Starting phenix.real_space_refine on Wed Sep 17 09:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u1d_8482/09_2025/5u1d_8482.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u1d_8482/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/5u1d_8482/09_2025/5u1d_8482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u1d_8482/09_2025/5u1d_8482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u1d_8482/09_2025/5u1d_8482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u1d_8482/09_2025/5u1d_8482.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.036 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 11, 'GLU:plan': 19, 'PHE:plan': 6, 'GLN:plan1': 26, 'ASN:plan1': 6, 'HIS:plan': 6, 'ASP:plan': 9, 'TYR:plan': 8, 'TRP:plan': 1} 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: {'ASP:plan': 15, 'GLN:plan1': 25, 'GLU:plan': 12, 'PHE:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 5, 'TYR:plan': 3, 'HIS:plan': 5, 'TRP:plan': 1} 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: 2.15, per 1000 atoms: 0.28 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: 0.62 Conformation dependent library (CDL) restraints added in 406.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.29 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: 1.15 Time building geometry restraints manager: 0.82 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: 1.660 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: 0.000 Extract box with map and model: 0.930 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- 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= 0.537 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 483 TYR 0.014 0.001 TYR B 446 PHE 0.013 0.001 PHE B 240 TRP 0.007 0.001 TRP A 214 HIS 0.002 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00732 ( 7919) covalent geometry : angle 1.17302 (10794) hydrogen bonds : bond 0.20476 ( 584) hydrogen bonds : angle 8.14630 ( 1707) *********************** 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 : 0.319 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: 0.7197 (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 281 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 292 LEU cc_start: 0.8587 (mt) cc_final: 0.8292 (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: 0.8667 (tmm) 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: 0.0926 time to fit residues: 44.3179 Evaluate side-chains 282 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 278 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 LEU 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 108 optimal weight: 20.0000 chunk 49 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 401 ASN A 469 GLN A 701 GLN B 171 HIS B 416 GLN B 539 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137848 restraints weight = 19818.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140924 restraints weight = 13092.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143145 restraints weight = 9565.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144615 restraints weight = 7490.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.145916 restraints weight = 6202.828| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7919 Z= 0.187 Angle : 0.609 10.282 10794 Z= 0.325 Chirality : 0.040 0.203 1301 Planarity : 0.004 0.051 1427 Dihedral : 4.675 46.878 1250 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 7.09 % Allowed : 16.05 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.24), residues: 1158 helix: 1.56 (0.17), residues: 798 sheet: -4.43 (0.70), residues: 37 loop : -2.18 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.023 0.002 TYR X 22 PHE 0.017 0.002 PHE B 240 TRP 0.030 0.002 TRP A 413 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7919) covalent geometry : angle 0.60903 (10794) hydrogen bonds : bond 0.04700 ( 584) hydrogen bonds : angle 4.42497 ( 1707) *********************** 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 315 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 214 TRP cc_start: 0.9105 (t60) cc_final: 0.8559 (t60) REVERT: A 223 THR cc_start: 0.7789 (p) cc_final: 0.7585 (t) REVERT: A 224 PHE cc_start: 0.8049 (t80) cc_final: 0.7672 (t80) REVERT: A 285 MET cc_start: 0.7863 (tpp) cc_final: 0.7557 (tpt) REVERT: A 374 MET cc_start: 0.8750 (tpt) cc_final: 0.8543 (tpt) REVERT: A 392 GLU cc_start: 0.8185 (tt0) cc_final: 0.7603 (mm-30) REVERT: A 417 ILE cc_start: 0.9175 (mm) cc_final: 0.8905 (mm) REVERT: A 439 VAL cc_start: 0.6842 (t) cc_final: 0.6346 (t) REVERT: A 443 ASN cc_start: 0.8993 (m-40) cc_final: 0.8768 (t0) REVERT: A 660 LYS cc_start: 0.8378 (mttt) cc_final: 0.8070 (mmtm) REVERT: B 131 GLN cc_start: 0.6716 (pm20) cc_final: 0.6494 (pm20) REVERT: B 243 GLU cc_start: 0.8959 (tp30) cc_final: 0.8741 (tt0) REVERT: B 248 GLU cc_start: 0.8799 (tp30) cc_final: 0.8480 (tp30) REVERT: B 300 MET cc_start: 0.9065 (mmt) cc_final: 0.8627 (mmp) REVERT: B 316 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6636 (tp30) REVERT: B 320 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 345 PHE cc_start: 0.8268 (m-80) cc_final: 0.8034 (m-80) REVERT: B 351 GLU cc_start: 0.8723 (tp30) cc_final: 0.8410 (tp30) REVERT: B 360 GLU cc_start: 0.8555 (tt0) cc_final: 0.8235 (tm-30) REVERT: B 370 ASP cc_start: 0.8856 (m-30) cc_final: 0.8585 (m-30) REVERT: B 372 GLU cc_start: 0.6990 (tp30) cc_final: 0.6655 (tp30) REVERT: B 373 ARG cc_start: 0.9164 (tmm-80) cc_final: 0.8795 (ttm170) REVERT: B 392 LEU cc_start: 0.9290 (tp) cc_final: 0.9053 (tt) REVERT: B 428 TYR cc_start: 0.9461 (t80) cc_final: 0.9159 (t80) REVERT: B 430 TYR cc_start: 0.8600 (t80) cc_final: 0.8227 (t80) REVERT: X 22 TYR cc_start: 0.8776 (t80) cc_final: 0.8235 (t80) REVERT: X 46 ASP cc_start: 0.8307 (p0) cc_final: 0.8005 (p0) REVERT: X 53 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7373 (mtt180) outliers start: 42 outliers final: 26 residues processed: 295 average time/residue: 0.0788 time to fit residues: 31.9434 Evaluate side-chains 264 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL 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 449 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 PHE 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 297 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 10 THR 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 79 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 102 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS B 416 GLN B 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.155993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135252 restraints weight = 19693.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138247 restraints weight = 12849.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140488 restraints weight = 9377.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142132 restraints weight = 7325.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143290 restraints weight = 5998.295| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7919 Z= 0.161 Angle : 0.588 11.374 10794 Z= 0.306 Chirality : 0.039 0.227 1301 Planarity : 0.004 0.035 1427 Dihedral : 4.167 35.378 1246 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 7.09 % Allowed : 20.10 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1158 helix: 1.95 (0.18), residues: 805 sheet: -3.75 (0.81), residues: 34 loop : -2.09 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 41 TYR 0.016 0.002 TYR A 349 PHE 0.018 0.002 PHE A 447 TRP 0.017 0.002 TRP A 348 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7919) covalent geometry : angle 0.58795 (10794) hydrogen bonds : bond 0.04143 ( 584) hydrogen bonds : angle 4.13200 ( 1707) *********************** 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 308 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8385 (m-80) cc_final: 0.8074 (m-80) REVERT: A 214 TRP cc_start: 0.9121 (t60) cc_final: 0.8850 (t60) REVERT: A 224 PHE cc_start: 0.8040 (t80) cc_final: 0.7682 (t80) REVERT: A 250 ASN cc_start: 0.9195 (m110) cc_final: 0.8971 (m110) REVERT: A 344 LYS cc_start: 0.8067 (tttt) cc_final: 0.7309 (ttpt) REVERT: A 355 GLN cc_start: 0.9072 (tp40) cc_final: 0.8551 (tm-30) REVERT: A 382 ASN cc_start: 0.8928 (t0) cc_final: 0.8655 (t0) REVERT: A 392 GLU cc_start: 0.8221 (tt0) cc_final: 0.7614 (mm-30) REVERT: A 429 ILE cc_start: 0.8900 (mm) cc_final: 0.8586 (mt) REVERT: A 443 ASN cc_start: 0.8983 (m-40) cc_final: 0.8727 (t0) REVERT: B 131 GLN cc_start: 0.6666 (pm20) cc_final: 0.6422 (pm20) REVERT: B 172 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 254 SER cc_start: 0.7488 (t) cc_final: 0.7075 (m) REVERT: B 300 MET cc_start: 0.9015 (mmt) cc_final: 0.8788 (mmm) REVERT: B 316 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6514 (tp30) REVERT: B 320 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 351 GLU cc_start: 0.8713 (tp30) cc_final: 0.8417 (tp30) REVERT: B 360 GLU cc_start: 0.8595 (tt0) cc_final: 0.8264 (tm-30) REVERT: B 372 GLU cc_start: 0.7294 (tp30) cc_final: 0.6916 (tp30) REVERT: B 373 ARG cc_start: 0.9097 (tmm-80) cc_final: 0.8759 (ttm170) REVERT: B 430 TYR cc_start: 0.8668 (t80) cc_final: 0.8355 (t80) REVERT: B 477 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6394 (m-10) REVERT: X 41 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8469 (ttp80) REVERT: X 46 ASP cc_start: 0.8392 (p0) cc_final: 0.8067 (p0) REVERT: X 53 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7398 (mtt180) outliers start: 42 outliers final: 33 residues processed: 287 average time/residue: 0.0750 time to fit residues: 29.4728 Evaluate side-chains 266 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 331 THR Chi-restraints excluded: chain A residue 352 LEU 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 414 THR Chi-restraints excluded: chain A residue 445 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 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 272 LEU Chi-restraints excluded: chain B residue 284 PHE 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 344 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 58 optimal weight: 3.9990 chunk 37 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 100 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 50.0000 chunk 35 optimal weight: 50.0000 overall best weight: 12.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 171 HIS B 267 ASN B 311 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127662 restraints weight = 20549.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130451 restraints weight = 13233.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132589 restraints weight = 9584.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134083 restraints weight = 7451.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135098 restraints weight = 6115.804| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7919 Z= 0.293 Angle : 0.746 9.882 10794 Z= 0.401 Chirality : 0.043 0.224 1301 Planarity : 0.005 0.040 1427 Dihedral : 5.308 38.282 1246 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 9.97 % Allowed : 22.13 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1158 helix: 1.13 (0.18), residues: 811 sheet: -3.86 (0.96), residues: 23 loop : -2.24 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 226 TYR 0.024 0.003 TYR B 477 PHE 0.034 0.003 PHE A 447 TRP 0.017 0.003 TRP B 139 HIS 0.006 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 7919) covalent geometry : angle 0.74599 (10794) hydrogen bonds : bond 0.05091 ( 584) hydrogen bonds : angle 4.93105 ( 1707) *********************** 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 297 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8888 (m-80) cc_final: 0.8110 (m-80) REVERT: A 214 TRP cc_start: 0.9225 (t60) cc_final: 0.8977 (t60) REVERT: A 224 PHE cc_start: 0.8091 (t80) cc_final: 0.7779 (t80) REVERT: A 234 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 249 TYR cc_start: 0.8680 (t80) cc_final: 0.8453 (t80) REVERT: A 309 TYR cc_start: 0.9054 (m-80) cc_final: 0.8709 (m-80) REVERT: A 312 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8846 (tpp80) REVERT: A 320 MET cc_start: 0.8829 (mtm) cc_final: 0.8493 (mtm) REVERT: A 344 LYS cc_start: 0.8049 (tttt) cc_final: 0.7237 (ttpt) REVERT: A 392 GLU cc_start: 0.8526 (tt0) cc_final: 0.8061 (mm-30) REVERT: A 420 MET cc_start: 0.8858 (mpp) cc_final: 0.8557 (mpp) REVERT: A 443 ASN cc_start: 0.8938 (m-40) cc_final: 0.8646 (t0) REVERT: A 601 TYR cc_start: 0.8733 (t80) cc_final: 0.8123 (t80) REVERT: B 172 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: B 254 SER cc_start: 0.7871 (t) cc_final: 0.7648 (m) REVERT: B 255 SER cc_start: 0.9150 (t) cc_final: 0.8836 (m) REVERT: B 300 MET cc_start: 0.9089 (mmt) cc_final: 0.8785 (mmp) REVERT: B 351 GLU cc_start: 0.8709 (tp30) cc_final: 0.8425 (tp30) REVERT: B 372 GLU cc_start: 0.7455 (tp30) cc_final: 0.6903 (tp30) REVERT: B 373 ARG cc_start: 0.9024 (tmm-80) cc_final: 0.8609 (ttm170) REVERT: B 477 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6570 (m-10) REVERT: X 38 GLU cc_start: 0.8673 (tp30) cc_final: 0.8407 (tp30) REVERT: X 41 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8476 (ttp80) REVERT: X 53 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7363 (mtt180) outliers start: 59 outliers final: 40 residues processed: 271 average time/residue: 0.0722 time to fit residues: 27.4125 Evaluate side-chains 269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 234 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL 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 354 VAL Chi-restraints excluded: chain A residue 376 THR 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 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 284 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 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 341 THR 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 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 5 LEU 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 115 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 382 ASN A 451 GLN A 456 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.154596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134069 restraints weight = 19848.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137076 restraints weight = 12824.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139253 restraints weight = 9254.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140756 restraints weight = 7185.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141571 restraints weight = 5919.774| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7919 Z= 0.130 Angle : 0.604 10.356 10794 Z= 0.310 Chirality : 0.039 0.170 1301 Planarity : 0.003 0.033 1427 Dihedral : 4.231 32.933 1243 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 6.93 % Allowed : 27.03 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1158 helix: 1.79 (0.18), residues: 806 sheet: -3.69 (0.77), residues: 35 loop : -2.13 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.023 0.002 TYR B 310 PHE 0.017 0.002 PHE B 412 TRP 0.013 0.002 TRP A 308 HIS 0.004 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7919) covalent geometry : angle 0.60384 (10794) hydrogen bonds : bond 0.03819 ( 584) hydrogen bonds : angle 4.07156 ( 1707) *********************** 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 288 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8677 (m-80) cc_final: 0.7639 (m-80) REVERT: A 214 TRP cc_start: 0.9220 (t60) cc_final: 0.8901 (t60) REVERT: A 224 PHE cc_start: 0.7949 (t80) cc_final: 0.7565 (t80) REVERT: A 231 MET cc_start: 0.8066 (ttt) cc_final: 0.7682 (mtp) REVERT: A 249 TYR cc_start: 0.8594 (t80) cc_final: 0.7790 (t80) REVERT: A 344 LYS cc_start: 0.8055 (tttt) cc_final: 0.7371 (pttt) REVERT: A 349 TYR cc_start: 0.8535 (t80) cc_final: 0.8231 (t80) REVERT: A 350 GLN cc_start: 0.8698 (mm110) cc_final: 0.8336 (mp10) REVERT: A 355 GLN cc_start: 0.9055 (tp40) cc_final: 0.8598 (tm-30) REVERT: A 382 ASN cc_start: 0.8840 (t0) cc_final: 0.8623 (t0) REVERT: A 392 GLU cc_start: 0.8313 (tt0) cc_final: 0.7623 (mt-10) REVERT: A 420 MET cc_start: 0.8928 (mpp) cc_final: 0.8610 (mpp) REVERT: A 443 ASN cc_start: 0.8935 (m-40) cc_final: 0.8699 (t0) REVERT: A 601 TYR cc_start: 0.8630 (t80) cc_final: 0.8112 (t80) REVERT: B 131 GLN cc_start: 0.6514 (pm20) cc_final: 0.6291 (pm20) REVERT: B 151 LEU cc_start: 0.8505 (tp) cc_final: 0.8297 (mt) REVERT: B 172 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: B 228 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8273 (tt0) REVERT: B 310 TYR cc_start: 0.9454 (t80) cc_final: 0.9008 (t80) REVERT: B 316 GLU cc_start: 0.7657 (tp30) cc_final: 0.6350 (tp30) REVERT: B 320 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 349 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 351 GLU cc_start: 0.8647 (tp30) cc_final: 0.8373 (tp30) REVERT: B 372 GLU cc_start: 0.7486 (tp30) cc_final: 0.6912 (tp30) REVERT: B 373 ARG cc_start: 0.8985 (tmm-80) cc_final: 0.8507 (ttm170) REVERT: B 430 TYR cc_start: 0.8147 (t80) cc_final: 0.7944 (t80) REVERT: B 477 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6330 (m-10) REVERT: X 26 ARG cc_start: 0.8815 (tpp80) cc_final: 0.8509 (tpp80) REVERT: X 38 GLU cc_start: 0.8642 (tp30) cc_final: 0.8277 (tp30) REVERT: X 41 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8457 (ttp80) REVERT: X 53 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7376 (mtt180) outliers start: 41 outliers final: 31 residues processed: 269 average time/residue: 0.0759 time to fit residues: 28.3242 Evaluate side-chains 267 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE 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 260 LEU 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 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 172 TYR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 PHE 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 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 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU 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 61 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 31 optimal weight: 50.0000 chunk 110 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 469 GLN B 250 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131983 restraints weight = 19971.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135025 restraints weight = 13013.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137107 restraints weight = 9431.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138727 restraints weight = 7349.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139672 restraints weight = 6048.761| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6265 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= 0.154 Angle : 0.606 8.693 10794 Z= 0.318 Chirality : 0.039 0.180 1301 Planarity : 0.003 0.041 1427 Dihedral : 4.251 32.920 1243 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.34 % Rotamer: Outliers : 8.45 % Allowed : 26.69 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.25), residues: 1158 helix: 1.78 (0.18), residues: 814 sheet: -3.43 (0.80), residues: 35 loop : -2.11 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 378 TYR 0.031 0.002 TYR B 376 PHE 0.018 0.002 PHE A 447 TRP 0.009 0.002 TRP B 139 HIS 0.004 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7919) covalent geometry : angle 0.60640 (10794) hydrogen bonds : bond 0.03955 ( 584) hydrogen bonds : angle 4.16610 ( 1707) *********************** 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 285 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8633 (m-80) cc_final: 0.7504 (m-80) REVERT: A 214 TRP cc_start: 0.9312 (t60) cc_final: 0.8931 (t60) REVERT: A 224 PHE cc_start: 0.7972 (t80) cc_final: 0.7543 (t80) REVERT: A 231 MET cc_start: 0.8056 (ttt) cc_final: 0.7666 (mtp) REVERT: A 251 ASN cc_start: 0.9412 (m110) cc_final: 0.7729 (m-40) REVERT: A 253 MET cc_start: 0.9072 (mtp) cc_final: 0.8747 (mtp) REVERT: A 344 LYS cc_start: 0.8066 (tttt) cc_final: 0.7380 (pttt) REVERT: A 349 TYR cc_start: 0.8596 (t80) cc_final: 0.8144 (t80) REVERT: A 350 GLN cc_start: 0.8680 (mm110) cc_final: 0.8298 (mp10) REVERT: A 355 GLN cc_start: 0.9023 (tp40) cc_final: 0.8611 (tm-30) REVERT: A 392 GLU cc_start: 0.8320 (tt0) cc_final: 0.7653 (mt-10) REVERT: A 420 MET cc_start: 0.8933 (mpp) cc_final: 0.8576 (mpp) REVERT: A 601 TYR cc_start: 0.8596 (t80) cc_final: 0.8059 (t80) REVERT: B 131 GLN cc_start: 0.6461 (pm20) cc_final: 0.6232 (pm20) REVERT: B 172 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: B 248 GLU cc_start: 0.8795 (tp30) cc_final: 0.8583 (tp30) REVERT: B 300 MET cc_start: 0.8947 (mmt) cc_final: 0.8528 (mmp) REVERT: B 316 GLU cc_start: 0.7716 (tp30) cc_final: 0.6774 (tp30) REVERT: B 320 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8501 (mm-30) REVERT: B 351 GLU cc_start: 0.8638 (tp30) cc_final: 0.8406 (tp30) REVERT: B 367 TRP cc_start: 0.9264 (t-100) cc_final: 0.8181 (t-100) REVERT: B 372 GLU cc_start: 0.7468 (tp30) cc_final: 0.6964 (tp30) REVERT: B 373 ARG cc_start: 0.9010 (tmm-80) cc_final: 0.8556 (ttm170) REVERT: B 430 TYR cc_start: 0.8395 (t80) cc_final: 0.8189 (t80) REVERT: B 477 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: X 26 ARG cc_start: 0.8834 (tpp80) cc_final: 0.8477 (tpp80) REVERT: X 38 GLU cc_start: 0.8662 (tp30) cc_final: 0.8260 (tp30) REVERT: X 41 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8408 (ttp80) REVERT: X 53 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7355 (mtt180) outliers start: 50 outliers final: 42 residues processed: 260 average time/residue: 0.0737 time to fit residues: 26.8032 Evaluate side-chains 275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 204 ILE 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 260 LEU 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 376 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 GLN 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 151 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 284 PHE 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 317 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 411 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 477 TYR Chi-restraints excluded: chain X residue 5 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 43 optimal weight: 40.0000 chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3926 r_free = 0.3926 target = 0.151727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131067 restraints weight = 19915.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134112 restraints weight = 12866.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136229 restraints weight = 9280.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137848 restraints weight = 7226.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138934 restraints weight = 5925.547| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7919 Z= 0.163 Angle : 0.629 10.739 10794 Z= 0.327 Chirality : 0.040 0.183 1301 Planarity : 0.003 0.043 1427 Dihedral : 4.274 33.696 1243 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 7.60 % Allowed : 28.72 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1158 helix: 1.80 (0.18), residues: 815 sheet: -3.27 (0.81), residues: 35 loop : -2.09 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 378 TYR 0.032 0.002 TYR B 310 PHE 0.035 0.002 PHE A 306 TRP 0.009 0.002 TRP A 308 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7919) covalent geometry : angle 0.62878 (10794) hydrogen bonds : bond 0.03887 ( 584) hydrogen bonds : angle 4.18605 ( 1707) *********************** 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 288 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8646 (m-80) cc_final: 0.8278 (m-80) REVERT: A 214 TRP cc_start: 0.9273 (t60) cc_final: 0.8852 (t60) REVERT: A 224 PHE cc_start: 0.8034 (t80) cc_final: 0.7678 (t80) REVERT: A 231 MET cc_start: 0.8092 (ttt) cc_final: 0.7748 (mtp) REVERT: A 251 ASN cc_start: 0.9410 (m110) cc_final: 0.7639 (m-40) REVERT: A 344 LYS cc_start: 0.8061 (tttt) cc_final: 0.7368 (pttt) REVERT: A 349 TYR cc_start: 0.8596 (t80) cc_final: 0.8182 (t80) REVERT: A 350 GLN cc_start: 0.8667 (mm110) cc_final: 0.8283 (mp10) REVERT: A 355 GLN cc_start: 0.9027 (tp40) cc_final: 0.8582 (tm-30) REVERT: A 356 VAL cc_start: 0.9249 (t) cc_final: 0.8850 (t) REVERT: A 392 GLU cc_start: 0.8292 (tt0) cc_final: 0.7630 (mt-10) REVERT: A 420 MET cc_start: 0.8900 (mpp) cc_final: 0.8535 (mpp) REVERT: A 479 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: A 601 TYR cc_start: 0.8593 (t80) cc_final: 0.7981 (t80) REVERT: B 131 GLN cc_start: 0.6436 (pm20) cc_final: 0.6212 (pm20) REVERT: B 172 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: B 228 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8346 (mt0) REVERT: B 248 GLU cc_start: 0.8816 (tp30) cc_final: 0.8562 (tp30) REVERT: B 316 GLU cc_start: 0.7747 (tp30) cc_final: 0.6805 (tp30) REVERT: B 320 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8489 (mm-30) REVERT: B 351 GLU cc_start: 0.8652 (tp30) cc_final: 0.8414 (tp30) REVERT: B 367 TRP cc_start: 0.9265 (t-100) cc_final: 0.8177 (t-100) REVERT: B 373 ARG cc_start: 0.9028 (tmm-80) cc_final: 0.8587 (ttm170) REVERT: B 430 TYR cc_start: 0.8434 (t80) cc_final: 0.8226 (t80) REVERT: B 477 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6250 (m-10) REVERT: X 26 ARG cc_start: 0.8804 (tpp80) cc_final: 0.8465 (tpp80) REVERT: X 38 GLU cc_start: 0.8669 (tp30) cc_final: 0.8242 (tp30) REVERT: X 41 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8441 (ttp80) REVERT: X 53 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7334 (mtt180) outliers start: 45 outliers final: 38 residues processed: 265 average time/residue: 0.0719 time to fit residues: 26.4173 Evaluate side-chains 271 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL 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 376 THR 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 460 VAL Chi-restraints excluded: chain A residue 479 PHE 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 284 PHE 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 317 VAL Chi-restraints excluded: chain B residue 339 LEU 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 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 477 TYR Chi-restraints excluded: chain X residue 5 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 388 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.154805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133895 restraints weight = 19864.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137005 restraints weight = 12912.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139300 restraints weight = 9387.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140948 restraints weight = 7281.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142095 restraints weight = 5957.588| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.6607 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= 0.129 Angle : 0.623 10.515 10794 Z= 0.320 Chirality : 0.039 0.190 1301 Planarity : 0.003 0.044 1427 Dihedral : 4.091 33.050 1243 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 7.43 % Allowed : 28.72 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1158 helix: 1.96 (0.18), residues: 816 sheet: -3.57 (0.68), residues: 45 loop : -1.85 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.020 0.002 TYR B 310 PHE 0.035 0.002 PHE A 306 TRP 0.006 0.001 TRP A 348 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7919) covalent geometry : angle 0.62326 (10794) hydrogen bonds : bond 0.03692 ( 584) hydrogen bonds : angle 3.99716 ( 1707) *********************** 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 294 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8583 (m-80) cc_final: 0.7464 (m-80) REVERT: A 214 TRP cc_start: 0.9247 (t60) cc_final: 0.8790 (t60) REVERT: A 224 PHE cc_start: 0.8012 (t80) cc_final: 0.7427 (t80) REVERT: A 251 ASN cc_start: 0.9370 (m110) cc_final: 0.7711 (m-40) REVERT: A 344 LYS cc_start: 0.8087 (tttt) cc_final: 0.7373 (tttt) REVERT: A 349 TYR cc_start: 0.8554 (t80) cc_final: 0.8066 (t80) REVERT: A 350 GLN cc_start: 0.8582 (mm110) cc_final: 0.8205 (mp10) REVERT: A 355 GLN cc_start: 0.8974 (tp40) cc_final: 0.8598 (tm-30) REVERT: A 356 VAL cc_start: 0.9216 (t) cc_final: 0.8790 (t) REVERT: A 392 GLU cc_start: 0.8214 (tt0) cc_final: 0.7535 (mt-10) REVERT: A 420 MET cc_start: 0.8930 (mpp) cc_final: 0.8556 (mpp) REVERT: A 479 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: A 601 TYR cc_start: 0.8549 (t80) cc_final: 0.7958 (t80) REVERT: B 172 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: B 228 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8379 (mt0) REVERT: B 248 GLU cc_start: 0.8829 (tp30) cc_final: 0.8593 (tp30) REVERT: B 316 GLU cc_start: 0.7679 (tp30) cc_final: 0.6720 (tp30) REVERT: B 320 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 351 GLU cc_start: 0.8643 (tp30) cc_final: 0.8423 (tp30) REVERT: B 367 TRP cc_start: 0.9239 (t-100) cc_final: 0.8175 (t-100) REVERT: B 372 GLU cc_start: 0.7504 (tp30) cc_final: 0.7008 (tp30) REVERT: B 373 ARG cc_start: 0.8991 (tmm-80) cc_final: 0.8603 (ttm170) REVERT: B 477 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.6073 (m-10) REVERT: X 26 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8444 (tpp80) REVERT: X 38 GLU cc_start: 0.8662 (tp30) cc_final: 0.8197 (tp30) REVERT: X 41 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8428 (ttp80) REVERT: X 53 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7295 (mtt180) outliers start: 44 outliers final: 37 residues processed: 273 average time/residue: 0.0765 time to fit residues: 29.1036 Evaluate side-chains 286 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 LEU 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 376 THR 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 A residue 479 PHE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 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 272 LEU Chi-restraints excluded: chain B residue 284 PHE 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 339 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 418 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 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 45 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 chunk 46 optimal weight: 30.0000 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** B 416 GLN ** 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 = 0.3934 r_free = 0.3934 target = 0.152420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131480 restraints weight = 19889.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134604 restraints weight = 12940.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136857 restraints weight = 9344.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138443 restraints weight = 7247.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139713 restraints weight = 5959.057| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7919 Z= 0.163 Angle : 0.651 10.314 10794 Z= 0.338 Chirality : 0.040 0.191 1301 Planarity : 0.004 0.046 1427 Dihedral : 4.236 34.533 1243 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.34 % Rotamer: Outliers : 8.28 % Allowed : 29.05 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1158 helix: 1.87 (0.19), residues: 813 sheet: -3.32 (0.71), residues: 44 loop : -1.68 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 378 TYR 0.022 0.002 TYR B 310 PHE 0.039 0.003 PHE A 306 TRP 0.008 0.001 TRP B 139 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7919) covalent geometry : angle 0.65100 (10794) hydrogen bonds : bond 0.03863 ( 584) hydrogen bonds : angle 4.16218 ( 1707) *********************** 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 295 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8691 (m-80) cc_final: 0.8320 (m-80) REVERT: A 214 TRP cc_start: 0.9204 (t60) cc_final: 0.8994 (t60) REVERT: A 251 ASN cc_start: 0.9395 (m110) cc_final: 0.7624 (m110) REVERT: A 344 LYS cc_start: 0.8074 (tttt) cc_final: 0.7352 (tttt) REVERT: A 349 TYR cc_start: 0.8578 (t80) cc_final: 0.8079 (t80) REVERT: A 350 GLN cc_start: 0.8608 (mm110) cc_final: 0.8213 (mp10) REVERT: A 355 GLN cc_start: 0.9015 (tp40) cc_final: 0.8572 (tm-30) REVERT: A 374 MET cc_start: 0.8659 (tpt) cc_final: 0.8458 (tmm) REVERT: A 392 GLU cc_start: 0.8251 (tt0) cc_final: 0.7541 (mt-10) REVERT: A 420 MET cc_start: 0.8926 (mpp) cc_final: 0.8551 (mpp) REVERT: A 479 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: B 172 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: B 228 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8443 (mt0) REVERT: B 248 GLU cc_start: 0.8841 (tp30) cc_final: 0.8568 (tp30) REVERT: B 316 GLU cc_start: 0.7758 (tp30) cc_final: 0.6789 (tp30) REVERT: B 320 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8477 (mm-30) REVERT: B 351 GLU cc_start: 0.8705 (tp30) cc_final: 0.8452 (tp30) REVERT: B 367 TRP cc_start: 0.9245 (t-100) cc_final: 0.8185 (t-100) REVERT: B 372 GLU cc_start: 0.7465 (tp30) cc_final: 0.6971 (tp30) REVERT: B 373 ARG cc_start: 0.8975 (tmm-80) cc_final: 0.8596 (ttm170) REVERT: B 477 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6204 (m-10) REVERT: X 26 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8427 (tpp80) REVERT: X 38 GLU cc_start: 0.8654 (tp30) cc_final: 0.8216 (tp30) REVERT: X 41 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8413 (ttp80) REVERT: X 53 ARG cc_start: 0.7832 (mtt180) cc_final: 0.7324 (mtt180) outliers start: 49 outliers final: 41 residues processed: 270 average time/residue: 0.0788 time to fit residues: 29.4899 Evaluate side-chains 286 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 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 376 THR Chi-restraints excluded: chain A residue 395 GLN 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 A residue 479 PHE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 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 272 LEU Chi-restraints excluded: chain B residue 284 PHE 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 339 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 418 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 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 14 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 50.0000 chunk 62 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 469 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.154371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133458 restraints weight = 19764.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136533 restraints weight = 12959.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138836 restraints weight = 9395.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140505 restraints weight = 7316.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141583 restraints weight = 5981.987| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6902 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= 0.143 Angle : 0.652 11.741 10794 Z= 0.334 Chirality : 0.041 0.265 1301 Planarity : 0.004 0.044 1427 Dihedral : 4.151 35.656 1243 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 7.09 % Allowed : 30.24 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1158 helix: 1.88 (0.18), residues: 812 sheet: -3.25 (0.72), residues: 45 loop : -1.66 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 378 TYR 0.020 0.002 TYR B 310 PHE 0.041 0.002 PHE A 306 TRP 0.007 0.001 TRP B 139 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7919) covalent geometry : angle 0.65156 (10794) hydrogen bonds : bond 0.03789 ( 584) hydrogen bonds : angle 4.08437 ( 1707) ********************** 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 292 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8618 (m-80) cc_final: 0.8267 (m-80) REVERT: A 214 TRP cc_start: 0.9196 (t60) cc_final: 0.8771 (t60) REVERT: A 224 PHE cc_start: 0.8016 (t80) cc_final: 0.7553 (t80) REVERT: A 251 ASN cc_start: 0.9379 (m110) cc_final: 0.7733 (m-40) REVERT: A 344 LYS cc_start: 0.8083 (tttt) cc_final: 0.7372 (tttt) REVERT: A 349 TYR cc_start: 0.8559 (t80) cc_final: 0.8041 (t80) REVERT: A 350 GLN cc_start: 0.8578 (mm110) cc_final: 0.8198 (mp10) REVERT: A 355 GLN cc_start: 0.8959 (tp40) cc_final: 0.8583 (tm-30) REVERT: A 392 GLU cc_start: 0.8286 (tt0) cc_final: 0.7613 (mt-10) REVERT: A 420 MET cc_start: 0.8911 (mpp) cc_final: 0.8551 (mpp) REVERT: A 479 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: B 172 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: B 228 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8437 (mt0) REVERT: B 248 GLU cc_start: 0.8855 (tp30) cc_final: 0.8604 (tp30) REVERT: B 316 GLU cc_start: 0.7716 (tp30) cc_final: 0.6742 (tp30) REVERT: B 320 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 322 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8631 (tt0) REVERT: B 351 GLU cc_start: 0.8685 (tp30) cc_final: 0.8428 (tp30) REVERT: B 367 TRP cc_start: 0.9238 (t-100) cc_final: 0.8186 (t-100) REVERT: B 372 GLU cc_start: 0.7506 (tp30) cc_final: 0.7001 (tp30) REVERT: B 373 ARG cc_start: 0.8985 (tmm-80) cc_final: 0.8613 (ttm170) REVERT: B 477 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6180 (m-10) REVERT: X 26 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8407 (tpp80) REVERT: X 38 GLU cc_start: 0.8648 (tp30) cc_final: 0.8204 (tp30) REVERT: X 41 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8440 (ttp80) REVERT: X 53 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7332 (mtt180) outliers start: 42 outliers final: 38 residues processed: 272 average time/residue: 0.0785 time to fit residues: 29.5460 Evaluate side-chains 280 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 260 LEU 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 376 THR Chi-restraints excluded: chain A residue 395 GLN 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 A residue 479 PHE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 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 272 LEU Chi-restraints excluded: chain B residue 284 PHE 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 339 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 418 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 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 20 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 382 ASN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 388 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132149 restraints weight = 19915.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135225 restraints weight = 12900.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137534 restraints weight = 9354.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139112 restraints weight = 7276.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140377 restraints weight = 5997.586| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7919 Z= 0.156 Angle : 0.651 11.087 10794 Z= 0.337 Chirality : 0.041 0.223 1301 Planarity : 0.004 0.044 1427 Dihedral : 4.225 36.306 1243 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 7.60 % Allowed : 30.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1158 helix: 1.87 (0.18), residues: 812 sheet: -3.13 (0.73), residues: 45 loop : -1.61 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 378 TYR 0.023 0.002 TYR X 22 PHE 0.039 0.002 PHE A 306 TRP 0.008 0.001 TRP B 139 HIS 0.007 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7919) covalent geometry : angle 0.65069 (10794) hydrogen bonds : bond 0.03836 ( 584) hydrogen bonds : angle 4.12160 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.61 seconds wall clock time: 37 minutes 27.65 seconds (2247.65 seconds total)