 MET cc_start: 0.9604 (ptt) cc_final: 0.9320 (tmm) REVERT: B 280 MET cc_start: 0.9233 (mmp) cc_final: 0.8689 (tpp) REVERT: B 341 MET cc_start: 0.9785 (tpt) cc_final: 0.9555 (mtp) REVERT: B 524 MET cc_start: 0.4003 (tpt) cc_final: 0.3676 (ttm) REVERT: D 444 MET cc_start: 0.7264 (ttm) cc_final: 0.6616 (ttm) REVERT: D 519 MET cc_start: 0.3168 (ppp) cc_final: 0.2918 (ppp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1085 time to fit residues: 13.6676 Evaluate side-chains 64 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 10.0000 chunk 17 optimal weight: 0.0040 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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 241 ASN A 731 GLN A 978 GLN A1056 ASN A1077 HIS ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035096 restraints weight = 201302.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035483 restraints weight = 168275.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.035752 restraints weight = 144891.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036003 restraints weight = 130436.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.036109 restraints weight = 122243.907| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14880 Z= 0.107 Angle : 0.581 11.613 20085 Z= 0.291 Chirality : 0.044 0.235 2252 Planarity : 0.004 0.095 2576 Dihedral : 4.495 29.217 1990 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1774 helix: -0.51 (0.21), residues: 533 sheet: -1.61 (0.28), residues: 309 loop : -1.38 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 200 TYR 0.013 0.001 TYR A 239 PHE 0.016 0.001 PHE A 140 TRP 0.037 0.001 TRP A1073 HIS 0.007 0.001 HIS A 991 Details of bonding type rmsd covalent geometry : bond 0.00238 (14876) covalent geometry : angle 0.58043 (20082) hydrogen bonds : bond 0.03209 ( 401) hydrogen bonds : angle 5.47705 ( 1137) metal coordination : bond 0.02043 ( 4) metal coordination : angle 1.69234 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.54 seconds wall clock time: 55 minutes 56.70 seconds (3356.70 seconds total)