Starting phenix.real_space_refine on Wed Feb 4 00:13:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ocg_70314/02_2026/9ocg_70314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ocg_70314/02_2026/9ocg_70314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ocg_70314/02_2026/9ocg_70314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ocg_70314/02_2026/9ocg_70314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ocg_70314/02_2026/9ocg_70314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ocg_70314/02_2026/9ocg_70314.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 33 5.16 5 C 4893 2.51 5 N 1386 2.21 5 O 1462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3710 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 20, 'TRANS': 530} Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 800 Unresolved non-hydrogen dihedrals: 489 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'ASN:plan1': 7, 'GLN:plan1': 22, 'PHE:plan': 5, 'ASP:plan': 13, 'TYR:plan': 6, 'ARG:plan': 12, 'GLU:plan': 11, 'HIS:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 363 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 414 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 5, 'TRANS': 49} Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 3650 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PTRANS': 18, 'TRANS': 539} Chain breaks: 1 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 16, 'GLN:plan1': 24, 'PHE:plan': 6, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 400 Time building chain proxies: 1.77, per 1000 atoms: 0.23 Number of scatterers: 7774 At special positions: 0 Unit cell: (140.4, 82.08, 124.2, 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 33 16.00 O 1462 8.00 N 1386 7.00 C 4893 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: 0.59 Conformation dependent library (CDL) restraints added in 256.5 milliseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 73.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 131 through 145 removed outlier: 4.072A pdb=" N LYS B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 181 removed outlier: 3.744A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 185 through 234 removed outlier: 3.712A pdb=" N SER B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.004A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 263 through 289 Processing helix chain 'B' and resid 289 through 298 removed outlier: 3.514A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 338 removed outlier: 3.689A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 317 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 348 through 402 removed outlier: 3.883A pdb=" N VAL B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 437 removed outlier: 3.689A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 437 " --> pdb=" O MET B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 591 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.679A pdb=" N GLY B 604 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.686A pdb=" N ALA B 636 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.870A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 650 " --> pdb=" O GLN B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 669 removed outlier: 3.917A pdb=" N VAL B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 12 through 14 No H-bonds generated for 'chain 'C' and resid 12 through 14' Processing helix chain 'C' and resid 35 through 58 removed outlier: 3.888A pdb=" N LEU C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.621A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.028A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 270 removed outlier: 3.548A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.680A pdb=" N PHE A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 324 removed outlier: 4.309A pdb=" N MET A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.960A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 373 Proline residue: A 342 - end of helix removed outlier: 3.802A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.782A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 424 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 484 removed outlier: 3.802A pdb=" N MET A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 3.655A pdb=" N SER A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 3.988A pdb=" N SER A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 660 removed outlier: 3.812A pdb=" N ARG A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 removed outlier: 4.980A pdb=" N GLN A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.861A pdb=" N SER A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.526A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 741 Processing sheet with id=AA1, first strand: chain 'B' and resid 486 through 493 removed outlier: 5.442A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 491 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN B 471 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 493 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS B 469 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP B 472 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLN B 526 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 627 through 630 removed outlier: 7.016A pdb=" N LEU B 628 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ILE B 659 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 630 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR B 499 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 528 removed outlier: 6.550A pdb=" N GLN A 522 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N SER A 509 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 524 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A 505 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU A 563 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP A 507 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLN A 561 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 533 through 534 removed outlier: 6.735A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 715 through 716 591 hydrogen bonds defined for protein. 1731 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: 1.04 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1394 1.30 - 1.43: 1850 1.43 - 1.56: 4595 1.56 - 1.69: 0 1.69 - 1.82: 54 Bond restraints: 7893 Sorted by residual: bond pdb=" C ARG B 381 " pdb=" O ARG B 381 " ideal model delta sigma weight residual 1.237 1.173 0.063 1.16e-02 7.43e+03 2.98e+01 bond pdb=" CG ASN A 227 " pdb=" OD1 ASN A 227 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.51e+01 bond pdb=" CD GLN B 340 " pdb=" OE1 GLN B 340 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.47e+01 bond pdb=" CD GLN A 453 " pdb=" OE1 GLN A 453 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.45e+01 bond pdb=" CD GLN A 453 " pdb=" NE2 GLN A 453 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.23e+01 ... (remaining 7888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 7813 1.73 - 3.46: 2542 3.46 - 5.18: 403 5.18 - 6.91: 31 6.91 - 8.64: 1 Bond angle restraints: 10790 Sorted by residual: angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 111.28 116.89 -5.61 1.09e+00 8.42e-01 2.65e+01 angle pdb=" N ALA B 374 " pdb=" CA ALA B 374 " pdb=" C ALA B 374 " ideal model delta sigma weight residual 111.28 116.08 -4.80 1.09e+00 8.42e-01 1.94e+01 angle pdb=" N LEU A 715 " pdb=" CA LEU A 715 " pdb=" C LEU A 715 " ideal model delta sigma weight residual 108.79 115.49 -6.70 1.53e+00 4.27e-01 1.92e+01 angle pdb=" N ASN B 436 " pdb=" CA ASN B 436 " pdb=" C ASN B 436 " ideal model delta sigma weight residual 111.28 116.02 -4.74 1.09e+00 8.42e-01 1.89e+01 angle pdb=" C VAL B 342 " pdb=" CA VAL B 342 " pdb=" CB VAL B 342 " ideal model delta sigma weight residual 111.97 106.62 5.35 1.28e+00 6.10e-01 1.75e+01 ... (remaining 10785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4374 17.12 - 34.23: 253 34.23 - 51.35: 50 51.35 - 68.46: 16 68.46 - 85.57: 5 Dihedral angle restraints: 4698 sinusoidal: 1372 harmonic: 3326 Sorted by residual: dihedral pdb=" CA HIS A 711 " pdb=" C HIS A 711 " pdb=" N ILE A 712 " pdb=" CA ILE A 712 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA A 535 " pdb=" C ALA A 535 " pdb=" N LEU A 536 " pdb=" CA LEU A 536 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLN A 586 " pdb=" C GLN A 586 " pdb=" N GLU A 587 " pdb=" CA GLU A 587 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 783 0.055 - 0.110: 318 0.110 - 0.164: 148 0.164 - 0.219: 48 0.219 - 0.274: 13 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CG LEU A 360 " pdb=" CB LEU A 360 " pdb=" CD1 LEU A 360 " pdb=" CD2 LEU A 360 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA THR A 328 " pdb=" N THR A 328 " pdb=" C THR A 328 " pdb=" CB THR A 328 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU A 338 " pdb=" N LEU A 338 " pdb=" C LEU A 338 " pdb=" CB LEU A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1307 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 422 " -0.077 2.00e-02 2.50e+03 5.07e-02 5.14e+01 pdb=" CG TYR B 422 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 422 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 422 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR B 422 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR B 422 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR B 422 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR B 422 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 447 " 0.084 2.00e-02 2.50e+03 5.14e-02 4.63e+01 pdb=" CG PHE A 447 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 447 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 447 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 447 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 447 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 447 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 249 " -0.059 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR A 249 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 249 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 249 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 249 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 249 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 249 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 249 " -0.068 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 474 2.76 - 3.29: 8338 3.29 - 3.83: 11909 3.83 - 4.36: 12967 4.36 - 4.90: 22304 Nonbonded interactions: 55992 Sorted by model distance: nonbonded pdb=" OE1 GLU B 307 " pdb=" NH2 ARG C 42 " model vdw 2.221 3.120 nonbonded pdb=" O ASN B 436 " pdb=" OD1 ASN B 436 " model vdw 2.346 3.040 nonbonded pdb=" O TYR A 349 " pdb=" C GLN A 350 " model vdw 2.462 3.270 nonbonded pdb=" OG SER A 220 " pdb=" OD1 ASP A 222 " model vdw 2.483 3.040 nonbonded pdb=" O ARG B 381 " pdb=" N HIS B 384 " model vdw 2.499 3.120 ... (remaining 55987 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.011 0.099 7893 Z= 0.691 Angle : 1.647 8.637 10790 Z= 1.118 Chirality : 0.077 0.274 1310 Planarity : 0.011 0.106 1432 Dihedral : 12.928 85.574 2552 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.34 % 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 are not related in a simple way. whole: -0.44 (0.23), residues: 1156 helix: -0.05 (0.17), residues: 756 sheet: -1.53 (1.18), residues: 13 loop : -0.46 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 210 TYR 0.094 0.016 TYR B 422 PHE 0.084 0.010 PHE A 447 TRP 0.041 0.012 TRP A 308 HIS 0.008 0.003 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.01102 ( 7893) covalent geometry : angle 1.64681 (10790) hydrogen bonds : bond 0.16290 ( 591) hydrogen bonds : angle 6.71863 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 ASP cc_start: 0.9208 (t0) cc_final: 0.8912 (t0) REVERT: B 198 LEU cc_start: 0.9516 (tp) cc_final: 0.9241 (tt) REVERT: B 218 MET cc_start: 0.9269 (ttm) cc_final: 0.8789 (tpp) REVERT: B 275 LEU cc_start: 0.9744 (tp) cc_final: 0.9497 (tt) REVERT: B 390 LEU cc_start: 0.9421 (tp) cc_final: 0.9205 (tt) REVERT: C 11 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 12 GLN cc_start: 0.8212 (mp10) cc_final: 0.7981 (mp10) REVERT: C 37 ASP cc_start: 0.9313 (m-30) cc_final: 0.9027 (m-30) REVERT: C 52 PHE cc_start: 0.9180 (t80) cc_final: 0.8663 (t80) REVERT: A 198 SER cc_start: 0.9334 (t) cc_final: 0.9070 (p) REVERT: A 202 MET cc_start: 0.8950 (mmm) cc_final: 0.8720 (mmm) REVERT: A 232 SER cc_start: 0.9363 (t) cc_final: 0.9073 (p) REVERT: A 250 ASN cc_start: 0.9018 (m-40) cc_final: 0.8618 (m-40) REVERT: A 283 ASN cc_start: 0.9624 (p0) cc_final: 0.9313 (p0) REVERT: A 285 MET cc_start: 0.9314 (mpp) cc_final: 0.8287 (mpp) REVERT: A 302 ASN cc_start: 0.9462 (m-40) cc_final: 0.9182 (m-40) REVERT: A 386 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8921 (mm-30) REVERT: A 411 ASN cc_start: 0.9508 (t0) cc_final: 0.9239 (t0) REVERT: A 451 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 452 MET cc_start: 0.9060 (mtp) cc_final: 0.8730 (mtp) REVERT: A 455 THR cc_start: 0.9292 (m) cc_final: 0.8851 (p) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.0651 time to fit residues: 19.6579 Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.074079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.057241 restraints weight = 35697.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058934 restraints weight = 18891.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060137 restraints weight = 12286.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060922 restraints weight = 9081.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061285 restraints weight = 7448.489| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7893 Z= 0.150 Angle : 0.615 8.079 10790 Z= 0.319 Chirality : 0.040 0.156 1310 Planarity : 0.005 0.099 1432 Dihedral : 3.965 27.548 1222 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.54 % Allowed : 16.56 % Favored : 79.90 % 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 are not related in a simple way. whole: 1.37 (0.25), residues: 1156 helix: 1.52 (0.18), residues: 795 sheet: -2.47 (0.58), residues: 54 loop : 0.13 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 287 TYR 0.018 0.002 TYR B 422 PHE 0.013 0.001 PHE A 224 TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7893) covalent geometry : angle 0.61480 (10790) hydrogen bonds : bond 0.06011 ( 591) hydrogen bonds : angle 4.26865 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 VAL cc_start: 0.9496 (t) cc_final: 0.9259 (p) REVERT: B 185 ASP cc_start: 0.8850 (t0) cc_final: 0.8445 (t0) REVERT: B 198 LEU cc_start: 0.9457 (tp) cc_final: 0.9118 (tt) REVERT: B 365 LEU cc_start: 0.9625 (tp) cc_final: 0.9422 (tp) REVERT: B 390 LEU cc_start: 0.9397 (tp) cc_final: 0.9111 (tt) REVERT: B 391 MET cc_start: 0.8873 (tmm) cc_final: 0.8416 (tmm) REVERT: B 399 MET cc_start: 0.9079 (tpp) cc_final: 0.8814 (tpp) REVERT: B 422 TYR cc_start: 0.9334 (m-80) cc_final: 0.8607 (m-80) REVERT: B 447 MET cc_start: 0.8780 (tpt) cc_final: 0.8336 (tmm) REVERT: B 448 ASP cc_start: 0.8670 (p0) cc_final: 0.8398 (p0) REVERT: C 9 LEU cc_start: 0.9674 (mp) cc_final: 0.9377 (mm) REVERT: C 11 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8108 (mt-10) REVERT: C 12 GLN cc_start: 0.8148 (mp10) cc_final: 0.7879 (mp10) REVERT: C 52 PHE cc_start: 0.9066 (t80) cc_final: 0.8837 (t80) REVERT: C 55 LEU cc_start: 0.9075 (tt) cc_final: 0.8708 (mm) REVERT: A 193 LEU cc_start: 0.9291 (mm) cc_final: 0.8980 (mt) REVERT: A 231 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8840 (ppp) REVERT: A 242 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8714 (tp30) REVERT: A 349 TYR cc_start: 0.9142 (t80) cc_final: 0.8867 (t80) REVERT: A 404 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.9180 (tm-30) REVERT: A 411 ASN cc_start: 0.9604 (t0) cc_final: 0.9328 (t0) REVERT: A 451 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 452 MET cc_start: 0.9017 (mtp) cc_final: 0.8626 (mtp) REVERT: A 455 THR cc_start: 0.9140 (m) cc_final: 0.8810 (p) outliers start: 22 outliers final: 13 residues processed: 160 average time/residue: 0.0589 time to fit residues: 14.1251 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 91 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.073918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.057506 restraints weight = 35828.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059170 restraints weight = 18983.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060286 restraints weight = 12394.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061084 restraints weight = 9207.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061634 restraints weight = 7511.366| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7893 Z= 0.132 Angle : 0.570 8.427 10790 Z= 0.291 Chirality : 0.038 0.121 1310 Planarity : 0.004 0.044 1432 Dihedral : 3.488 16.617 1220 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.70 % Allowed : 19.29 % Favored : 77.01 % 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 are not related in a simple way. whole: 1.88 (0.25), residues: 1156 helix: 1.87 (0.19), residues: 805 sheet: -2.08 (0.62), residues: 54 loop : 0.32 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 27 TYR 0.012 0.001 TYR B 172 PHE 0.013 0.001 PHE A 224 TRP 0.008 0.001 TRP B 263 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7893) covalent geometry : angle 0.57037 (10790) hydrogen bonds : bond 0.05299 ( 591) hydrogen bonds : angle 3.92105 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: B 163 VAL cc_start: 0.9504 (t) cc_final: 0.9248 (p) REVERT: B 185 ASP cc_start: 0.8885 (t0) cc_final: 0.8469 (t0) REVERT: B 198 LEU cc_start: 0.9423 (tp) cc_final: 0.9130 (tt) REVERT: B 237 ASP cc_start: 0.7996 (p0) cc_final: 0.7731 (m-30) REVERT: B 307 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 355 TYR cc_start: 0.9419 (t80) cc_final: 0.9080 (t80) REVERT: B 365 LEU cc_start: 0.9641 (tp) cc_final: 0.9427 (tp) REVERT: B 390 LEU cc_start: 0.9418 (tp) cc_final: 0.9105 (tt) REVERT: B 399 MET cc_start: 0.9063 (tpp) cc_final: 0.8793 (tpp) REVERT: B 401 ASP cc_start: 0.8630 (t0) cc_final: 0.8392 (m-30) REVERT: B 417 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8606 (mm-30) REVERT: B 422 TYR cc_start: 0.9324 (m-80) cc_final: 0.8581 (m-10) REVERT: B 430 TYR cc_start: 0.8962 (t80) cc_final: 0.8657 (t80) REVERT: B 447 MET cc_start: 0.8848 (tpt) cc_final: 0.8400 (tmm) REVERT: B 448 ASP cc_start: 0.8471 (p0) cc_final: 0.8239 (p0) REVERT: C 9 LEU cc_start: 0.9672 (mp) cc_final: 0.9454 (mm) REVERT: C 11 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8096 (mt-10) REVERT: C 12 GLN cc_start: 0.8308 (mp10) cc_final: 0.7980 (mp10) REVERT: C 55 LEU cc_start: 0.9151 (tt) cc_final: 0.8768 (mm) REVERT: A 231 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8769 (ppp) REVERT: A 242 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8767 (tp30) REVERT: A 311 VAL cc_start: 0.9804 (t) cc_final: 0.9581 (p) REVERT: A 349 TYR cc_start: 0.9191 (t80) cc_final: 0.8888 (t80) REVERT: A 404 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9183 (tm-30) REVERT: A 411 ASN cc_start: 0.9608 (t0) cc_final: 0.9398 (t0) REVERT: A 451 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 452 MET cc_start: 0.9032 (mtp) cc_final: 0.8708 (mtp) REVERT: A 455 THR cc_start: 0.9164 (m) cc_final: 0.8792 (p) outliers start: 23 outliers final: 10 residues processed: 158 average time/residue: 0.0614 time to fit residues: 14.3547 Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 1.9990 chunk 91 optimal weight: 40.0000 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054900 restraints weight = 37242.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056447 restraints weight = 19923.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057560 restraints weight = 13195.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058320 restraints weight = 9835.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.058593 restraints weight = 8070.601| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7893 Z= 0.239 Angle : 0.645 6.842 10790 Z= 0.336 Chirality : 0.040 0.145 1310 Planarity : 0.004 0.043 1432 Dihedral : 3.515 15.963 1220 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.14 % Allowed : 19.13 % Favored : 75.72 % 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 are not related in a simple way. whole: 1.88 (0.25), residues: 1156 helix: 1.89 (0.19), residues: 807 sheet: -1.63 (0.59), residues: 64 loop : 0.24 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 27 TYR 0.015 0.001 TYR B 310 PHE 0.013 0.002 PHE A 224 TRP 0.008 0.002 TRP B 367 HIS 0.002 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7893) covalent geometry : angle 0.64521 (10790) hydrogen bonds : bond 0.05345 ( 591) hydrogen bonds : angle 4.25972 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.9444 (tp) cc_final: 0.9088 (tt) REVERT: B 237 ASP cc_start: 0.8148 (p0) cc_final: 0.7779 (m-30) REVERT: B 307 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8419 (tm-30) REVERT: B 365 LEU cc_start: 0.9646 (tp) cc_final: 0.9312 (tp) REVERT: B 390 LEU cc_start: 0.9420 (tp) cc_final: 0.9167 (tt) REVERT: B 391 MET cc_start: 0.9007 (tmm) cc_final: 0.8499 (tmm) REVERT: B 417 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8413 (mm-30) REVERT: B 432 ASP cc_start: 0.9104 (t70) cc_final: 0.8762 (t0) REVERT: B 447 MET cc_start: 0.8906 (tpt) cc_final: 0.8518 (tmm) REVERT: C 9 LEU cc_start: 0.9719 (mp) cc_final: 0.9453 (mm) REVERT: C 11 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8535 (mt-10) REVERT: C 12 GLN cc_start: 0.8601 (mp10) cc_final: 0.8141 (mp10) REVERT: A 193 LEU cc_start: 0.9363 (mm) cc_final: 0.9112 (mt) REVERT: A 242 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8801 (tp30) REVERT: A 311 VAL cc_start: 0.9835 (t) cc_final: 0.9604 (p) REVERT: A 349 TYR cc_start: 0.9374 (t80) cc_final: 0.9069 (t80) REVERT: A 374 MET cc_start: 0.8897 (mmm) cc_final: 0.8665 (tpp) REVERT: A 404 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.9162 (tm-30) REVERT: A 411 ASN cc_start: 0.9639 (t0) cc_final: 0.9413 (t0) REVERT: A 421 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8759 (tt) REVERT: A 452 MET cc_start: 0.9194 (mtp) cc_final: 0.8898 (mtp) outliers start: 32 outliers final: 21 residues processed: 143 average time/residue: 0.0645 time to fit residues: 13.6363 Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.072405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055802 restraints weight = 36532.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.057492 restraints weight = 19353.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058321 restraints weight = 12647.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059288 restraints weight = 9776.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059818 restraints weight = 7812.497| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7893 Z= 0.127 Angle : 0.562 8.136 10790 Z= 0.283 Chirality : 0.038 0.161 1310 Planarity : 0.003 0.045 1432 Dihedral : 3.316 15.701 1220 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.38 % Allowed : 23.63 % Favored : 72.99 % 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 are not related in a simple way. whole: 2.25 (0.26), residues: 1156 helix: 2.19 (0.19), residues: 800 sheet: -1.48 (0.61), residues: 64 loop : 0.31 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.009 0.001 TYR B 310 PHE 0.014 0.001 PHE A 224 TRP 0.009 0.001 TRP B 263 HIS 0.003 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7893) covalent geometry : angle 0.56160 (10790) hydrogen bonds : bond 0.05030 ( 591) hydrogen bonds : angle 3.78895 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.9401 (tp) cc_final: 0.9076 (tt) REVERT: B 218 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8700 (tpp) REVERT: B 237 ASP cc_start: 0.8085 (p0) cc_final: 0.7750 (m-30) REVERT: B 307 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 390 LEU cc_start: 0.9399 (tp) cc_final: 0.9099 (tt) REVERT: B 391 MET cc_start: 0.8953 (tmm) cc_final: 0.8419 (tmm) REVERT: B 432 ASP cc_start: 0.9078 (t70) cc_final: 0.8713 (t0) REVERT: B 447 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8478 (tmm) REVERT: C 9 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9405 (mm) REVERT: C 11 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8464 (mt-10) REVERT: C 12 GLN cc_start: 0.8577 (mp10) cc_final: 0.8078 (mp10) REVERT: C 55 LEU cc_start: 0.9180 (tt) cc_final: 0.8846 (mm) REVERT: A 193 LEU cc_start: 0.9346 (mm) cc_final: 0.9086 (mt) REVERT: A 242 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8757 (tp30) REVERT: A 349 TYR cc_start: 0.9322 (t80) cc_final: 0.9010 (t80) REVERT: A 404 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9144 (tm-30) REVERT: A 420 MET cc_start: 0.9062 (ttm) cc_final: 0.8801 (mtt) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 0.0688 time to fit residues: 14.4454 Evaluate side-chains 134 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS ** A 401 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.072829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055819 restraints weight = 36560.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057518 restraints weight = 19217.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058681 restraints weight = 12526.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059482 restraints weight = 9219.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060024 restraints weight = 7452.502| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7893 Z= 0.130 Angle : 0.578 9.034 10790 Z= 0.290 Chirality : 0.038 0.169 1310 Planarity : 0.003 0.044 1432 Dihedral : 3.256 15.707 1220 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.54 % Allowed : 23.95 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.26), residues: 1156 helix: 2.28 (0.19), residues: 802 sheet: -1.34 (0.61), residues: 64 loop : 0.29 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.012 0.001 TYR B 428 PHE 0.013 0.001 PHE A 224 TRP 0.006 0.001 TRP B 263 HIS 0.021 0.002 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7893) covalent geometry : angle 0.57795 (10790) hydrogen bonds : bond 0.04836 ( 591) hydrogen bonds : angle 3.75591 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.9413 (tp) cc_final: 0.9108 (tt) REVERT: B 218 MET cc_start: 0.9277 (ttm) cc_final: 0.8639 (tmm) REVERT: B 262 ASN cc_start: 0.8989 (m-40) cc_final: 0.8481 (m110) REVERT: B 307 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 390 LEU cc_start: 0.9385 (tp) cc_final: 0.9082 (tt) REVERT: B 432 ASP cc_start: 0.9092 (t70) cc_final: 0.8714 (t0) REVERT: B 447 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8534 (tmm) REVERT: B 448 ASP cc_start: 0.8319 (p0) cc_final: 0.8087 (p0) REVERT: C 9 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9378 (mm) REVERT: C 11 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 12 GLN cc_start: 0.8636 (mp10) cc_final: 0.8127 (mp10) REVERT: C 55 LEU cc_start: 0.9199 (tt) cc_final: 0.8915 (mm) REVERT: A 231 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8693 (ppp) REVERT: A 242 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8741 (tp30) REVERT: A 311 VAL cc_start: 0.9798 (t) cc_final: 0.9571 (p) REVERT: A 349 TYR cc_start: 0.9348 (t80) cc_final: 0.9024 (t80) REVERT: A 404 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9175 (tm-30) REVERT: A 420 MET cc_start: 0.9025 (ttm) cc_final: 0.8709 (mtt) REVERT: A 451 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 459 GLU cc_start: 0.9463 (tt0) cc_final: 0.8776 (mt-10) outliers start: 22 outliers final: 14 residues processed: 139 average time/residue: 0.0628 time to fit residues: 12.9002 Evaluate side-chains 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS ** A 401 ASN ** 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 = 0.3457 r_free = 0.3457 target = 0.073106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056195 restraints weight = 36527.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057929 restraints weight = 19456.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059046 restraints weight = 12705.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059806 restraints weight = 9450.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060341 restraints weight = 7684.160| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7893 Z= 0.125 Angle : 0.574 9.271 10790 Z= 0.288 Chirality : 0.038 0.180 1310 Planarity : 0.003 0.044 1432 Dihedral : 3.185 15.335 1220 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.02 % Allowed : 24.28 % Favored : 71.70 % 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 are not related in a simple way. whole: 2.47 (0.26), residues: 1156 helix: 2.37 (0.19), residues: 803 sheet: -1.29 (0.60), residues: 64 loop : 0.33 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.008 0.001 TYR B 310 PHE 0.013 0.001 PHE A 224 TRP 0.006 0.001 TRP B 263 HIS 0.014 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7893) covalent geometry : angle 0.57375 (10790) hydrogen bonds : bond 0.04665 ( 591) hydrogen bonds : angle 3.65103 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 198 LEU cc_start: 0.9401 (tp) cc_final: 0.9103 (tt) REVERT: B 237 ASP cc_start: 0.7954 (p0) cc_final: 0.7743 (m-30) REVERT: B 262 ASN cc_start: 0.8891 (m-40) cc_final: 0.8579 (m110) REVERT: B 307 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 370 ASP cc_start: 0.9232 (m-30) cc_final: 0.8891 (m-30) REVERT: B 432 ASP cc_start: 0.9078 (t70) cc_final: 0.8765 (t0) REVERT: B 436 ASN cc_start: 0.8948 (t0) cc_final: 0.8731 (t0) REVERT: B 447 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8489 (tmm) REVERT: C 9 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9351 (mm) REVERT: C 11 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8490 (mt-10) REVERT: C 12 GLN cc_start: 0.8661 (mp10) cc_final: 0.8131 (mp10) REVERT: C 55 LEU cc_start: 0.9185 (tt) cc_final: 0.8889 (mm) REVERT: A 193 LEU cc_start: 0.9373 (mm) cc_final: 0.9132 (mt) REVERT: A 231 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8695 (ppp) REVERT: A 242 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8730 (tp30) REVERT: A 311 VAL cc_start: 0.9807 (t) cc_final: 0.9586 (p) REVERT: A 349 TYR cc_start: 0.9332 (t80) cc_final: 0.9015 (t80) REVERT: A 404 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9171 (tm-30) REVERT: A 420 MET cc_start: 0.8987 (ttm) cc_final: 0.8679 (mtt) REVERT: A 451 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 0.0611 time to fit residues: 13.3685 Evaluate side-chains 146 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS A 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.073160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056212 restraints weight = 36714.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057949 restraints weight = 19368.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059119 restraints weight = 12516.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059911 restraints weight = 9232.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060274 restraints weight = 7440.612| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7893 Z= 0.126 Angle : 0.583 10.384 10790 Z= 0.289 Chirality : 0.038 0.168 1310 Planarity : 0.003 0.043 1432 Dihedral : 3.134 14.907 1220 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.02 % Allowed : 24.28 % Favored : 71.70 % 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 are not related in a simple way. whole: 2.54 (0.26), residues: 1156 helix: 2.42 (0.19), residues: 803 sheet: -1.25 (0.60), residues: 64 loop : 0.34 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.013 0.001 TYR B 428 PHE 0.013 0.001 PHE B 412 TRP 0.005 0.001 TRP B 263 HIS 0.011 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7893) covalent geometry : angle 0.58304 (10790) hydrogen bonds : bond 0.04559 ( 591) hydrogen bonds : angle 3.62811 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 198 LEU cc_start: 0.9382 (tp) cc_final: 0.9099 (tt) REVERT: B 262 ASN cc_start: 0.8870 (m-40) cc_final: 0.8544 (m110) REVERT: B 307 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 370 ASP cc_start: 0.9258 (m-30) cc_final: 0.8931 (m-30) REVERT: B 391 MET cc_start: 0.8988 (tmm) cc_final: 0.8678 (tmm) REVERT: B 432 ASP cc_start: 0.9101 (t70) cc_final: 0.8792 (t0) REVERT: B 436 ASN cc_start: 0.8927 (t0) cc_final: 0.8695 (t0) REVERT: B 447 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8571 (tmm) REVERT: C 9 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9331 (mm) REVERT: C 11 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8493 (mt-10) REVERT: C 12 GLN cc_start: 0.8652 (mp10) cc_final: 0.8077 (mp10) REVERT: C 55 LEU cc_start: 0.9202 (tt) cc_final: 0.8892 (mm) REVERT: A 193 LEU cc_start: 0.9344 (mm) cc_final: 0.9091 (mt) REVERT: A 231 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8710 (ppp) REVERT: A 242 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8740 (tp30) REVERT: A 311 VAL cc_start: 0.9810 (t) cc_final: 0.9585 (p) REVERT: A 349 TYR cc_start: 0.9378 (t80) cc_final: 0.9052 (t80) REVERT: A 404 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9167 (tm-30) REVERT: A 459 GLU cc_start: 0.9469 (tt0) cc_final: 0.8779 (mt-10) outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 0.0572 time to fit residues: 12.4631 Evaluate side-chains 143 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 95 optimal weight: 50.0000 chunk 17 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** A 401 ASN ** 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 = 0.3466 r_free = 0.3466 target = 0.073600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.056777 restraints weight = 36204.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058458 restraints weight = 19064.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059660 restraints weight = 12236.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060246 restraints weight = 9023.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060877 restraints weight = 7568.287| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7893 Z= 0.124 Angle : 0.600 11.344 10790 Z= 0.295 Chirality : 0.038 0.183 1310 Planarity : 0.003 0.043 1432 Dihedral : 3.100 13.988 1220 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.70 % Allowed : 24.92 % Favored : 71.38 % 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 are not related in a simple way. whole: 2.60 (0.26), residues: 1156 helix: 2.45 (0.19), residues: 807 sheet: -1.15 (0.61), residues: 64 loop : 0.36 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.008 0.001 TYR B 310 PHE 0.012 0.001 PHE B 412 TRP 0.005 0.001 TRP B 263 HIS 0.016 0.002 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7893) covalent geometry : angle 0.60046 (10790) hydrogen bonds : bond 0.04469 ( 591) hydrogen bonds : angle 3.57139 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.276 Fit side-chains REVERT: B 198 LEU cc_start: 0.9375 (tp) cc_final: 0.9095 (tt) REVERT: B 262 ASN cc_start: 0.8874 (m-40) cc_final: 0.8583 (m-40) REVERT: B 307 GLU cc_start: 0.8826 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 311 ASN cc_start: 0.9113 (m-40) cc_final: 0.8676 (m-40) REVERT: B 370 ASP cc_start: 0.9259 (m-30) cc_final: 0.8920 (m-30) REVERT: B 391 MET cc_start: 0.9007 (tmm) cc_final: 0.8713 (tmm) REVERT: B 432 ASP cc_start: 0.9101 (t70) cc_final: 0.8893 (t0) REVERT: B 436 ASN cc_start: 0.8896 (t0) cc_final: 0.8654 (t0) REVERT: B 447 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8581 (tmm) REVERT: C 9 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9269 (mm) REVERT: C 11 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8498 (mt-10) REVERT: C 12 GLN cc_start: 0.8663 (mp10) cc_final: 0.8065 (mp10) REVERT: C 55 LEU cc_start: 0.9201 (tt) cc_final: 0.8906 (mm) REVERT: A 193 LEU cc_start: 0.9332 (mm) cc_final: 0.9072 (mt) REVERT: A 231 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8691 (ppp) REVERT: A 242 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8751 (tp30) REVERT: A 311 VAL cc_start: 0.9792 (t) cc_final: 0.9569 (p) REVERT: A 349 TYR cc_start: 0.9369 (t80) cc_final: 0.9046 (t80) REVERT: A 404 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9173 (tm-30) REVERT: A 451 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8030 (tm-30) outliers start: 23 outliers final: 18 residues processed: 143 average time/residue: 0.0641 time to fit residues: 13.7420 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** A 401 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.073594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056668 restraints weight = 36287.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058363 restraints weight = 19207.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059599 restraints weight = 12357.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060425 restraints weight = 9055.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060934 restraints weight = 7308.694| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7893 Z= 0.126 Angle : 0.624 15.930 10790 Z= 0.303 Chirality : 0.038 0.171 1310 Planarity : 0.003 0.044 1432 Dihedral : 3.061 13.549 1220 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.70 % Allowed : 25.24 % Favored : 71.06 % 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 are not related in a simple way. whole: 2.65 (0.26), residues: 1156 helix: 2.48 (0.19), residues: 807 sheet: -1.06 (0.62), residues: 64 loop : 0.38 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.013 0.001 TYR B 428 PHE 0.013 0.001 PHE B 412 TRP 0.005 0.001 TRP B 263 HIS 0.009 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7893) covalent geometry : angle 0.62364 (10790) hydrogen bonds : bond 0.04395 ( 591) hydrogen bonds : angle 3.52548 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.275 Fit side-chains REVERT: B 198 LEU cc_start: 0.9368 (tp) cc_final: 0.9089 (tt) REVERT: B 262 ASN cc_start: 0.8847 (m-40) cc_final: 0.8549 (m-40) REVERT: B 307 GLU cc_start: 0.8840 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 311 ASN cc_start: 0.9142 (m-40) cc_final: 0.8714 (m-40) REVERT: B 370 ASP cc_start: 0.9284 (m-30) cc_final: 0.8940 (m-30) REVERT: B 391 MET cc_start: 0.9029 (tmm) cc_final: 0.8733 (tmm) REVERT: B 416 GLN cc_start: 0.9392 (tm-30) cc_final: 0.8925 (tm-30) REVERT: B 436 ASN cc_start: 0.8966 (t0) cc_final: 0.8702 (t0) REVERT: B 447 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8568 (tmm) REVERT: C 5 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8302 (tp) REVERT: C 9 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9279 (mm) REVERT: C 11 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8493 (mt-10) REVERT: C 12 GLN cc_start: 0.8676 (mp10) cc_final: 0.8089 (mp10) REVERT: C 48 LEU cc_start: 0.9528 (tp) cc_final: 0.9241 (mt) REVERT: C 55 LEU cc_start: 0.9194 (tt) cc_final: 0.8906 (mm) REVERT: A 193 LEU cc_start: 0.9329 (mm) cc_final: 0.9064 (mt) REVERT: A 231 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8683 (ppp) REVERT: A 242 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8753 (tp30) REVERT: A 311 VAL cc_start: 0.9785 (t) cc_final: 0.9571 (p) REVERT: A 349 TYR cc_start: 0.9378 (t80) cc_final: 0.9063 (t80) REVERT: A 404 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9177 (tm-30) REVERT: A 451 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 459 GLU cc_start: 0.9476 (tt0) cc_final: 0.8783 (mt-10) outliers start: 23 outliers final: 15 residues processed: 136 average time/residue: 0.0550 time to fit residues: 11.4546 Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS A 227 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.072135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.055835 restraints weight = 37020.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057465 restraints weight = 19548.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058625 restraints weight = 12629.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059377 restraints weight = 9369.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059903 restraints weight = 7591.769| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7893 Z= 0.171 Angle : 0.632 11.242 10790 Z= 0.316 Chirality : 0.038 0.167 1310 Planarity : 0.003 0.043 1432 Dihedral : 3.088 13.434 1220 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.02 % Allowed : 25.08 % Favored : 70.90 % 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 are not related in a simple way. whole: 2.63 (0.26), residues: 1156 helix: 2.49 (0.19), residues: 801 sheet: -1.08 (0.61), residues: 64 loop : 0.36 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.008 0.001 TYR B 172 PHE 0.012 0.001 PHE B 412 TRP 0.005 0.001 TRP A 308 HIS 0.015 0.002 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7893) covalent geometry : angle 0.63182 (10790) hydrogen bonds : bond 0.04449 ( 591) hydrogen bonds : angle 3.68853 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.82 seconds wall clock time: 22 minutes 2.82 seconds (1322.82 seconds total)