Starting phenix.real_space_refine on Sat Apr 6 19:25:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf6_12296/04_2024/7nf6_12296_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf6_12296/04_2024/7nf6_12296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf6_12296/04_2024/7nf6_12296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf6_12296/04_2024/7nf6_12296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf6_12296/04_2024/7nf6_12296_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nf6_12296/04_2024/7nf6_12296_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 49 5.16 5 C 5754 2.51 5 N 1417 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "A ARG 665": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8817 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3506 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5090 Classifications: {'peptide': 623} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 596} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 109 Unusual residues: {' CA': 1, 'LBN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8817 At special positions: 0 Unit cell: (87.8848, 95.5747, 139.517, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 49 16.00 P 1 15.00 O 1595 8.00 N 1417 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS A 114 " distance=2.08 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.04 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 703 " - " ASN A 513 " " NAG A 704 " - " ASN A 246 " " NAG A 705 " - " ASN A 228 " " NAG A 706 " - " ASN A 523 " " NAG C 1 " - " ASN A 332 " " NAG D 1 " - " ASN A 261 " Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 48.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 32 through 43 removed outlier: 4.440A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.949A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 89 removed outlier: 4.078A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 86 " --> pdb=" O CYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.701A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.636A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.708A pdb=" N SER B 133 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.771A pdb=" N ALA B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 177 through 200 removed outlier: 3.530A pdb=" N ALA B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.585A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.550A pdb=" N GLU B 243 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.586A pdb=" N MET B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.200A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 285' Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.647A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 333 removed outlier: 3.501A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY B 325 " --> pdb=" O CYS B 321 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.502A pdb=" N MET B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 371 through 398 removed outlier: 3.603A pdb=" N ASN B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.774A pdb=" N ILE B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 435 through 454 removed outlier: 3.563A pdb=" N TYR B 439 " --> pdb=" O TRP B 435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 444 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 3.942A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 464' Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.829A pdb=" N MET B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.544A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 76' Processing helix chain 'A' and resid 84 through 110 removed outlier: 3.645A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.698A pdb=" N THR A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.600A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.762A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 355 through 369 removed outlier: 4.404A pdb=" N HIS A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 361 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 362 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.664A pdb=" N VAL A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.893A pdb=" N ASN A 463 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 464 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 465 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 467 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 469 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 518 Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.529A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing sheet with id= A, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.480A pdb=" N THR A 475 " --> pdb=" O TRP A 443 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 159 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 126 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP A 161 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 206 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE A 162 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 208 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 310 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 380 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE A 313 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 382 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 407 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.776A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 569 through 571 removed outlier: 3.659A pdb=" N LEU A 622 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU A 649 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE A 620 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 605 Processing sheet with id= E, first strand: chain 'A' and resid 673 through 675 284 hydrogen bonds defined for protein. 789 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: 2.44 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1546 1.33 - 1.45: 2438 1.45 - 1.57: 4988 1.57 - 1.70: 2 1.70 - 1.82: 81 Bond restraints: 9055 Sorted by residual: bond pdb=" C9 LBN A 701 " pdb=" O2 LBN A 701 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" O2 LBN A 701 " pdb=" P1 LBN A 701 " ideal model delta sigma weight residual 1.650 1.605 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 LBN A 701 " pdb=" O1 LBN A 701 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.71e+00 bond pdb=" C11 LBN A 701 " pdb=" C8 LBN A 701 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" N ALA A 66 " pdb=" CA ALA A 66 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.34e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.75: 212 105.75 - 112.83: 4814 112.83 - 119.91: 3133 119.91 - 127.00: 4034 127.00 - 134.08: 129 Bond angle restraints: 12322 Sorted by residual: angle pdb=" C GLU B 96 " pdb=" N TYR B 97 " pdb=" CA TYR B 97 " ideal model delta sigma weight residual 120.09 125.56 -5.47 1.25e+00 6.40e-01 1.92e+01 angle pdb=" C PHE A 173 " pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" CA TYR A 65 " pdb=" CB TYR A 65 " pdb=" CG TYR A 65 " ideal model delta sigma weight residual 113.90 120.26 -6.36 1.80e+00 3.09e-01 1.25e+01 angle pdb=" C TYR A 65 " pdb=" N ALA A 66 " pdb=" CA ALA A 66 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 111.02 114.55 -3.53 1.22e+00 6.72e-01 8.35e+00 ... (remaining 12317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 5112 26.26 - 52.52: 361 52.52 - 78.78: 42 78.78 - 105.05: 9 105.05 - 131.31: 4 Dihedral angle restraints: 5528 sinusoidal: 2383 harmonic: 3145 Sorted by residual: dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N HIS A 175 " pdb=" CA HIS A 175 " ideal model delta harmonic sigma weight residual 180.00 137.18 42.82 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA GLN A 79 " pdb=" C GLN A 79 " pdb=" N ALA A 80 " pdb=" CA ALA A 80 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA TYR A 65 " pdb=" C TYR A 65 " pdb=" N ALA A 66 " pdb=" CA ALA A 66 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1314 0.086 - 0.172: 82 0.172 - 0.259: 1 0.259 - 0.345: 2 0.345 - 0.431: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.30e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1397 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 523 " 0.233 2.00e-02 2.50e+03 3.33e-01 1.38e+03 pdb=" CG ASN A 523 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 523 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 523 " -0.559 2.00e-02 2.50e+03 pdb=" C1 NAG A 706 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 513 " -0.080 2.00e-02 2.50e+03 2.29e-01 6.58e+02 pdb=" CG ASN A 513 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 513 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN A 513 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " -0.037 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" CG ASN A 246 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " 0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " -0.275 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.194 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 184 2.67 - 3.23: 8513 3.23 - 3.79: 13350 3.79 - 4.34: 19409 4.34 - 4.90: 31150 Nonbonded interactions: 72606 Sorted by model distance: nonbonded pdb=" O GLY B 47 " pdb=" OG SER B 51 " model vdw 2.114 2.440 nonbonded pdb=" OG SER B 345 " pdb=" O ARG B 348 " model vdw 2.141 2.440 nonbonded pdb=" O LEU A 565 " pdb=" NH2 ARG A 584 " model vdw 2.174 2.520 nonbonded pdb=" OG1 THR A 471 " pdb=" OH TYR A 582 " model vdw 2.223 2.440 nonbonded pdb=" NE2 GLN B 474 " pdb=" O VAL B 479 " model vdw 2.281 2.520 ... (remaining 72601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.350 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: 6.870 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.290 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9055 Z= 0.393 Angle : 0.746 9.759 12322 Z= 0.416 Chirality : 0.047 0.431 1400 Planarity : 0.005 0.043 1520 Dihedral : 17.273 131.306 3498 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 8.17 % Allowed : 22.27 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.19), residues: 1074 helix: -4.12 (0.12), residues: 486 sheet: -2.26 (0.45), residues: 88 loop : -2.20 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.023 0.001 PHE A 407 TYR 0.019 0.001 TYR A 65 ARG 0.002 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 143 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 71 MET cc_start: 0.7689 (ttt) cc_final: 0.7288 (ttt) REVERT: B 233 ASP cc_start: 0.8265 (t70) cc_final: 0.7786 (t70) REVERT: B 237 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: B 244 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 338 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8751 (tp) REVERT: B 356 MET cc_start: 0.6922 (mmm) cc_final: 0.6637 (mmt) REVERT: B 360 MET cc_start: 0.7974 (ttp) cc_final: 0.7408 (tmm) REVERT: B 436 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: B 471 MET cc_start: 0.7639 (pp-130) cc_final: 0.7432 (ppp) REVERT: A 284 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: A 377 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8020 (mtp180) REVERT: A 465 MET cc_start: 0.9099 (tpt) cc_final: 0.8816 (mmm) REVERT: A 495 ASN cc_start: 0.8308 (t0) cc_final: 0.7849 (t0) REVERT: A 524 HIS cc_start: 0.7906 (p90) cc_final: 0.7688 (p-80) REVERT: A 574 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7777 (ppp-140) REVERT: A 662 PHE cc_start: 0.8497 (m-80) cc_final: 0.7648 (m-80) outliers start: 77 outliers final: 44 residues processed: 206 average time/residue: 0.2487 time to fit residues: 68.6786 Evaluate side-chains 171 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 121 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 675 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 203 ASN B 251 ASN B 372 ASN B 456 HIS B 463 GLN A 79 GLN A 146 GLN A 181 GLN A 220 HIS A 224 GLN A 282 GLN A 293 GLN A 301 GLN A 335 GLN A 345 GLN A 366 GLN A 370 GLN A 403 GLN A 442 ASN A 466 ASN A 510 GLN A 544 GLN A 561 ASN A 575 ASN A 606 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9055 Z= 0.226 Angle : 0.641 8.380 12322 Z= 0.328 Chirality : 0.044 0.319 1400 Planarity : 0.005 0.038 1520 Dihedral : 11.446 126.960 1600 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 6.47 % Allowed : 22.80 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.22), residues: 1074 helix: -1.98 (0.19), residues: 478 sheet: -1.92 (0.42), residues: 90 loop : -1.66 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.018 0.001 PHE A 407 TYR 0.015 0.001 TYR A 65 ARG 0.006 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 127 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 233 ASP cc_start: 0.8250 (t70) cc_final: 0.7795 (t70) REVERT: B 356 MET cc_start: 0.6976 (mmm) cc_final: 0.6459 (mmt) REVERT: B 360 MET cc_start: 0.7782 (ttp) cc_final: 0.7374 (tmm) REVERT: B 394 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 436 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: B 444 MET cc_start: 0.7686 (mpp) cc_final: 0.7097 (mtt) REVERT: B 475 MET cc_start: 0.7886 (mtp) cc_final: 0.7593 (tmm) REVERT: A 100 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 240 HIS cc_start: 0.7380 (t70) cc_final: 0.7132 (m-70) REVERT: A 284 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: A 465 MET cc_start: 0.9106 (tpt) cc_final: 0.8857 (mmm) REVERT: A 495 ASN cc_start: 0.8212 (t0) cc_final: 0.7931 (t0) REVERT: A 666 CYS cc_start: 0.5443 (m) cc_final: 0.5137 (m) outliers start: 61 outliers final: 30 residues processed: 174 average time/residue: 0.2782 time to fit residues: 64.2523 Evaluate side-chains 144 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 96 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN A 314 ASN A 403 GLN A 561 ASN A 679 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9055 Z= 0.188 Angle : 0.597 9.624 12322 Z= 0.299 Chirality : 0.043 0.314 1400 Planarity : 0.004 0.041 1520 Dihedral : 9.947 130.393 1552 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 5.83 % Allowed : 22.80 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.24), residues: 1074 helix: -0.75 (0.23), residues: 475 sheet: -1.60 (0.43), residues: 90 loop : -1.30 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.018 0.001 PHE A 407 TYR 0.017 0.001 TYR A 65 ARG 0.006 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 122 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8193 (tpt) cc_final: 0.7971 (tpt) REVERT: B 102 GLU cc_start: 0.8255 (tp30) cc_final: 0.7793 (tp30) REVERT: B 233 ASP cc_start: 0.8287 (t70) cc_final: 0.7701 (t70) REVERT: B 343 TYR cc_start: 0.8284 (m-10) cc_final: 0.7732 (m-10) REVERT: B 356 MET cc_start: 0.7100 (mmm) cc_final: 0.6622 (mmt) REVERT: B 360 MET cc_start: 0.7679 (ttp) cc_final: 0.7284 (tmm) REVERT: B 435 TRP cc_start: 0.7444 (m-90) cc_final: 0.6255 (m-10) REVERT: B 436 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: B 444 MET cc_start: 0.7719 (mpp) cc_final: 0.7144 (mtt) REVERT: B 471 MET cc_start: 0.8214 (ppp) cc_final: 0.7729 (ppp) REVERT: A 100 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7566 (mt) REVERT: A 284 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: A 465 MET cc_start: 0.9094 (tpt) cc_final: 0.8863 (mmm) REVERT: A 574 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7235 (ttp80) REVERT: A 658 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8100 (mmt180) REVERT: A 666 CYS cc_start: 0.5132 (m) cc_final: 0.4866 (m) outliers start: 55 outliers final: 36 residues processed: 163 average time/residue: 0.2314 time to fit residues: 51.3397 Evaluate side-chains 151 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.0030 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 GLN B 474 GLN A 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9055 Z= 0.182 Angle : 0.578 8.057 12322 Z= 0.290 Chirality : 0.043 0.312 1400 Planarity : 0.004 0.038 1520 Dihedral : 9.612 130.023 1551 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 5.09 % Allowed : 23.65 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1074 helix: -0.21 (0.24), residues: 469 sheet: -1.43 (0.43), residues: 90 loop : -1.16 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.022 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.003 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 116 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8267 (tp30) cc_final: 0.7833 (tp30) REVERT: B 233 ASP cc_start: 0.8242 (t70) cc_final: 0.7649 (t70) REVERT: B 343 TYR cc_start: 0.8284 (m-10) cc_final: 0.7723 (m-10) REVERT: B 356 MET cc_start: 0.7091 (mmm) cc_final: 0.6609 (mmt) REVERT: B 360 MET cc_start: 0.7690 (ttp) cc_final: 0.7431 (tmm) REVERT: B 435 TRP cc_start: 0.7351 (m-90) cc_final: 0.6259 (m-10) REVERT: B 436 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: B 444 MET cc_start: 0.7768 (mpp) cc_final: 0.7100 (mtt) REVERT: B 471 MET cc_start: 0.8161 (ppp) cc_final: 0.7736 (ppp) REVERT: A 100 LEU cc_start: 0.7775 (mp) cc_final: 0.7496 (mt) REVERT: A 284 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: A 465 MET cc_start: 0.9096 (tpt) cc_final: 0.8867 (mmm) REVERT: A 574 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7218 (ttp80) REVERT: A 658 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.8118 (mmt180) REVERT: A 666 CYS cc_start: 0.5270 (m) cc_final: 0.5001 (m) outliers start: 48 outliers final: 32 residues processed: 154 average time/residue: 0.2202 time to fit residues: 46.6629 Evaluate side-chains 145 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 GLN B 474 GLN A 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9055 Z= 0.230 Angle : 0.590 7.879 12322 Z= 0.294 Chirality : 0.044 0.310 1400 Planarity : 0.004 0.037 1520 Dihedral : 9.153 129.186 1543 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 5.73 % Allowed : 23.01 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.25), residues: 1074 helix: -0.02 (0.25), residues: 473 sheet: -1.40 (0.44), residues: 90 loop : -1.11 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.020 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.003 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 113 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8292 (tp30) cc_final: 0.7869 (tp30) REVERT: B 233 ASP cc_start: 0.8242 (t70) cc_final: 0.7656 (t70) REVERT: B 343 TYR cc_start: 0.8294 (m-10) cc_final: 0.7738 (m-10) REVERT: B 356 MET cc_start: 0.7097 (mmm) cc_final: 0.6610 (mmt) REVERT: B 360 MET cc_start: 0.7703 (ttp) cc_final: 0.7454 (tmm) REVERT: B 435 TRP cc_start: 0.7369 (m-90) cc_final: 0.6272 (m-10) REVERT: B 436 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: B 471 MET cc_start: 0.8207 (ppp) cc_final: 0.7793 (ppp) REVERT: A 100 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7524 (mt) REVERT: A 284 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: A 465 MET cc_start: 0.9109 (tpt) cc_final: 0.8873 (mmm) REVERT: A 574 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7160 (ttp80) REVERT: A 658 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.8132 (mmt180) REVERT: A 666 CYS cc_start: 0.5341 (m) cc_final: 0.5112 (m) outliers start: 54 outliers final: 39 residues processed: 157 average time/residue: 0.2194 time to fit residues: 47.6837 Evaluate side-chains 154 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.0010 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN A 403 GLN A 679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9055 Z= 0.190 Angle : 0.582 8.166 12322 Z= 0.290 Chirality : 0.043 0.308 1400 Planarity : 0.004 0.037 1520 Dihedral : 8.946 127.410 1541 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 5.09 % Allowed : 24.07 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1074 helix: 0.14 (0.25), residues: 473 sheet: -1.30 (0.45), residues: 90 loop : -1.04 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.022 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.003 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 115 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8266 (tp30) cc_final: 0.7840 (tp30) REVERT: B 233 ASP cc_start: 0.8234 (t70) cc_final: 0.7646 (t70) REVERT: B 343 TYR cc_start: 0.8281 (m-10) cc_final: 0.7715 (m-10) REVERT: B 356 MET cc_start: 0.7093 (mmm) cc_final: 0.6598 (mmt) REVERT: B 360 MET cc_start: 0.7720 (ttp) cc_final: 0.7416 (tmm) REVERT: B 390 ILE cc_start: 0.8364 (mm) cc_final: 0.8047 (mm) REVERT: B 435 TRP cc_start: 0.7309 (m-90) cc_final: 0.6244 (m-10) REVERT: B 436 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: B 471 MET cc_start: 0.8169 (ppp) cc_final: 0.7748 (ppp) REVERT: A 100 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 284 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: A 465 MET cc_start: 0.9096 (tpt) cc_final: 0.8866 (mmm) REVERT: A 574 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7096 (ttp80) REVERT: A 658 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8186 (mmt180) REVERT: A 666 CYS cc_start: 0.5344 (m) cc_final: 0.5109 (m) REVERT: A 679 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8134 (t0) outliers start: 48 outliers final: 36 residues processed: 155 average time/residue: 0.2251 time to fit residues: 47.6471 Evaluate side-chains 152 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 679 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN A 679 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9055 Z= 0.298 Angle : 0.610 8.426 12322 Z= 0.305 Chirality : 0.045 0.308 1400 Planarity : 0.004 0.038 1520 Dihedral : 8.970 126.375 1540 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 5.62 % Allowed : 23.01 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1074 helix: 0.12 (0.25), residues: 473 sheet: -1.25 (0.46), residues: 88 loop : -1.05 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.024 0.001 PHE A 407 TYR 0.016 0.001 TYR B 299 ARG 0.002 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 112 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8295 (tp30) cc_final: 0.7869 (tp30) REVERT: B 233 ASP cc_start: 0.8251 (t70) cc_final: 0.7668 (t70) REVERT: B 343 TYR cc_start: 0.8294 (m-10) cc_final: 0.7737 (m-10) REVERT: B 356 MET cc_start: 0.7124 (mmm) cc_final: 0.6624 (mmt) REVERT: B 360 MET cc_start: 0.7786 (ttp) cc_final: 0.7492 (tmm) REVERT: B 390 ILE cc_start: 0.8368 (mm) cc_final: 0.8045 (mm) REVERT: B 435 TRP cc_start: 0.7325 (m-90) cc_final: 0.6239 (m-10) REVERT: B 436 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: B 471 MET cc_start: 0.8168 (ppp) cc_final: 0.7863 (ppp) REVERT: A 100 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7552 (mt) REVERT: A 284 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: A 465 MET cc_start: 0.9119 (tpt) cc_final: 0.8875 (mmm) outliers start: 53 outliers final: 45 residues processed: 155 average time/residue: 0.2274 time to fit residues: 48.2650 Evaluate side-chains 157 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9055 Z= 0.201 Angle : 0.574 8.211 12322 Z= 0.287 Chirality : 0.043 0.304 1400 Planarity : 0.004 0.038 1520 Dihedral : 8.865 122.367 1540 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 5.51 % Allowed : 23.33 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1074 helix: 0.30 (0.25), residues: 473 sheet: -1.12 (0.48), residues: 88 loop : -0.98 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.007 0.001 HIS A 175 PHE 0.020 0.001 PHE A 407 TYR 0.017 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 114 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8286 (tp30) cc_final: 0.7858 (tp30) REVERT: B 201 GLN cc_start: 0.6484 (mm110) cc_final: 0.6140 (mm110) REVERT: B 233 ASP cc_start: 0.8244 (t70) cc_final: 0.7663 (t70) REVERT: B 271 ASN cc_start: 0.8038 (t0) cc_final: 0.7796 (t0) REVERT: B 343 TYR cc_start: 0.8280 (m-10) cc_final: 0.7713 (m-10) REVERT: B 360 MET cc_start: 0.7766 (ttp) cc_final: 0.7440 (tmm) REVERT: B 390 ILE cc_start: 0.8316 (mm) cc_final: 0.7975 (mm) REVERT: B 435 TRP cc_start: 0.7296 (m-90) cc_final: 0.6230 (m-10) REVERT: B 436 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: B 471 MET cc_start: 0.8216 (ppp) cc_final: 0.7851 (ppp) REVERT: A 100 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 284 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: A 465 MET cc_start: 0.9096 (tpt) cc_final: 0.8869 (mmm) REVERT: A 656 LEU cc_start: 0.8623 (mp) cc_final: 0.8405 (mp) outliers start: 52 outliers final: 41 residues processed: 154 average time/residue: 0.2310 time to fit residues: 49.1254 Evaluate side-chains 155 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 111 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 663 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.0370 chunk 101 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS A 679 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9055 Z= 0.209 Angle : 0.586 8.088 12322 Z= 0.292 Chirality : 0.044 0.304 1400 Planarity : 0.004 0.038 1520 Dihedral : 8.759 118.247 1538 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 5.62 % Allowed : 23.12 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1074 helix: 0.22 (0.25), residues: 486 sheet: -1.13 (0.47), residues: 88 loop : -0.94 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.008 0.001 HIS A 240 PHE 0.019 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 113 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8282 (tp30) cc_final: 0.7849 (tp30) REVERT: B 233 ASP cc_start: 0.8239 (t70) cc_final: 0.7657 (t70) REVERT: B 278 MET cc_start: 0.8449 (ptp) cc_final: 0.8146 (ptp) REVERT: B 343 TYR cc_start: 0.8278 (m-10) cc_final: 0.7721 (m-10) REVERT: B 360 MET cc_start: 0.7769 (ttp) cc_final: 0.7427 (tmm) REVERT: B 390 ILE cc_start: 0.8253 (mm) cc_final: 0.7950 (mm) REVERT: B 435 TRP cc_start: 0.7272 (m-90) cc_final: 0.6207 (m-10) REVERT: B 436 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: B 471 MET cc_start: 0.8282 (ppp) cc_final: 0.7860 (ppp) REVERT: A 73 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7866 (tt) REVERT: A 100 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 284 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: A 465 MET cc_start: 0.9114 (tpt) cc_final: 0.8892 (mmm) REVERT: A 656 LEU cc_start: 0.8618 (mp) cc_final: 0.8418 (mp) outliers start: 53 outliers final: 40 residues processed: 154 average time/residue: 0.2186 time to fit residues: 46.4859 Evaluate side-chains 156 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 112 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 663 LYS Chi-restraints excluded: chain A residue 679 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 67 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 240 HIS A 679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9055 Z= 0.173 Angle : 0.588 8.969 12322 Z= 0.291 Chirality : 0.043 0.303 1400 Planarity : 0.004 0.039 1520 Dihedral : 8.674 116.087 1537 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 4.45 % Allowed : 24.18 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1074 helix: 0.26 (0.24), residues: 493 sheet: -1.05 (0.47), residues: 88 loop : -0.92 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 383 HIS 0.010 0.001 HIS A 240 PHE 0.018 0.001 PHE A 407 TYR 0.017 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8242 (tp30) cc_final: 0.7827 (tp30) REVERT: B 233 ASP cc_start: 0.8229 (t70) cc_final: 0.7651 (t70) REVERT: B 278 MET cc_start: 0.8438 (ptp) cc_final: 0.8140 (ptp) REVERT: B 343 TYR cc_start: 0.8287 (m-10) cc_final: 0.7722 (m-10) REVERT: B 360 MET cc_start: 0.7755 (ttp) cc_final: 0.7407 (tmm) REVERT: B 390 ILE cc_start: 0.8234 (mm) cc_final: 0.7933 (mm) REVERT: B 435 TRP cc_start: 0.7297 (m-90) cc_final: 0.6237 (m-10) REVERT: B 436 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: B 471 MET cc_start: 0.8280 (ppp) cc_final: 0.7778 (ppp) REVERT: A 73 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 100 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7541 (mt) REVERT: A 284 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: A 465 MET cc_start: 0.9107 (tpt) cc_final: 0.8893 (mmm) REVERT: A 656 LEU cc_start: 0.8614 (mp) cc_final: 0.8393 (mp) outliers start: 42 outliers final: 34 residues processed: 142 average time/residue: 0.2269 time to fit residues: 44.4686 Evaluate side-chains 147 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 663 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099779 restraints weight = 10537.887| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.46 r_work: 0.2843 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9055 Z= 0.238 Angle : 0.603 9.066 12322 Z= 0.298 Chirality : 0.044 0.304 1400 Planarity : 0.004 0.040 1520 Dihedral : 8.318 113.318 1533 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 4.67 % Allowed : 23.75 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1074 helix: 0.20 (0.24), residues: 494 sheet: -1.04 (0.47), residues: 88 loop : -0.94 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 239 HIS 0.011 0.001 HIS A 240 PHE 0.021 0.001 PHE A 407 TYR 0.017 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.50 seconds wall clock time: 45 minutes 36.89 seconds (2736.89 seconds total)