Starting phenix.real_space_refine on Wed Feb 12 08:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u1d_8482/02_2025/5u1d_8482.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u1d_8482/02_2025/5u1d_8482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u1d_8482/02_2025/5u1d_8482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u1d_8482/02_2025/5u1d_8482.map" model { file = "/net/cci-nas-00/data/ceres_data/5u1d_8482/02_2025/5u1d_8482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u1d_8482/02_2025/5u1d_8482.cif" } resolution = 3.97 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= 0.036 sd= 0.252 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4900 2.51 5 N 1426 2.21 5 O 1458 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-5592/modules/chem_data/mon_lib" Total number of atoms: 7815 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3635 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 18, 'TRANS': 542} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 962 Unresolved non-hydrogen dihedrals: 594 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 9, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 411 Chain: "B" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 3732 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 20, 'TRANS': 531} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 790 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 327 Chain: "X" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 448 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG A 529 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG A 529 " occ=0.50 residue: pdb=" N ARG B 494 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B 494 " occ=0.50 Time building chain proxies: 5.14, per 1000 atoms: 0.66 Number of scatterers: 7815 At special positions: 0 Unit cell: (92.8618, 120.53, 116.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1458 8.00 N 1426 7.00 C 4900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 73.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 202 removed outlier: 4.083A pdb=" N GLY A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.637A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 271 removed outlier: 3.871A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 removed outlier: 4.230A pdb=" N PHE A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 4.009A pdb=" N ILE A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 320 removed outlier: 3.564A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 373 removed outlier: 3.648A pdb=" N ILE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.223A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 4.023A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 352 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.659A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.640A pdb=" N ALA A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 removed outlier: 3.809A pdb=" N VAL A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 483 removed outlier: 4.162A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ALA A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.751A pdb=" N THR A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.055A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.662A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.648A pdb=" N LYS B 143 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.073A pdb=" N LEU B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 4.414A pdb=" N HIS B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 236 removed outlier: 3.678A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.134A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 289 removed outlier: 4.797A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 264 " --> pdb=" O MET B 260 " (cutoff:3.500A) Proline residue: B 265 - end of helix removed outlier: 3.549A pdb=" N ILE B 288 " --> pdb=" O PHE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.791A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 338 removed outlier: 3.685A pdb=" N ALA B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 401 removed outlier: 3.538A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 366 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 433 removed outlier: 3.790A pdb=" N LEU B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 3.896A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 584 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.529A pdb=" N ALA B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 4.359A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 654 removed outlier: 3.760A pdb=" N SER B 650 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 654 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.883A pdb=" N GLU X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 44 removed outlier: 3.845A pdb=" N ASP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL X 25 " --> pdb=" O THR X 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG X 41 " --> pdb=" O ARG X 37 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 527 removed outlier: 5.019A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 526 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN A 506 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.903A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 714 through 716 removed outlier: 3.727A pdb=" N GLU A 722 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.093A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 549 removed outlier: 6.559A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1707 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: 2.63 Time building geometry restraints manager: 2.08 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: 2692 1.34 - 1.46: 649 1.46 - 1.58: 4523 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 7919 Sorted by residual: bond pdb=" CA ILE A 204 " pdb=" CB ILE A 204 " ideal model delta sigma weight residual 1.534 1.565 -0.031 6.80e-03 2.16e+04 2.05e+01 bond pdb=" CA ILE A 204 " pdb=" C ILE A 204 " ideal model delta sigma weight residual 1.520 1.545 -0.025 8.80e-03 1.29e+04 8.27e+00 bond pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 1.462 1.484 -0.023 9.50e-03 1.11e+04 5.67e+00 bond pdb=" N GLY B 524 " pdb=" CA GLY B 524 " ideal model delta sigma weight residual 1.446 1.469 -0.023 9.50e-03 1.11e+04 5.62e+00 bond pdb=" N ASP B 130 " pdb=" CA ASP B 130 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.87e+00 ... (remaining 7914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 9939 2.08 - 4.16: 812 4.16 - 6.23: 37 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 10794 Sorted by residual: angle pdb=" C ASP B 624 " pdb=" N PRO B 625 " pdb=" CA PRO B 625 " ideal model delta sigma weight residual 120.11 130.50 -10.39 1.12e+00 7.97e-01 8.61e+01 angle pdb=" C SER A 688 " pdb=" N PRO A 689 " pdb=" CA PRO A 689 " ideal model delta sigma weight residual 119.05 129.31 -10.26 1.11e+00 8.12e-01 8.54e+01 angle pdb=" C LYS A 660 " pdb=" N PRO A 661 " pdb=" CA PRO A 661 " ideal model delta sigma weight residual 120.31 128.17 -7.86 9.80e-01 1.04e+00 6.44e+01 angle pdb=" C LEU A 569 " pdb=" N PRO A 570 " pdb=" CA PRO A 570 " ideal model delta sigma weight residual 119.28 127.08 -7.80 1.10e+00 8.26e-01 5.03e+01 angle pdb=" C THR A 495 " pdb=" N PRO A 496 " pdb=" CA PRO A 496 " ideal model delta sigma weight residual 119.84 128.32 -8.48 1.25e+00 6.40e-01 4.60e+01 ... (remaining 10789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 4369 15.80 - 31.60: 210 31.60 - 47.40: 79 47.40 - 63.20: 20 63.20 - 79.00: 1 Dihedral angle restraints: 4679 sinusoidal: 1333 harmonic: 3346 Sorted by residual: dihedral pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N GLU A 183 " pdb=" CA GLU A 183 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 183 " pdb=" C GLU A 183 " pdb=" N THR A 184 " pdb=" CA THR A 184 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA THR A 184 " pdb=" C THR A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta harmonic sigma weight residual 180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 837 0.038 - 0.076: 297 0.076 - 0.114: 117 0.114 - 0.152: 36 0.152 - 0.190: 14 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CA HIS X 45 " pdb=" N HIS X 45 " pdb=" C HIS X 45 " pdb=" CB HIS X 45 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ASP A 483 " pdb=" N ASP A 483 " pdb=" C ASP A 483 " pdb=" CB ASP A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1298 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 300 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO B 301 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 146 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 147 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 465 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 466 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.019 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3099 2.94 - 3.43: 8317 3.43 - 3.92: 12011 3.92 - 4.41: 12091 4.41 - 4.90: 21589 Nonbonded interactions: 57107 Sorted by model distance: nonbonded pdb=" O GLU A 183 " pdb=" OG1 THR A 184 " model vdw 2.452 3.040 nonbonded pdb=" O MET B 218 " pdb=" OG SER B 261 " model vdw 2.513 3.040 nonbonded pdb=" O ARG X 20 " pdb=" OG1 THR X 21 " model vdw 2.563 3.040 nonbonded pdb=" O SER B 255 " pdb=" OG1 THR B 258 " model vdw 2.571 3.040 nonbonded pdb=" O LEU A 360 " pdb=" OG SER A 363 " model vdw 2.582 3.040 ... (remaining 57102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.490 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 7919 Z= 0.493 Angle : 1.173 10.391 10794 Z= 0.861 Chirality : 0.050 0.190 1301 Planarity : 0.003 0.046 1427 Dihedral : 12.049 78.999 2521 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 0.84 % Allowed : 1.69 % Favored : 97.47 % 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: -2.16 (0.21), residues: 1158 helix: -0.58 (0.15), residues: 765 sheet: -4.63 (0.65), residues: 37 loop : -2.79 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.002 0.001 HIS B 539 PHE 0.013 0.001 PHE B 240 TYR 0.014 0.001 TYR B 446 ARG 0.005 0.001 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 363 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7526 (t60) cc_final: 0.7319 (t60) REVERT: A 304 SER cc_start: 0.8176 (t) cc_final: 0.7835 (p) REVERT: A 317 LEU cc_start: 0.8945 (mt) cc_final: 0.8468 (mt) REVERT: A 351 LEU cc_start: 0.8574 (tt) cc_final: 0.8295 (pp) REVERT: A 374 MET cc_start: 0.6740 (tpt) cc_final: 0.5995 (tpt) REVERT: A 383 GLU cc_start: 0.7744 (pt0) cc_final: 0.7504 (pt0) REVERT: A 392 GLU cc_start: 0.7150 (tt0) cc_final: 0.6871 (mm-30) REVERT: A 417 ILE cc_start: 0.7832 (mm) cc_final: 0.7611 (mm) REVERT: A 439 VAL cc_start: 0.6634 (t) cc_final: 0.6243 (m) REVERT: A 443 ASN cc_start: 0.9299 (m-40) cc_final: 0.9075 (t0) REVERT: A 452 MET cc_start: 0.7528 (ttt) cc_final: 0.7199 (tpp) REVERT: A 655 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6995 (ptm160) REVERT: A 660 LYS cc_start: 0.7518 (mttt) cc_final: 0.7258 (mmtm) REVERT: A 702 HIS cc_start: 0.7329 (m-70) cc_final: 0.6930 (m-70) REVERT: B 218 MET cc_start: 0.7298 (ttm) cc_final: 0.7032 (mtt) REVERT: B 243 GLU cc_start: 0.8711 (tp30) cc_final: 0.8492 (tt0) REVERT: B 248 GLU cc_start: 0.7216 (tp30) cc_final: 0.6960 (tp30) REVERT: B 267 ASN cc_start: 0.6832 (m-40) cc_final: 0.6604 (m-40) REVERT: B 292 LEU cc_start: 0.8587 (mt) cc_final: 0.8273 (mt) REVERT: B 316 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7032 (tp30) REVERT: B 345 PHE cc_start: 0.7333 (m-80) cc_final: 0.6845 (m-80) REVERT: B 360 GLU cc_start: 0.7579 (tt0) cc_final: 0.7370 (tm-30) REVERT: B 372 GLU cc_start: 0.6172 (tp30) cc_final: 0.5885 (tp30) REVERT: B 389 MET cc_start: 0.9184 (mmt) cc_final: 0.8666 (tmm) REVERT: B 416 GLN cc_start: 0.7558 (tp40) cc_final: 0.7284 (tp40) REVERT: B 428 TYR cc_start: 0.7588 (t80) cc_final: 0.7366 (t80) REVERT: B 430 TYR cc_start: 0.7824 (t80) cc_final: 0.7617 (t80) REVERT: B 446 TYR cc_start: 0.6981 (m-80) cc_final: 0.6772 (m-10) REVERT: B 452 ASN cc_start: 0.3719 (m-40) cc_final: 0.3458 (m-40) REVERT: X 1 MET cc_start: 0.4101 (ttm) cc_final: 0.3416 (ttt) REVERT: X 3 TRP cc_start: 0.6559 (t60) cc_final: 0.5842 (t60) REVERT: X 5 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6242 (tt) REVERT: X 46 ASP cc_start: 0.6712 (p0) cc_final: 0.6489 (p0) outliers start: 5 outliers final: 2 residues processed: 366 average time/residue: 0.2209 time to fit residues: 104.6105 Evaluate side-chains 279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain X residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 251 ASN A 257 HIS A 382 ASN A 701 GLN B 171 HIS B 539 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139764 restraints weight = 19557.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142828 restraints weight = 12900.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145065 restraints weight = 9442.881| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7919 Z= 0.226 Angle : 0.582 10.623 10794 Z= 0.310 Chirality : 0.039 0.192 1301 Planarity : 0.004 0.051 1427 Dihedral : 4.358 47.533 1248 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 5.91 % Allowed : 15.88 % Favored : 78.21 % 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: 0.59 (0.24), residues: 1158 helix: 1.62 (0.17), residues: 789 sheet: -4.00 (0.98), residues: 25 loop : -2.28 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 413 HIS 0.005 0.001 HIS B 299 PHE 0.018 0.002 PHE B 240 TYR 0.021 0.002 TYR X 22 ARG 0.007 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 292 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.9073 (t60) cc_final: 0.8526 (t60) REVERT: A 223 THR cc_start: 0.7829 (p) cc_final: 0.7613 (t) REVERT: A 224 PHE cc_start: 0.8014 (t80) cc_final: 0.7587 (t80) REVERT: A 227 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8368 (t0) REVERT: A 285 MET cc_start: 0.7752 (tpp) cc_final: 0.7507 (tpp) REVERT: A 392 GLU cc_start: 0.8085 (tt0) cc_final: 0.7484 (mt-10) REVERT: A 417 ILE cc_start: 0.9146 (mm) cc_final: 0.8875 (mm) REVERT: A 420 MET cc_start: 0.8854 (mpp) cc_final: 0.8654 (mpp) REVERT: A 439 VAL cc_start: 0.6854 (t) cc_final: 0.6304 (t) REVERT: A 443 ASN cc_start: 0.9024 (m-40) cc_final: 0.8801 (t0) REVERT: A 466 PRO cc_start: 0.9245 (Cg_exo) cc_final: 0.9041 (Cg_endo) REVERT: A 660 LYS cc_start: 0.8335 (mttt) cc_final: 0.8129 (mmtm) REVERT: B 131 GLN cc_start: 0.6675 (pm20) cc_final: 0.6437 (pm20) REVERT: B 243 GLU cc_start: 0.8993 (tp30) cc_final: 0.8745 (tt0) REVERT: B 248 GLU cc_start: 0.8750 (tp30) cc_final: 0.8422 (tp30) REVERT: B 300 MET cc_start: 0.9011 (mmt) cc_final: 0.8570 (mmp) REVERT: B 316 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6590 (tp30) REVERT: B 320 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8572 (mm-30) REVERT: B 351 GLU cc_start: 0.8755 (tp30) cc_final: 0.8420 (tp30) REVERT: B 360 GLU cc_start: 0.8556 (tt0) cc_final: 0.8263 (tm-30) REVERT: B 370 ASP cc_start: 0.8877 (m-30) cc_final: 0.8602 (m-30) REVERT: B 372 GLU cc_start: 0.6921 (tp30) cc_final: 0.6576 (tp30) REVERT: B 373 ARG cc_start: 0.9179 (tmm-80) cc_final: 0.8832 (ttm170) REVERT: B 391 MET cc_start: 0.9056 (ttm) cc_final: 0.8151 (ttt) REVERT: B 416 GLN cc_start: 0.8772 (tp40) cc_final: 0.8486 (tp40) REVERT: B 428 TYR cc_start: 0.9437 (t80) cc_final: 0.9166 (t80) REVERT: B 430 TYR cc_start: 0.8576 (t80) cc_final: 0.8192 (t80) REVERT: X 46 ASP cc_start: 0.8278 (p0) cc_final: 0.7950 (p0) REVERT: X 53 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7372 (mtt180) outliers start: 35 outliers final: 20 residues processed: 305 average time/residue: 0.1867 time to fit residues: 77.0267 Evaluate side-chains 263 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 45 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN B 171 HIS B 311 ASN B 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131746 restraints weight = 20165.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134730 restraints weight = 13275.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136793 restraints weight = 9703.263| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7919 Z= 0.317 Angle : 0.657 9.935 10794 Z= 0.349 Chirality : 0.041 0.235 1301 Planarity : 0.005 0.035 1427 Dihedral : 4.631 34.826 1246 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 8.78 % Allowed : 18.75 % Favored : 72.47 % 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: 0.64 (0.25), residues: 1158 helix: 1.63 (0.18), residues: 795 sheet: -3.77 (0.79), residues: 34 loop : -2.17 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 348 HIS 0.004 0.001 HIS A 255 PHE 0.030 0.003 PHE A 190 TYR 0.021 0.002 TYR A 349 ARG 0.004 0.001 ARG X 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8418 (m-80) cc_final: 0.8176 (m-80) REVERT: A 214 TRP cc_start: 0.9148 (t60) cc_final: 0.8897 (t60) REVERT: A 224 PHE cc_start: 0.8126 (t80) cc_final: 0.7854 (t80) REVERT: A 250 ASN cc_start: 0.9202 (m110) cc_final: 0.8982 (m110) REVERT: A 344 LYS cc_start: 0.8057 (tttt) cc_final: 0.7271 (ttpt) REVERT: A 382 ASN cc_start: 0.8982 (t0) cc_final: 0.8748 (t0) REVERT: A 392 GLU cc_start: 0.8382 (tt0) cc_final: 0.7861 (mm-30) REVERT: A 417 ILE cc_start: 0.9188 (mm) cc_final: 0.8904 (mm) REVERT: A 420 MET cc_start: 0.8785 (mpp) cc_final: 0.8482 (mpp) REVERT: A 428 TYR cc_start: 0.8194 (t80) cc_final: 0.7954 (t80) REVERT: A 443 ASN cc_start: 0.8980 (m-40) cc_final: 0.8705 (t0) REVERT: A 601 TYR cc_start: 0.8813 (t80) cc_final: 0.8445 (t80) REVERT: B 131 GLN cc_start: 0.6689 (pm20) cc_final: 0.6435 (pm20) REVERT: B 172 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: B 210 ARG cc_start: 0.8889 (ptt-90) cc_final: 0.8628 (ttp-170) REVERT: B 254 SER cc_start: 0.7673 (t) cc_final: 0.7283 (m) REVERT: B 285 MET cc_start: 0.8239 (mtm) cc_final: 0.7535 (mtm) REVERT: B 300 MET cc_start: 0.9068 (mmt) cc_final: 0.8741 (mmp) REVERT: B 316 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6914 (tp30) REVERT: B 320 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8609 (mm-30) REVERT: B 343 ARG cc_start: 0.8991 (mtp85) cc_final: 0.8660 (tpp80) REVERT: B 351 GLU cc_start: 0.8765 (tp30) cc_final: 0.8466 (tp30) REVERT: B 360 GLU cc_start: 0.8681 (tt0) cc_final: 0.8123 (tm-30) REVERT: B 372 GLU cc_start: 0.7373 (tp30) cc_final: 0.6941 (tp30) REVERT: B 373 ARG cc_start: 0.9098 (tmm-80) cc_final: 0.8707 (ttm170) REVERT: B 477 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6562 (m-10) REVERT: X 41 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8471 (ttp80) REVERT: X 46 ASP cc_start: 0.8368 (p0) cc_final: 0.8076 (p0) REVERT: X 53 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7438 (mtt180) outliers start: 52 outliers final: 35 residues processed: 275 average time/residue: 0.1842 time to fit residues: 68.8563 Evaluate side-chains 275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 14 ASN Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 45 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 91 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 chunk 83 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.154772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133916 restraints weight = 19732.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136893 restraints weight = 12949.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139073 restraints weight = 9453.806| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7919 Z= 0.215 Angle : 0.585 9.665 10794 Z= 0.302 Chirality : 0.039 0.210 1301 Planarity : 0.003 0.039 1427 Dihedral : 4.285 38.404 1246 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 7.26 % Allowed : 23.31 % Favored : 69.43 % 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: 1.12 (0.25), residues: 1158 helix: 1.98 (0.18), residues: 807 sheet: -3.88 (0.75), residues: 34 loop : -2.08 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 348 HIS 0.003 0.001 HIS B 299 PHE 0.023 0.002 PHE A 447 TYR 0.015 0.002 TYR A 249 ARG 0.003 0.000 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8550 (m-80) cc_final: 0.8127 (m-80) REVERT: A 214 TRP cc_start: 0.9205 (t60) cc_final: 0.8921 (t60) REVERT: A 224 PHE cc_start: 0.8048 (t80) cc_final: 0.7735 (t80) REVERT: A 344 LYS cc_start: 0.8063 (tttt) cc_final: 0.7309 (ttpt) REVERT: A 382 ASN cc_start: 0.8894 (t0) cc_final: 0.8676 (t0) REVERT: A 392 GLU cc_start: 0.8367 (tt0) cc_final: 0.7810 (mm-30) REVERT: A 420 MET cc_start: 0.8825 (mpp) cc_final: 0.8559 (mpp) REVERT: A 428 TYR cc_start: 0.8173 (t80) cc_final: 0.7947 (t80) REVERT: A 443 ASN cc_start: 0.8950 (m-40) cc_final: 0.8697 (t0) REVERT: A 601 TYR cc_start: 0.8753 (t80) cc_final: 0.8342 (t80) REVERT: B 131 GLN cc_start: 0.6584 (pm20) cc_final: 0.6340 (pm20) REVERT: B 151 LEU cc_start: 0.8619 (mt) cc_final: 0.8364 (mt) REVERT: B 172 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: B 248 GLU cc_start: 0.8847 (tp30) cc_final: 0.8593 (tp30) REVERT: B 254 SER cc_start: 0.7639 (t) cc_final: 0.7317 (m) REVERT: B 285 MET cc_start: 0.8110 (mtm) cc_final: 0.7833 (mtm) REVERT: B 300 MET cc_start: 0.9017 (mmt) cc_final: 0.8763 (mmm) REVERT: B 310 TYR cc_start: 0.9478 (t80) cc_final: 0.9152 (t80) REVERT: B 316 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6836 (tp30) REVERT: B 320 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8561 (mm-30) REVERT: B 343 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8607 (tpp80) REVERT: B 351 GLU cc_start: 0.8750 (tp30) cc_final: 0.8420 (tp30) REVERT: B 372 GLU cc_start: 0.7466 (tp30) cc_final: 0.7076 (tp30) REVERT: B 373 ARG cc_start: 0.9056 (tmm-80) cc_final: 0.8609 (ttm170) REVERT: B 421 SER cc_start: 0.9248 (t) cc_final: 0.8847 (t) REVERT: B 450 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6681 (pp30) REVERT: B 477 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: X 46 ASP cc_start: 0.8345 (p0) cc_final: 0.8021 (p0) REVERT: X 53 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7392 (mtt180) outliers start: 43 outliers final: 32 residues processed: 275 average time/residue: 0.1893 time to fit residues: 71.8042 Evaluate side-chains 272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 14 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 29 optimal weight: 0.0770 chunk 60 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 8 optimal weight: 6.9990 overall best weight: 2.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN B 388 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135829 restraints weight = 19670.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138849 restraints weight = 13090.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141132 restraints weight = 9670.974| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7919 Z= 0.171 Angle : 0.573 10.048 10794 Z= 0.291 Chirality : 0.038 0.189 1301 Planarity : 0.003 0.050 1427 Dihedral : 4.091 40.953 1246 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 6.42 % Allowed : 26.18 % Favored : 67.40 % 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: 1.39 (0.26), residues: 1158 helix: 2.17 (0.18), residues: 808 sheet: -3.81 (0.74), residues: 34 loop : -1.95 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.003 0.001 HIS B 299 PHE 0.018 0.002 PHE A 390 TYR 0.027 0.002 TYR A 249 ARG 0.006 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8597 (m-80) cc_final: 0.7974 (m-80) REVERT: A 214 TRP cc_start: 0.9259 (t60) cc_final: 0.8956 (t60) REVERT: A 224 PHE cc_start: 0.8006 (t80) cc_final: 0.7628 (t80) REVERT: A 344 LYS cc_start: 0.8088 (tttt) cc_final: 0.7420 (pttt) REVERT: A 388 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8505 (mm-40) REVERT: A 392 GLU cc_start: 0.8309 (tt0) cc_final: 0.7645 (mt-10) REVERT: A 420 MET cc_start: 0.8837 (mpp) cc_final: 0.8566 (mpp) REVERT: A 443 ASN cc_start: 0.8939 (m-40) cc_final: 0.8697 (t0) REVERT: A 601 TYR cc_start: 0.8691 (t80) cc_final: 0.8274 (t80) REVERT: B 131 GLN cc_start: 0.6588 (pm20) cc_final: 0.6324 (pm20) REVERT: B 151 LEU cc_start: 0.8570 (mt) cc_final: 0.8312 (mt) REVERT: B 172 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: B 228 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8360 (mt0) REVERT: B 248 GLU cc_start: 0.8824 (tp30) cc_final: 0.8583 (tp30) REVERT: B 254 SER cc_start: 0.7700 (t) cc_final: 0.7413 (m) REVERT: B 285 MET cc_start: 0.8089 (mtm) cc_final: 0.7588 (mtm) REVERT: B 316 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6767 (tp30) REVERT: B 320 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 343 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8467 (tpp80) REVERT: B 351 GLU cc_start: 0.8758 (tp30) cc_final: 0.8447 (tp30) REVERT: B 372 GLU cc_start: 0.7527 (tp30) cc_final: 0.7009 (tp30) REVERT: B 373 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8684 (ttm170) REVERT: B 424 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.9029 (mp10) REVERT: B 450 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6798 (pp30) REVERT: B 477 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6325 (m-10) REVERT: X 38 GLU cc_start: 0.8716 (tp30) cc_final: 0.8274 (tp30) REVERT: X 46 ASP cc_start: 0.8342 (p0) cc_final: 0.7972 (p0) REVERT: X 53 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7362 (mtt180) outliers start: 38 outliers final: 29 residues processed: 268 average time/residue: 0.1899 time to fit residues: 68.9031 Evaluate side-chains 272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 14 ASN Chi-restraints excluded: chain X residue 45 HIS Chi-restraints excluded: chain X residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 50.0000 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 50.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.155592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134255 restraints weight = 19637.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137293 restraints weight = 13113.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139454 restraints weight = 9683.239| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7919 Z= 0.213 Angle : 0.597 10.393 10794 Z= 0.309 Chirality : 0.040 0.214 1301 Planarity : 0.003 0.034 1427 Dihedral : 4.192 43.836 1246 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 6.59 % Allowed : 27.53 % Favored : 65.88 % 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: 1.44 (0.26), residues: 1158 helix: 2.17 (0.18), residues: 807 sheet: -3.60 (0.76), residues: 34 loop : -1.84 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 367 HIS 0.003 0.001 HIS B 299 PHE 0.013 0.002 PHE B 195 TYR 0.024 0.002 TYR A 249 ARG 0.006 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8667 (m-80) cc_final: 0.7874 (m-80) REVERT: A 214 TRP cc_start: 0.9265 (t60) cc_final: 0.8967 (t60) REVERT: A 224 PHE cc_start: 0.8024 (t80) cc_final: 0.7666 (t80) REVERT: A 251 ASN cc_start: 0.9433 (m-40) cc_final: 0.7870 (m110) REVERT: A 284 ILE cc_start: 0.9081 (pt) cc_final: 0.8863 (tp) REVERT: A 344 LYS cc_start: 0.8088 (tttt) cc_final: 0.7418 (pttt) REVERT: A 392 GLU cc_start: 0.8311 (tt0) cc_final: 0.7660 (mt-10) REVERT: A 420 MET cc_start: 0.8866 (mpp) cc_final: 0.8564 (mpp) REVERT: A 429 ILE cc_start: 0.9293 (mm) cc_final: 0.8736 (mt) REVERT: A 601 TYR cc_start: 0.8674 (t80) cc_final: 0.8248 (t80) REVERT: B 131 GLN cc_start: 0.6534 (pm20) cc_final: 0.6295 (pm20) REVERT: B 172 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7812 (m-10) REVERT: B 248 GLU cc_start: 0.8843 (tp30) cc_final: 0.8580 (tp30) REVERT: B 254 SER cc_start: 0.7840 (t) cc_final: 0.7588 (m) REVERT: B 300 MET cc_start: 0.9013 (mmt) cc_final: 0.8595 (mmp) REVERT: B 316 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6768 (tp30) REVERT: B 320 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8558 (mm-30) REVERT: B 343 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8518 (tpp80) REVERT: B 351 GLU cc_start: 0.8737 (tp30) cc_final: 0.8453 (tp30) REVERT: B 367 TRP cc_start: 0.9221 (t-100) cc_final: 0.8171 (t-100) REVERT: B 372 GLU cc_start: 0.7476 (tp30) cc_final: 0.6939 (tp30) REVERT: B 373 ARG cc_start: 0.9046 (tmm-80) cc_final: 0.8630 (ttm170) REVERT: B 450 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6822 (pp30) REVERT: B 477 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.6359 (m-10) REVERT: X 38 GLU cc_start: 0.8720 (tp30) cc_final: 0.8340 (tp30) REVERT: X 46 ASP cc_start: 0.8386 (p0) cc_final: 0.8053 (p0) REVERT: X 53 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7348 (mtt180) outliers start: 39 outliers final: 31 residues processed: 264 average time/residue: 0.1771 time to fit residues: 64.8572 Evaluate side-chains 274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 45 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN X 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133712 restraints weight = 19623.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136694 restraints weight = 13005.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138839 restraints weight = 9522.038| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7919 Z= 0.209 Angle : 0.603 9.115 10794 Z= 0.311 Chirality : 0.040 0.233 1301 Planarity : 0.003 0.033 1427 Dihedral : 4.270 48.034 1246 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 7.60 % Allowed : 27.20 % Favored : 65.20 % 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: 1.45 (0.26), residues: 1158 helix: 2.15 (0.18), residues: 809 sheet: -3.34 (0.80), residues: 34 loop : -1.81 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 367 HIS 0.003 0.001 HIS B 299 PHE 0.037 0.002 PHE A 306 TYR 0.025 0.002 TYR A 249 ARG 0.007 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8703 (m-80) cc_final: 0.7811 (m-80) REVERT: A 214 TRP cc_start: 0.9233 (t60) cc_final: 0.8949 (t60) REVERT: A 224 PHE cc_start: 0.8032 (t80) cc_final: 0.7667 (t80) REVERT: A 249 TYR cc_start: 0.8112 (t80) cc_final: 0.7434 (t80) REVERT: A 251 ASN cc_start: 0.9491 (m-40) cc_final: 0.9240 (m-40) REVERT: A 253 MET cc_start: 0.9084 (mtp) cc_final: 0.8461 (mtp) REVERT: A 344 LYS cc_start: 0.8113 (tttt) cc_final: 0.7440 (pttt) REVERT: A 349 TYR cc_start: 0.8577 (t80) cc_final: 0.8282 (t80) REVERT: A 350 GLN cc_start: 0.8698 (mm110) cc_final: 0.8352 (mp10) REVERT: A 388 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8515 (mm-40) REVERT: A 392 GLU cc_start: 0.8321 (tt0) cc_final: 0.7665 (mt-10) REVERT: A 420 MET cc_start: 0.8864 (mpp) cc_final: 0.8531 (mpp) REVERT: A 429 ILE cc_start: 0.8950 (mm) cc_final: 0.8625 (mt) REVERT: A 601 TYR cc_start: 0.8636 (t80) cc_final: 0.8170 (t80) REVERT: B 131 GLN cc_start: 0.6484 (pm20) cc_final: 0.6268 (pm20) REVERT: B 172 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: B 187 HIS cc_start: 0.8334 (m-70) cc_final: 0.8084 (p90) REVERT: B 248 GLU cc_start: 0.8849 (tp30) cc_final: 0.8406 (tp30) REVERT: B 316 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6785 (tp30) REVERT: B 320 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8547 (mm-30) REVERT: B 343 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8543 (tpp80) REVERT: B 351 GLU cc_start: 0.8722 (tp30) cc_final: 0.8445 (tp30) REVERT: B 372 GLU cc_start: 0.7427 (tp30) cc_final: 0.6811 (tp30) REVERT: B 373 ARG cc_start: 0.9029 (tmm-80) cc_final: 0.8579 (ttm170) REVERT: B 477 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6305 (m-10) REVERT: X 38 GLU cc_start: 0.8711 (tp30) cc_final: 0.8349 (tp30) REVERT: X 46 ASP cc_start: 0.8416 (p0) cc_final: 0.8166 (p0) REVERT: X 53 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7367 (mtt180) outliers start: 45 outliers final: 35 residues processed: 275 average time/residue: 0.1761 time to fit residues: 66.5273 Evaluate side-chains 274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 14 ASN Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 48 optimal weight: 50.0000 chunk 59 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 103 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129913 restraints weight = 19872.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132827 restraints weight = 12966.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134671 restraints weight = 9433.521| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7919 Z= 0.296 Angle : 0.682 10.350 10794 Z= 0.358 Chirality : 0.042 0.238 1301 Planarity : 0.004 0.031 1427 Dihedral : 4.455 33.340 1243 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 7.77 % Allowed : 27.87 % Favored : 64.36 % 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: 1.03 (0.25), residues: 1158 helix: 1.76 (0.18), residues: 816 sheet: -3.10 (0.83), residues: 34 loop : -1.87 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 139 HIS 0.003 0.001 HIS B 171 PHE 0.039 0.003 PHE A 306 TYR 0.032 0.003 TYR A 249 ARG 0.007 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.916 Fit side-chains REVERT: A 207 PHE cc_start: 0.8891 (m-80) cc_final: 0.7875 (m-80) REVERT: A 214 TRP cc_start: 0.9253 (t60) cc_final: 0.8954 (t60) REVERT: A 224 PHE cc_start: 0.8082 (t80) cc_final: 0.7720 (t80) REVERT: A 250 ASN cc_start: 0.9043 (m-40) cc_final: 0.8757 (m110) REVERT: A 251 ASN cc_start: 0.9510 (m-40) cc_final: 0.7707 (m-40) REVERT: A 344 LYS cc_start: 0.8059 (tttt) cc_final: 0.7364 (pttt) REVERT: A 392 GLU cc_start: 0.8394 (tt0) cc_final: 0.7877 (mm-30) REVERT: A 420 MET cc_start: 0.8854 (mpp) cc_final: 0.8482 (mpp) REVERT: A 429 ILE cc_start: 0.8937 (mm) cc_final: 0.8622 (mt) REVERT: A 470 LYS cc_start: 0.9229 (tptm) cc_final: 0.8996 (mmtt) REVERT: B 131 GLN cc_start: 0.6423 (pm20) cc_final: 0.6217 (pm20) REVERT: B 172 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: B 187 HIS cc_start: 0.8388 (m-70) cc_final: 0.8175 (p90) REVERT: B 248 GLU cc_start: 0.8814 (tp30) cc_final: 0.8594 (tp30) REVERT: B 300 MET cc_start: 0.9018 (mmt) cc_final: 0.8559 (mmp) REVERT: B 316 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6893 (tp30) REVERT: B 320 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8509 (mm-30) REVERT: B 343 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8597 (tpp80) REVERT: B 351 GLU cc_start: 0.8731 (tp30) cc_final: 0.8466 (tp30) REVERT: B 367 TRP cc_start: 0.9266 (t-100) cc_final: 0.8711 (t-100) REVERT: B 372 GLU cc_start: 0.7556 (tp30) cc_final: 0.6964 (tp30) REVERT: B 373 ARG cc_start: 0.9029 (tmm-80) cc_final: 0.8643 (ttm170) REVERT: B 477 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6338 (m-10) REVERT: X 38 GLU cc_start: 0.8739 (tp30) cc_final: 0.8417 (tp30) REVERT: X 46 ASP cc_start: 0.8461 (p0) cc_final: 0.8260 (p0) REVERT: X 53 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7345 (mtt180) outliers start: 46 outliers final: 36 residues processed: 261 average time/residue: 0.1733 time to fit residues: 62.7536 Evaluate side-chains 268 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 40.0000 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 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 = 0.3939 r_free = 0.3939 target = 0.152526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131714 restraints weight = 20048.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134615 restraints weight = 13158.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136785 restraints weight = 9630.442| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7919 Z= 0.243 Angle : 0.674 11.547 10794 Z= 0.347 Chirality : 0.041 0.294 1301 Planarity : 0.004 0.033 1427 Dihedral : 4.321 34.698 1243 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 6.93 % Allowed : 28.72 % Favored : 64.36 % 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: 1.05 (0.25), residues: 1158 helix: 1.79 (0.18), residues: 813 sheet: -3.17 (0.82), residues: 35 loop : -1.87 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 367 HIS 0.004 0.001 HIS B 299 PHE 0.037 0.002 PHE A 306 TYR 0.037 0.002 TYR B 310 ARG 0.009 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8826 (m-80) cc_final: 0.7789 (m-80) REVERT: A 214 TRP cc_start: 0.9225 (t60) cc_final: 0.8886 (t60) REVERT: A 224 PHE cc_start: 0.8018 (t80) cc_final: 0.7621 (t80) REVERT: A 249 TYR cc_start: 0.8165 (t80) cc_final: 0.7746 (t80) REVERT: A 251 ASN cc_start: 0.9335 (m-40) cc_final: 0.9108 (m110) REVERT: A 344 LYS cc_start: 0.8076 (tttt) cc_final: 0.7393 (pttt) REVERT: A 350 GLN cc_start: 0.8724 (mm110) cc_final: 0.8383 (mp10) REVERT: A 392 GLU cc_start: 0.8440 (tt0) cc_final: 0.7787 (mt-10) REVERT: A 420 MET cc_start: 0.8849 (mpp) cc_final: 0.8493 (mpp) REVERT: A 470 LYS cc_start: 0.9243 (tptm) cc_final: 0.9000 (mmtt) REVERT: B 131 GLN cc_start: 0.6448 (pm20) cc_final: 0.6241 (pm20) REVERT: B 172 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: B 300 MET cc_start: 0.8978 (mmt) cc_final: 0.8528 (mmp) REVERT: B 316 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7144 (tp30) REVERT: B 343 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8549 (tpp80) REVERT: B 351 GLU cc_start: 0.8663 (tp30) cc_final: 0.8410 (tp30) REVERT: B 370 ASP cc_start: 0.8876 (m-30) cc_final: 0.8510 (t0) REVERT: B 372 GLU cc_start: 0.7455 (tp30) cc_final: 0.7040 (tp30) REVERT: B 373 ARG cc_start: 0.8886 (tmm-80) cc_final: 0.8476 (ttm170) REVERT: B 477 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6195 (m-10) REVERT: X 38 GLU cc_start: 0.8731 (tp30) cc_final: 0.8401 (tp30) REVERT: X 53 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7361 (mtt180) outliers start: 41 outliers final: 35 residues processed: 263 average time/residue: 0.1921 time to fit residues: 68.6093 Evaluate side-chains 264 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132140 restraints weight = 19520.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135244 restraints weight = 12662.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137501 restraints weight = 9160.403| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7919 Z= 0.221 Angle : 0.672 12.036 10794 Z= 0.342 Chirality : 0.040 0.239 1301 Planarity : 0.003 0.032 1427 Dihedral : 4.210 36.114 1243 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 6.59 % Allowed : 29.39 % Favored : 64.02 % 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: 1.11 (0.26), residues: 1158 helix: 1.84 (0.18), residues: 816 sheet: -3.39 (0.71), residues: 45 loop : -1.75 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 367 HIS 0.004 0.001 HIS B 299 PHE 0.038 0.002 PHE A 306 TYR 0.034 0.002 TYR B 310 ARG 0.009 0.001 ARG X 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8759 (m-80) cc_final: 0.7694 (m-80) REVERT: A 214 TRP cc_start: 0.9220 (t60) cc_final: 0.8833 (t60) REVERT: A 224 PHE cc_start: 0.7983 (t80) cc_final: 0.7526 (t80) REVERT: A 250 ASN cc_start: 0.9034 (m-40) cc_final: 0.8605 (m110) REVERT: A 344 LYS cc_start: 0.8100 (tttt) cc_final: 0.7384 (tttt) REVERT: A 349 TYR cc_start: 0.8602 (t80) cc_final: 0.8268 (t80) REVERT: A 350 GLN cc_start: 0.8679 (mm110) cc_final: 0.8360 (mp10) REVERT: A 392 GLU cc_start: 0.8366 (tt0) cc_final: 0.7699 (mt-10) REVERT: A 420 MET cc_start: 0.8855 (mpp) cc_final: 0.8503 (mpp) REVERT: B 172 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7754 (m-10) REVERT: B 316 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7088 (tp30) REVERT: B 343 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8546 (tpp80) REVERT: B 351 GLU cc_start: 0.8712 (tp30) cc_final: 0.8468 (tp30) REVERT: B 370 ASP cc_start: 0.8818 (m-30) cc_final: 0.8613 (t0) REVERT: B 372 GLU cc_start: 0.7577 (tp30) cc_final: 0.7220 (tp30) REVERT: B 373 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8514 (ttm170) REVERT: B 477 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: X 38 GLU cc_start: 0.8746 (tp30) cc_final: 0.8422 (tp30) REVERT: X 53 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7322 (mtt180) outliers start: 39 outliers final: 35 residues processed: 262 average time/residue: 0.1830 time to fit residues: 66.2706 Evaluate side-chains 268 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 96 optimal weight: 0.1980 chunk 104 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132894 restraints weight = 19578.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135988 restraints weight = 12737.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138304 restraints weight = 9214.174| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7919 Z= 0.215 Angle : 0.674 11.802 10794 Z= 0.342 Chirality : 0.040 0.209 1301 Planarity : 0.003 0.032 1427 Dihedral : 4.141 37.337 1243 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 6.42 % Allowed : 31.25 % Favored : 62.33 % 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: 1.16 (0.26), residues: 1158 helix: 1.86 (0.18), residues: 816 sheet: -3.29 (0.71), residues: 45 loop : -1.70 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 367 HIS 0.004 0.001 HIS B 299 PHE 0.040 0.002 PHE A 306 TYR 0.032 0.002 TYR B 310 ARG 0.009 0.001 ARG X 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.06 seconds wall clock time: 67 minutes 24.42 seconds (4044.42 seconds total)