Starting phenix.real_space_refine on Wed Mar 12 09:44:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmh_30406/03_2025/7cmh_30406.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmh_30406/03_2025/7cmh_30406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cmh_30406/03_2025/7cmh_30406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmh_30406/03_2025/7cmh_30406.map" model { file = "/net/cci-nas-00/data/ceres_data/7cmh_30406/03_2025/7cmh_30406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmh_30406/03_2025/7cmh_30406.cif" } resolution = 3.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4830 2.51 5 N 1179 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7368 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3480 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 60 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: "E" 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: "F" 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: 30 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Conformer: "B" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP B 601 " occ=0.50 ... (28 atoms not shown) pdb=" OXTBTRP B 601 " occ=0.50 Time building chain proxies: 5.27, per 1000 atoms: 0.72 Number of scatterers: 7368 At special positions: 0 Unit cell: (82.916, 84.007, 127.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1330 8.00 N 1179 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 3 sheets defined 56.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 167 through 175 removed outlier: 3.584A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.747A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.916A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.704A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.574A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.889A pdb=" N THR A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.548A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 342 removed outlier: 3.723A pdb=" N ALA A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.526A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.588A pdb=" N ILE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 4.015A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.701A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.974A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 removed outlier: 3.501A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.613A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 4.182A pdb=" N ASP A 583 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 585 through 589 removed outlier: 4.006A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.860A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.175A pdb=" N GLY B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 100 removed outlier: 3.657A pdb=" N ILE B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 111 removed outlier: 3.734A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.922A pdb=" N PHE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.634A pdb=" N GLN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.708A pdb=" N CYS B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 186 through 210 removed outlier: 3.542A pdb=" N PHE B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.547A pdb=" N GLN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.920A pdb=" N GLU B 257 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 289 removed outlier: 3.954A pdb=" N ILE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 3.521A pdb=" N TYR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.732A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 336 removed outlier: 4.050A pdb=" N ILE B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Proline residue: B 319 - end of helix removed outlier: 3.762A pdb=" N VAL B 322 " --> pdb=" O MET B 318 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.660A pdb=" N ALA B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.689A pdb=" N LEU B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.709A pdb=" N ILE B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 412 removed outlier: 4.025A pdb=" N ASN B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 403 " --> pdb=" O TYR B 399 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 445 removed outlier: 4.169A pdb=" N TYR B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.551A pdb=" N CYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 465 removed outlier: 3.690A pdb=" N VAL B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 491 removed outlier: 3.707A pdb=" N ASP B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 479 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227 removed outlier: 7.090A pdb=" N CYS A 432 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 466 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 removed outlier: 7.224A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ARG A 349 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 400 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544 removed outlier: 5.988A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 610 " --> pdb=" O ALA A 594 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 804 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: 2.03 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2161 1.34 - 1.45: 1262 1.45 - 1.57: 4079 1.57 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 7545 Sorted by residual: bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.452 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C21 3PH B 603 " pdb=" O21 3PH B 603 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.451 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.00e-02 2.50e+03 3.81e+01 bond pdb=" O11 3PH B 602 " pdb=" P 3PH B 602 " ideal model delta sigma weight residual 1.703 1.608 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 7540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9720 2.09 - 4.17: 435 4.17 - 6.26: 66 6.26 - 8.35: 32 8.35 - 10.43: 6 Bond angle restraints: 10259 Sorted by residual: angle pdb=" C GLY A 175 " pdb=" N SER A 176 " pdb=" CA SER A 176 " ideal model delta sigma weight residual 122.83 129.01 -6.18 1.08e+00 8.57e-01 3.28e+01 angle pdb=" N ASN B 176 " pdb=" CA ASN B 176 " pdb=" C ASN B 176 " ideal model delta sigma weight residual 111.28 116.28 -5.00 1.09e+00 8.42e-01 2.10e+01 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 113.25 118.96 -5.71 1.30e+00 5.92e-01 1.93e+01 angle pdb=" N SER B 178 " pdb=" CA SER B 178 " pdb=" C SER B 178 " ideal model delta sigma weight residual 110.28 116.55 -6.27 1.48e+00 4.57e-01 1.80e+01 angle pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " ideal model delta sigma weight residual 118.09 121.55 -3.46 8.20e-01 1.49e+00 1.78e+01 ... (remaining 10254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 4137 21.77 - 43.54: 342 43.54 - 65.31: 42 65.31 - 87.09: 12 87.09 - 108.86: 8 Dihedral angle restraints: 4541 sinusoidal: 1887 harmonic: 2654 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual -86.00 -37.22 -48.78 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA THR B 381 " pdb=" C THR B 381 " pdb=" N SER B 382 " pdb=" CA SER B 382 " ideal model delta harmonic sigma weight residual 180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 4538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1088 0.089 - 0.178: 103 0.178 - 0.267: 8 0.267 - 0.356: 1 0.356 - 0.445: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CB VAL B 492 " pdb=" CA VAL B 492 " pdb=" CG1 VAL B 492 " pdb=" CG2 VAL B 492 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1198 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 228 " -0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 229 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 131 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 132 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 460 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.69e+00 pdb=" N PRO B 461 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " -0.034 5.00e-02 4.00e+02 ... (remaining 1262 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1084 2.75 - 3.29: 6682 3.29 - 3.83: 11635 3.83 - 4.36: 13972 4.36 - 4.90: 23671 Nonbonded interactions: 57044 Sorted by model distance: nonbonded pdb=" O PHE B 243 " pdb=" CE3ATRP B 601 " model vdw 2.214 3.340 nonbonded pdb=" OD1 ASN B 134 " pdb=" N ATRP B 601 " model vdw 2.224 3.120 nonbonded pdb=" O PHE B 59 " pdb=" OH TYR B 145 " model vdw 2.251 3.040 nonbonded pdb=" O VAL B 129 " pdb=" OG1 THR B 133 " model vdw 2.257 3.040 nonbonded pdb=" O PHE B 243 " pdb=" N BTRP B 601 " model vdw 2.279 3.120 ... (remaining 57039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.910 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.127 7545 Z= 0.403 Angle : 1.060 10.434 10259 Z= 0.558 Chirality : 0.056 0.445 1201 Planarity : 0.007 0.081 1261 Dihedral : 16.328 108.858 2836 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.56 % Favored : 90.68 % Rotamer: Outliers : 1.18 % Allowed : 10.08 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.98 (0.17), residues: 923 helix: -4.53 (0.10), residues: 463 sheet: -1.57 (0.58), residues: 70 loop : -3.54 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.006 0.002 HIS B 358 PHE 0.018 0.002 PHE B 335 TYR 0.034 0.002 TYR B 145 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.807 Fit side-chains REVERT: A 192 LEU cc_start: 0.8554 (tp) cc_final: 0.8234 (tp) REVERT: A 383 SER cc_start: 0.8874 (m) cc_final: 0.8385 (m) REVERT: A 430 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8128 (mtm180) REVERT: B 204 MET cc_start: 0.8038 (mmt) cc_final: 0.7653 (mmm) REVERT: B 257 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5925 (tm-30) REVERT: B 263 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8102 (ptpp) REVERT: B 443 TRP cc_start: 0.5862 (t-100) cc_final: 0.5494 (t60) REVERT: B 479 PHE cc_start: 0.7763 (t80) cc_final: 0.7519 (t80) outliers start: 9 outliers final: 2 residues processed: 197 average time/residue: 0.1996 time to fit residues: 52.3649 Evaluate side-chains 143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 363 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 296 GLN A 317 ASN A 353 ASN A 560 GLN A 601 GLN B 284 ASN B 331 ASN B 349 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108106 restraints weight = 11543.698| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.80 r_work: 0.3165 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7545 Z= 0.214 Angle : 0.710 9.248 10259 Z= 0.352 Chirality : 0.045 0.295 1201 Planarity : 0.006 0.059 1261 Dihedral : 11.819 94.140 1253 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer: Outliers : 2.36 % Allowed : 17.02 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.22), residues: 923 helix: -2.64 (0.18), residues: 491 sheet: -0.64 (0.66), residues: 57 loop : -2.99 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.003 0.001 HIS A 539 PHE 0.010 0.001 PHE A 627 TYR 0.014 0.002 TYR B 495 ARG 0.006 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.812 Fit side-chains REVERT: A 192 LEU cc_start: 0.8606 (tp) cc_final: 0.8303 (tp) REVERT: A 383 SER cc_start: 0.9072 (m) cc_final: 0.8870 (p) REVERT: A 430 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8415 (mtm180) REVERT: A 451 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9211 (tt) REVERT: B 46 CYS cc_start: 0.8799 (m) cc_final: 0.8570 (m) REVERT: B 111 LYS cc_start: 0.8241 (tptm) cc_final: 0.7580 (ttpp) REVERT: B 257 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5668 (tm-30) REVERT: B 469 TRP cc_start: 0.5907 (t-100) cc_final: 0.5106 (t-100) outliers start: 17 outliers final: 7 residues processed: 163 average time/residue: 0.1721 time to fit residues: 39.3014 Evaluate side-chains 138 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 7 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 396 ASN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 284 ASN B 349 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109451 restraints weight = 11935.405| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.90 r_work: 0.3179 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7545 Z= 0.167 Angle : 0.626 9.106 10259 Z= 0.308 Chirality : 0.043 0.295 1201 Planarity : 0.005 0.050 1261 Dihedral : 10.693 84.614 1246 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer: Outliers : 3.40 % Allowed : 19.50 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.25), residues: 923 helix: -1.57 (0.22), residues: 490 sheet: -0.57 (0.68), residues: 57 loop : -2.67 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 PHE 0.012 0.001 PHE A 627 TYR 0.009 0.001 TYR B 253 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 344 ASP cc_start: 0.8035 (t70) cc_final: 0.7516 (t0) REVERT: A 451 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9122 (tt) REVERT: A 508 MET cc_start: 0.7427 (ttm) cc_final: 0.7148 (ttm) REVERT: A 595 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7802 (p0) REVERT: B 46 CYS cc_start: 0.8723 (m) cc_final: 0.8509 (m) REVERT: B 111 LYS cc_start: 0.8282 (tptm) cc_final: 0.7610 (ttpp) REVERT: B 469 TRP cc_start: 0.5829 (t-100) cc_final: 0.5064 (t-100) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 0.1666 time to fit residues: 35.4128 Evaluate side-chains 143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN B 208 GLN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107097 restraints weight = 12614.735| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.94 r_work: 0.3144 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7545 Z= 0.211 Angle : 0.637 9.694 10259 Z= 0.309 Chirality : 0.043 0.248 1201 Planarity : 0.004 0.049 1261 Dihedral : 9.686 72.250 1243 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer: Outliers : 3.93 % Allowed : 19.90 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.26), residues: 923 helix: -0.91 (0.23), residues: 485 sheet: -0.46 (0.69), residues: 57 loop : -2.37 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 179 HIS 0.004 0.001 HIS B 471 PHE 0.019 0.001 PHE A 346 TYR 0.012 0.001 TYR A 251 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.856 Fit side-chains REVERT: A 183 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7204 (mtm110) REVERT: A 344 ASP cc_start: 0.7975 (t70) cc_final: 0.7449 (t0) REVERT: A 430 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8309 (mtm180) REVERT: A 451 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9136 (tt) REVERT: A 508 MET cc_start: 0.7467 (ttm) cc_final: 0.7113 (ttm) REVERT: B 46 CYS cc_start: 0.8769 (m) cc_final: 0.8527 (m) REVERT: B 111 LYS cc_start: 0.8264 (tptm) cc_final: 0.7604 (ttpp) REVERT: B 458 THR cc_start: 0.8912 (p) cc_final: 0.8632 (t) REVERT: B 469 TRP cc_start: 0.5825 (t-100) cc_final: 0.5024 (t-100) outliers start: 30 outliers final: 17 residues processed: 151 average time/residue: 0.2778 time to fit residues: 57.6566 Evaluate side-chains 146 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 75 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN B 208 GLN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109927 restraints weight = 11713.689| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.83 r_work: 0.3182 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7545 Z= 0.156 Angle : 0.595 8.302 10259 Z= 0.288 Chirality : 0.042 0.261 1201 Planarity : 0.004 0.048 1261 Dihedral : 8.946 62.001 1243 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 4.45 % Allowed : 19.50 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.27), residues: 923 helix: -0.44 (0.24), residues: 485 sheet: -0.32 (0.69), residues: 57 loop : -2.13 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 124 HIS 0.003 0.001 HIS B 358 PHE 0.012 0.001 PHE A 346 TYR 0.008 0.001 TYR A 251 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.896 Fit side-chains REVERT: A 183 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7230 (mtm110) REVERT: A 344 ASP cc_start: 0.7974 (t70) cc_final: 0.7465 (t0) REVERT: A 451 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9080 (tt) REVERT: A 595 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7795 (p0) REVERT: B 111 LYS cc_start: 0.8210 (tptm) cc_final: 0.7549 (ttpp) REVERT: B 458 THR cc_start: 0.8817 (p) cc_final: 0.8571 (t) REVERT: B 469 TRP cc_start: 0.5601 (t-100) cc_final: 0.4883 (t-100) outliers start: 34 outliers final: 18 residues processed: 161 average time/residue: 0.2072 time to fit residues: 45.9966 Evaluate side-chains 146 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107404 restraints weight = 11876.788| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.84 r_work: 0.3137 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7545 Z= 0.217 Angle : 0.624 9.000 10259 Z= 0.301 Chirality : 0.043 0.273 1201 Planarity : 0.004 0.047 1261 Dihedral : 8.552 62.744 1243 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 4.58 % Allowed : 21.47 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 923 helix: -0.33 (0.24), residues: 491 sheet: -0.31 (0.69), residues: 57 loop : -1.96 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.004 0.001 HIS B 471 PHE 0.012 0.001 PHE A 346 TYR 0.011 0.001 TYR A 554 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.731 Fit side-chains REVERT: A 344 ASP cc_start: 0.7995 (t70) cc_final: 0.7458 (t0) REVERT: A 440 ARG cc_start: 0.8264 (mmt90) cc_final: 0.8033 (mmt90) REVERT: A 451 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9058 (tt) REVERT: A 508 MET cc_start: 0.7440 (ttm) cc_final: 0.7139 (ttm) REVERT: A 595 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7839 (p0) REVERT: B 111 LYS cc_start: 0.8259 (tptm) cc_final: 0.7645 (ttpp) REVERT: B 406 GLN cc_start: 0.9283 (tm-30) cc_final: 0.8984 (tm-30) REVERT: B 458 THR cc_start: 0.8849 (p) cc_final: 0.8648 (t) REVERT: B 469 TRP cc_start: 0.5749 (t-100) cc_final: 0.4858 (t-100) outliers start: 35 outliers final: 29 residues processed: 155 average time/residue: 0.2760 time to fit residues: 59.8939 Evaluate side-chains 154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.0370 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108195 restraints weight = 11948.400| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.86 r_work: 0.3151 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7545 Z= 0.180 Angle : 0.607 8.204 10259 Z= 0.292 Chirality : 0.043 0.304 1201 Planarity : 0.004 0.047 1261 Dihedral : 8.162 62.400 1243 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer: Outliers : 4.32 % Allowed : 22.25 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 923 helix: -0.09 (0.24), residues: 494 sheet: -0.22 (0.70), residues: 57 loop : -1.94 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.025 0.001 PHE A 346 TYR 0.009 0.001 TYR A 554 ARG 0.004 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.863 Fit side-chains REVERT: A 344 ASP cc_start: 0.8035 (t70) cc_final: 0.7541 (t0) REVERT: A 440 ARG cc_start: 0.8233 (mmt90) cc_final: 0.7993 (mmt90) REVERT: A 451 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9028 (tt) REVERT: A 508 MET cc_start: 0.7449 (ttm) cc_final: 0.7169 (ttm) REVERT: A 595 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7874 (p0) REVERT: B 111 LYS cc_start: 0.8220 (tptm) cc_final: 0.7618 (ttpp) REVERT: B 406 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8991 (tm-30) outliers start: 33 outliers final: 23 residues processed: 157 average time/residue: 0.2343 time to fit residues: 50.5232 Evaluate side-chains 148 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109272 restraints weight = 11685.701| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.81 r_work: 0.3170 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7545 Z= 0.168 Angle : 0.594 8.014 10259 Z= 0.285 Chirality : 0.042 0.331 1201 Planarity : 0.004 0.049 1261 Dihedral : 7.814 61.741 1243 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer: Outliers : 3.53 % Allowed : 23.82 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 923 helix: 0.25 (0.24), residues: 489 sheet: -0.19 (0.69), residues: 57 loop : -1.90 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.002 0.001 HIS B 471 PHE 0.025 0.001 PHE B 436 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.919 Fit side-chains REVERT: A 344 ASP cc_start: 0.8055 (t70) cc_final: 0.7591 (t0) REVERT: A 440 ARG cc_start: 0.8251 (mmt90) cc_final: 0.8016 (mmt90) REVERT: A 451 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8973 (tt) REVERT: A 508 MET cc_start: 0.7468 (ttm) cc_final: 0.7186 (ttm) REVERT: A 595 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7906 (p0) REVERT: B 111 LYS cc_start: 0.8210 (tptm) cc_final: 0.7611 (ttpp) REVERT: B 263 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7145 (tttt) REVERT: B 406 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8932 (tm-30) outliers start: 27 outliers final: 22 residues processed: 149 average time/residue: 0.2767 time to fit residues: 58.3819 Evaluate side-chains 149 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 37 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.132904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107922 restraints weight = 11897.215| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.82 r_work: 0.3151 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7545 Z= 0.205 Angle : 0.632 9.198 10259 Z= 0.305 Chirality : 0.043 0.337 1201 Planarity : 0.004 0.049 1261 Dihedral : 7.775 62.390 1243 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 3.53 % Allowed : 23.56 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 923 helix: 0.26 (0.24), residues: 493 sheet: -0.15 (0.70), residues: 57 loop : -1.90 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 179 HIS 0.003 0.001 HIS B 471 PHE 0.010 0.001 PHE A 542 TYR 0.010 0.001 TYR A 554 ARG 0.004 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.842 Fit side-chains REVERT: A 210 ARG cc_start: 0.6039 (mmm160) cc_final: 0.4945 (mmt90) REVERT: A 344 ASP cc_start: 0.7939 (t70) cc_final: 0.7461 (t0) REVERT: A 440 ARG cc_start: 0.8289 (mmt90) cc_final: 0.8052 (mmt90) REVERT: A 451 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8975 (tt) REVERT: A 508 MET cc_start: 0.7485 (ttm) cc_final: 0.7228 (ttm) REVERT: A 595 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7916 (p0) REVERT: B 111 LYS cc_start: 0.8217 (tptm) cc_final: 0.7627 (ttpp) REVERT: B 406 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8947 (tm-30) outliers start: 27 outliers final: 21 residues processed: 145 average time/residue: 0.1700 time to fit residues: 34.7200 Evaluate side-chains 146 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.133863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108764 restraints weight = 11934.269| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.84 r_work: 0.3159 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7545 Z= 0.186 Angle : 0.619 8.288 10259 Z= 0.297 Chirality : 0.043 0.342 1201 Planarity : 0.004 0.049 1261 Dihedral : 7.713 62.844 1243 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer: Outliers : 3.14 % Allowed : 24.35 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 923 helix: 0.33 (0.24), residues: 496 sheet: -0.13 (0.69), residues: 57 loop : -1.94 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.010 0.001 PHE B 306 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG B 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.125 Fit side-chains REVERT: A 210 ARG cc_start: 0.6063 (mmm160) cc_final: 0.5109 (mmt90) REVERT: A 344 ASP cc_start: 0.7976 (t70) cc_final: 0.7490 (t0) REVERT: A 440 ARG cc_start: 0.8285 (mmt90) cc_final: 0.8049 (mmt90) REVERT: A 451 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8965 (tt) REVERT: A 508 MET cc_start: 0.7469 (ttm) cc_final: 0.7221 (ttm) REVERT: A 595 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7901 (p0) REVERT: B 111 LYS cc_start: 0.8221 (tptm) cc_final: 0.7637 (ttpp) REVERT: B 263 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7136 (tttt) REVERT: B 406 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8934 (tm-30) REVERT: B 497 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7655 (tm-30) outliers start: 24 outliers final: 20 residues processed: 145 average time/residue: 0.1786 time to fit residues: 36.2577 Evaluate side-chains 147 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.0010 chunk 45 optimal weight: 3.9990 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** 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 = 0.3632 r_free = 0.3632 target = 0.135727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110823 restraints weight = 11796.917| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.82 r_work: 0.3175 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7545 Z= 0.156 Angle : 0.603 8.333 10259 Z= 0.289 Chirality : 0.042 0.345 1201 Planarity : 0.004 0.050 1261 Dihedral : 7.580 62.682 1243 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 2.88 % Allowed : 25.00 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.28), residues: 923 helix: 0.45 (0.25), residues: 493 sheet: -0.04 (0.70), residues: 57 loop : -1.88 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.012 0.001 PHE B 306 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG B 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.84 seconds wall clock time: 68 minutes 56.33 seconds (4136.33 seconds total)