Starting phenix.real_space_refine on Mon May 26 05:33:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrm_39544/05_2025/8yrm_39544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrm_39544/05_2025/8yrm_39544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yrm_39544/05_2025/8yrm_39544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrm_39544/05_2025/8yrm_39544.map" model { file = "/net/cci-nas-00/data/ceres_data/8yrm_39544/05_2025/8yrm_39544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrm_39544/05_2025/8yrm_39544.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 42 5.16 5 C 17367 2.51 5 N 4550 2.21 5 O 5880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27853 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3977 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 491} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 11.55, per 1000 atoms: 0.41 Number of scatterers: 27853 At special positions: 0 Unit cell: (176.85, 172.8, 161.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 42 16.00 O 5880 8.00 N 4550 7.00 C 17367 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: 7.31 Conformation dependent library (CDL) restraints added in 3.7 seconds 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 78 sheets defined 15.7% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.589A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.708A pdb=" N SER A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.931A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.590A pdb=" N ILE B 428 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.709A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.930A pdb=" N LYS B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.589A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 502 through 512 removed outlier: 4.705A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 592 removed outlier: 3.930A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.589A pdb=" N ILE D 428 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 502 through 512 removed outlier: 4.707A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.930A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.589A pdb=" N ILE E 428 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 502 through 512 removed outlier: 4.708A pdb=" N SER E 507 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 580 through 592 removed outlier: 3.931A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 232 Processing helix chain 'F' and resid 245 through 249 Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.589A pdb=" N ILE F 428 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 502 through 512 removed outlier: 4.709A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.930A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 424 through 428 removed outlier: 3.589A pdb=" N ILE G 428 " --> pdb=" O ASP G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 470 Processing helix chain 'G' and resid 502 through 512 removed outlier: 4.704A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN G 508 " --> pdb=" O ASN G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 3.930A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 310 removed outlier: 6.840A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.697A pdb=" N ILE A 459 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 422 removed outlier: 6.798A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 431 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 422 removed outlier: 6.798A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS A 404 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY A 484 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR A 406 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL A 482 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 530 Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 617 through 619 Processing sheet with id=AB2, first strand: chain 'A' and resid 617 through 619 removed outlier: 5.716A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A 667 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 672 " --> pdb=" O PHE A 706 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 652 through 657 Processing sheet with id=AB4, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB5, first strand: chain 'B' and resid 299 through 310 removed outlier: 6.843A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 437 through 438 removed outlier: 4.694A pdb=" N ILE B 459 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 416 through 422 removed outlier: 6.796A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 416 through 422 removed outlier: 6.796A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AC1, first strand: chain 'B' and resid 524 through 530 Processing sheet with id=AC2, first strand: chain 'B' and resid 557 through 559 Processing sheet with id=AC3, first strand: chain 'B' and resid 617 through 619 Processing sheet with id=AC4, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.716A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG B 667 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 672 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 652 through 657 Processing sheet with id=AC6, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC7, first strand: chain 'C' and resid 299 through 310 removed outlier: 6.841A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 306 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN C 389 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 308 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 387 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 437 through 438 removed outlier: 4.698A pdb=" N ILE C 459 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 416 through 422 removed outlier: 6.796A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR C 403 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN C 431 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 416 through 422 removed outlier: 6.796A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AD3, first strand: chain 'C' and resid 524 through 530 Processing sheet with id=AD4, first strand: chain 'C' and resid 557 through 559 Processing sheet with id=AD5, first strand: chain 'C' and resid 617 through 619 Processing sheet with id=AD6, first strand: chain 'C' and resid 617 through 619 removed outlier: 5.716A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C 667 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 672 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 652 through 657 Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD9, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.841A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 437 through 438 removed outlier: 4.695A pdb=" N ILE D 459 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.795A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.795A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS D 404 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY D 484 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR D 406 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL D 482 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR D 408 " --> pdb=" O THR D 480 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AE5, first strand: chain 'D' and resid 524 through 530 Processing sheet with id=AE6, first strand: chain 'D' and resid 557 through 559 Processing sheet with id=AE7, first strand: chain 'D' and resid 617 through 619 Processing sheet with id=AE8, first strand: chain 'D' and resid 617 through 619 removed outlier: 5.716A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG D 667 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY D 672 " --> pdb=" O PHE D 706 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 652 through 657 Processing sheet with id=AF1, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AF2, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.843A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 437 through 438 removed outlier: 4.696A pdb=" N ILE E 459 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 416 through 422 removed outlier: 6.797A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR E 403 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN E 431 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 416 through 422 removed outlier: 6.797A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS E 404 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY E 484 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR E 406 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL E 482 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AF7, first strand: chain 'E' and resid 524 through 530 Processing sheet with id=AF8, first strand: chain 'E' and resid 557 through 559 Processing sheet with id=AF9, first strand: chain 'E' and resid 617 through 619 Processing sheet with id=AG1, first strand: chain 'E' and resid 617 through 619 removed outlier: 5.716A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG E 667 " --> pdb=" O LEU E 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY E 672 " --> pdb=" O PHE E 706 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 652 through 657 Processing sheet with id=AG3, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AG4, first strand: chain 'F' and resid 299 through 310 removed outlier: 6.839A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU F 306 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN F 389 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE F 308 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR F 387 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 437 through 438 removed outlier: 4.696A pdb=" N ILE F 459 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 416 through 422 removed outlier: 6.797A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR F 403 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN F 431 " --> pdb=" O TYR F 403 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 416 through 422 removed outlier: 6.797A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS F 404 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY F 484 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR F 406 " --> pdb=" O VAL F 482 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL F 482 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 408 " --> pdb=" O THR F 480 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AG9, first strand: chain 'F' and resid 524 through 530 Processing sheet with id=AH1, first strand: chain 'F' and resid 557 through 559 Processing sheet with id=AH2, first strand: chain 'F' and resid 617 through 619 Processing sheet with id=AH3, first strand: chain 'F' and resid 617 through 619 removed outlier: 5.715A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG F 667 " --> pdb=" O LEU F 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 672 " --> pdb=" O PHE F 706 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 652 through 657 Processing sheet with id=AH5, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AH6, first strand: chain 'G' and resid 299 through 310 removed outlier: 6.843A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU G 306 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN G 389 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE G 308 " --> pdb=" O TYR G 387 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR G 387 " --> pdb=" O ILE G 308 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 437 through 438 removed outlier: 4.696A pdb=" N ILE G 459 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 416 through 422 removed outlier: 6.797A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 416 through 422 removed outlier: 6.797A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS G 404 " --> pdb=" O GLY G 484 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY G 484 " --> pdb=" O LYS G 404 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR G 406 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL G 482 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR G 408 " --> pdb=" O THR G 480 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AI2, first strand: chain 'G' and resid 524 through 530 Processing sheet with id=AI3, first strand: chain 'G' and resid 557 through 559 Processing sheet with id=AI4, first strand: chain 'G' and resid 617 through 619 Processing sheet with id=AI5, first strand: chain 'G' and resid 617 through 619 removed outlier: 5.715A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG G 667 " --> pdb=" O LEU G 740 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY G 672 " --> pdb=" O PHE G 706 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 652 through 657 1267 hydrogen bonds defined for protein. 3213 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: 11.06 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7756 1.34 - 1.46: 7594 1.46 - 1.58: 12881 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 28308 Sorted by residual: bond pdb=" CA SER D 515 " pdb=" CB SER D 515 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.43e-02 4.89e+03 9.43e+00 bond pdb=" CA SER E 515 " pdb=" CB SER E 515 " ideal model delta sigma weight residual 1.529 1.486 0.044 1.43e-02 4.89e+03 9.29e+00 bond pdb=" CA SER G 515 " pdb=" CB SER G 515 " ideal model delta sigma weight residual 1.529 1.486 0.044 1.43e-02 4.89e+03 9.28e+00 bond pdb=" CA SER B 515 " pdb=" CB SER B 515 " ideal model delta sigma weight residual 1.529 1.486 0.044 1.43e-02 4.89e+03 9.28e+00 bond pdb=" CA SER C 515 " pdb=" CB SER C 515 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.43e-02 4.89e+03 9.24e+00 ... (remaining 28303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 30652 1.22 - 2.45: 6403 2.45 - 3.67: 1129 3.67 - 4.90: 181 4.90 - 6.12: 23 Bond angle restraints: 38388 Sorted by residual: angle pdb=" CA ASP G 622 " pdb=" CB ASP G 622 " pdb=" CG ASP G 622 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASP B 622 " pdb=" CB ASP B 622 " pdb=" CG ASP B 622 " ideal model delta sigma weight residual 112.60 116.78 -4.18 1.00e+00 1.00e+00 1.75e+01 angle pdb=" CA ASP F 622 " pdb=" CB ASP F 622 " pdb=" CG ASP F 622 " ideal model delta sigma weight residual 112.60 116.78 -4.18 1.00e+00 1.00e+00 1.74e+01 angle pdb=" CA ASP C 622 " pdb=" CB ASP C 622 " pdb=" CG ASP C 622 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" CA ASP E 622 " pdb=" CB ASP E 622 " pdb=" CG ASP E 622 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 38383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 14957 15.93 - 31.87: 1735 31.87 - 47.80: 353 47.80 - 63.74: 140 63.74 - 79.67: 63 Dihedral angle restraints: 17248 sinusoidal: 6769 harmonic: 10479 Sorted by residual: dihedral pdb=" CA LEU E 448 " pdb=" C LEU E 448 " pdb=" N ASN E 449 " pdb=" CA ASN E 449 " ideal model delta harmonic sigma weight residual -180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU G 448 " pdb=" C LEU G 448 " pdb=" N ASN G 449 " pdb=" CA ASN G 449 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA LEU B 448 " pdb=" C LEU B 448 " pdb=" N ASN B 449 " pdb=" CA ASN B 449 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 17245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2606 0.061 - 0.123: 1473 0.123 - 0.184: 228 0.184 - 0.246: 40 0.246 - 0.307: 14 Chirality restraints: 4361 Sorted by residual: chirality pdb=" CA PRO G 269 " pdb=" N PRO G 269 " pdb=" C PRO G 269 " pdb=" CB PRO G 269 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO B 269 " pdb=" N PRO B 269 " pdb=" C PRO B 269 " pdb=" CB PRO B 269 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA PRO A 269 " pdb=" N PRO A 269 " pdb=" C PRO A 269 " pdb=" CB PRO A 269 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 4358 not shown) Planarity restraints: 4998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 457 " -0.300 9.50e-02 1.11e+02 1.35e-01 1.15e+01 pdb=" NE ARG G 457 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG G 457 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 457 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 457 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 457 " -0.296 9.50e-02 1.11e+02 1.33e-01 1.12e+01 pdb=" NE ARG B 457 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 457 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 457 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 457 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 457 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG E 457 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG E 457 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 457 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 457 " 0.007 2.00e-02 2.50e+03 ... (remaining 4995 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 398 2.64 - 3.20: 24449 3.20 - 3.77: 43083 3.77 - 4.33: 63447 4.33 - 4.90: 104593 Nonbonded interactions: 235970 Sorted by model distance: nonbonded pdb=" OD1 ASP F 221 " pdb="CA CA F 802 " model vdw 2.069 2.510 nonbonded pdb=" OD1 ASP A 221 " pdb="CA CA A 802 " model vdw 2.071 2.510 nonbonded pdb=" OD1 ASP B 221 " pdb="CA CA B 802 " model vdw 2.072 2.510 nonbonded pdb=" OD1 ASP E 221 " pdb="CA CA E 802 " model vdw 2.073 2.510 nonbonded pdb=" OD1 ASP D 221 " pdb="CA CA D 802 " model vdw 2.080 2.510 ... (remaining 235965 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 0.030 Extract box with map and model: 1.310 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 57.820 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 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 : 0.008 0.055 28308 Z= 0.488 Angle : 1.042 6.120 38388 Z= 0.682 Chirality : 0.071 0.307 4361 Planarity : 0.007 0.135 4998 Dihedral : 15.561 79.674 10528 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.28 % Rotamer: Outliers : 0.88 % Allowed : 13.05 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3549 helix: -0.45 (0.24), residues: 441 sheet: 1.99 (0.15), residues: 1197 loop : -1.22 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 502 HIS 0.004 0.002 HIS C 313 PHE 0.026 0.004 PHE A 248 TYR 0.031 0.004 TYR C 273 ARG 0.011 0.002 ARG F 457 Details of bonding type rmsd hydrogen bonds : bond 0.19256 ( 1218) hydrogen bonds : angle 7.78017 ( 3213) covalent geometry : bond 0.00822 (28308) covalent geometry : angle 1.04157 (38388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 3.348 Fit side-chains REVERT: A 593 TYR cc_start: 0.8767 (m-80) cc_final: 0.8497 (m-10) REVERT: B 593 TYR cc_start: 0.8761 (m-80) cc_final: 0.8483 (m-10) REVERT: C 589 GLU cc_start: 0.8702 (tp30) cc_final: 0.8496 (tp30) REVERT: D 589 GLU cc_start: 0.8700 (tp30) cc_final: 0.8472 (tp30) REVERT: D 593 TYR cc_start: 0.8697 (m-80) cc_final: 0.8385 (m-80) REVERT: F 589 GLU cc_start: 0.8687 (tp30) cc_final: 0.8402 (tp30) outliers start: 28 outliers final: 21 residues processed: 210 average time/residue: 1.4061 time to fit residues: 345.1473 Evaluate side-chains 187 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 557 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 279 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 324 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 362 ASN A 500 ASN A 508 GLN B 318 GLN B 362 ASN B 500 ASN B 508 GLN B 590 GLN C 318 GLN C 362 ASN C 500 ASN C 508 GLN D 318 GLN D 362 ASN D 508 GLN D 590 GLN E 318 GLN E 362 ASN E 508 GLN E 590 GLN F 318 GLN F 362 ASN F 508 GLN F 590 GLN G 500 ASN G 508 GLN G 590 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.062527 restraints weight = 43590.246| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.27 r_work: 0.2622 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 28308 Z= 0.112 Angle : 0.505 5.364 38388 Z= 0.283 Chirality : 0.045 0.152 4361 Planarity : 0.003 0.033 4998 Dihedral : 5.296 52.817 3849 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.55 % Allowed : 12.55 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 3549 helix: 0.46 (0.25), residues: 441 sheet: 2.29 (0.14), residues: 1197 loop : -1.16 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 244 HIS 0.002 0.001 HIS E 313 PHE 0.013 0.001 PHE F 248 TYR 0.009 0.001 TYR F 438 ARG 0.001 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1218) hydrogen bonds : angle 5.08218 ( 3213) covalent geometry : bond 0.00247 (28308) covalent geometry : angle 0.50546 (38388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 3.355 Fit side-chains REVERT: A 378 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 589 GLU cc_start: 0.8461 (tp30) cc_final: 0.8243 (tp30) REVERT: A 593 TYR cc_start: 0.8651 (m-80) cc_final: 0.8343 (m-10) REVERT: B 589 GLU cc_start: 0.8580 (tp30) cc_final: 0.8364 (tp30) REVERT: B 593 TYR cc_start: 0.8726 (m-80) cc_final: 0.8455 (m-10) REVERT: C 317 ASP cc_start: 0.8543 (m-30) cc_final: 0.8287 (m-30) REVERT: C 589 GLU cc_start: 0.8514 (tp30) cc_final: 0.8014 (tp30) REVERT: D 589 GLU cc_start: 0.8506 (tp30) cc_final: 0.8241 (tp30) REVERT: D 593 TYR cc_start: 0.8624 (m-80) cc_final: 0.8303 (m-80) REVERT: E 317 ASP cc_start: 0.8467 (m-30) cc_final: 0.8264 (m-30) REVERT: E 589 GLU cc_start: 0.8564 (tp30) cc_final: 0.8262 (tp30) REVERT: F 330 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7441 (tmtm) REVERT: F 589 GLU cc_start: 0.8516 (tp30) cc_final: 0.8235 (tp30) REVERT: F 593 TYR cc_start: 0.8603 (m-80) cc_final: 0.8232 (m-10) REVERT: G 330 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6830 (tptp) REVERT: G 589 GLU cc_start: 0.8501 (tp30) cc_final: 0.8187 (tp30) REVERT: G 593 TYR cc_start: 0.8737 (m-80) cc_final: 0.8447 (m-10) outliers start: 49 outliers final: 22 residues processed: 224 average time/residue: 1.2607 time to fit residues: 338.1532 Evaluate side-chains 201 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 330 LYS Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 330 LYS Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 196 optimal weight: 5.9990 chunk 351 optimal weight: 0.0670 chunk 82 optimal weight: 0.7980 chunk 325 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 324 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 318 GLN A 559 ASN A 590 GLN B 318 GLN B 559 ASN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 500 ASN D 559 ASN D 590 GLN E 318 GLN E 500 ASN E 559 ASN F 311 ASN F 318 GLN F 500 ASN F 559 ASN F 590 GLN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061637 restraints weight = 43580.955| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.25 r_work: 0.2603 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 28308 Z= 0.139 Angle : 0.488 5.296 38388 Z= 0.273 Chirality : 0.044 0.147 4361 Planarity : 0.003 0.038 4998 Dihedral : 4.831 50.084 3821 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.83 % Allowed : 12.90 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 3549 helix: 0.58 (0.26), residues: 441 sheet: 2.31 (0.14), residues: 1148 loop : -1.04 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 631 HIS 0.002 0.001 HIS E 358 PHE 0.018 0.001 PHE F 248 TYR 0.014 0.001 TYR C 438 ARG 0.001 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 1218) hydrogen bonds : angle 4.67669 ( 3213) covalent geometry : bond 0.00316 (28308) covalent geometry : angle 0.48845 (38388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 3.235 Fit side-chains REVERT: A 378 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8471 (tt) REVERT: A 589 GLU cc_start: 0.8528 (tp30) cc_final: 0.8195 (tp30) REVERT: A 593 TYR cc_start: 0.8734 (m-80) cc_final: 0.8350 (m-10) REVERT: B 589 GLU cc_start: 0.8613 (tp30) cc_final: 0.8228 (tp30) REVERT: B 593 TYR cc_start: 0.8805 (m-80) cc_final: 0.8437 (m-80) REVERT: C 317 ASP cc_start: 0.8523 (m-30) cc_final: 0.8314 (m-30) REVERT: C 589 GLU cc_start: 0.8584 (tp30) cc_final: 0.8025 (tp30) REVERT: D 378 LEU cc_start: 0.8795 (pt) cc_final: 0.8540 (tp) REVERT: D 589 GLU cc_start: 0.8577 (tp30) cc_final: 0.8207 (tp30) REVERT: D 593 TYR cc_start: 0.8698 (m-80) cc_final: 0.8315 (m-80) REVERT: E 589 GLU cc_start: 0.8615 (tp30) cc_final: 0.8255 (tp30) REVERT: E 593 TYR cc_start: 0.8880 (m-80) cc_final: 0.8667 (m-10) REVERT: F 589 GLU cc_start: 0.8579 (tp30) cc_final: 0.8204 (tp30) REVERT: F 593 TYR cc_start: 0.8680 (m-80) cc_final: 0.8229 (m-10) REVERT: G 330 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6810 (tptp) REVERT: G 378 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8442 (tp) REVERT: G 589 GLU cc_start: 0.8558 (tp30) cc_final: 0.8085 (tp30) REVERT: G 593 TYR cc_start: 0.8805 (m-80) cc_final: 0.8440 (m-10) outliers start: 58 outliers final: 26 residues processed: 208 average time/residue: 1.2787 time to fit residues: 316.2590 Evaluate side-chains 200 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 330 LYS Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 236 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 559 ASN A 590 GLN B 318 GLN B 367 GLN B 559 ASN B 590 GLN C 318 GLN C 367 GLN C 559 ASN C 590 GLN D 318 GLN D 367 GLN D 559 ASN D 590 GLN E 318 GLN E 367 GLN E 559 ASN E 590 GLN F 311 ASN F 318 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 GLN F 559 ASN F 590 GLN G 318 GLN G 367 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.060565 restraints weight = 43934.816| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.27 r_work: 0.2582 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 28308 Z= 0.170 Angle : 0.494 5.255 38388 Z= 0.276 Chirality : 0.045 0.162 4361 Planarity : 0.004 0.041 4998 Dihedral : 4.912 49.460 3819 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.90 % Allowed : 13.46 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 3549 helix: 0.56 (0.26), residues: 441 sheet: 2.32 (0.14), residues: 1148 loop : -1.04 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 631 HIS 0.002 0.001 HIS D 358 PHE 0.020 0.001 PHE A 248 TYR 0.016 0.001 TYR F 438 ARG 0.001 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 1218) hydrogen bonds : angle 4.55679 ( 3213) covalent geometry : bond 0.00394 (28308) covalent geometry : angle 0.49428 (38388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 3.174 Fit side-chains REVERT: A 378 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8471 (tt) REVERT: A 589 GLU cc_start: 0.8586 (tp30) cc_final: 0.8198 (tp30) REVERT: A 593 TYR cc_start: 0.8769 (m-80) cc_final: 0.8390 (m-80) REVERT: B 589 GLU cc_start: 0.8666 (tp30) cc_final: 0.8177 (tp30) REVERT: B 593 TYR cc_start: 0.8843 (m-80) cc_final: 0.8415 (m-80) REVERT: C 317 ASP cc_start: 0.8562 (m-30) cc_final: 0.8339 (m-30) REVERT: C 589 GLU cc_start: 0.8611 (tp30) cc_final: 0.8006 (tp30) REVERT: D 378 LEU cc_start: 0.8835 (pt) cc_final: 0.8530 (tt) REVERT: D 589 GLU cc_start: 0.8609 (tp30) cc_final: 0.8184 (tp30) REVERT: D 593 TYR cc_start: 0.8725 (m-80) cc_final: 0.8281 (m-80) REVERT: E 589 GLU cc_start: 0.8629 (tp30) cc_final: 0.8207 (tp30) REVERT: E 593 TYR cc_start: 0.8930 (m-80) cc_final: 0.8702 (m-10) REVERT: F 589 GLU cc_start: 0.8615 (tp30) cc_final: 0.8206 (tp30) REVERT: F 593 TYR cc_start: 0.8732 (m-80) cc_final: 0.8247 (m-10) REVERT: G 330 LYS cc_start: 0.7287 (tptp) cc_final: 0.6833 (tptp) REVERT: G 378 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8463 (tp) REVERT: G 589 GLU cc_start: 0.8583 (tp30) cc_final: 0.8156 (tp30) REVERT: G 593 TYR cc_start: 0.8850 (m-80) cc_final: 0.8461 (m-10) outliers start: 60 outliers final: 33 residues processed: 214 average time/residue: 1.2845 time to fit residues: 329.6595 Evaluate side-chains 209 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 110 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 210 optimal weight: 0.9990 chunk 306 optimal weight: 0.5980 chunk 293 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 559 ASN B 590 GLN C 318 GLN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 559 ASN F 590 GLN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.062285 restraints weight = 43559.653| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.27 r_work: 0.2619 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28308 Z= 0.112 Angle : 0.461 5.043 38388 Z= 0.257 Chirality : 0.044 0.151 4361 Planarity : 0.003 0.039 4998 Dihedral : 4.675 46.853 3819 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.96 % Allowed : 13.50 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 3549 helix: 0.63 (0.25), residues: 441 sheet: 2.38 (0.14), residues: 1197 loop : -1.04 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 631 HIS 0.002 0.001 HIS E 313 PHE 0.016 0.001 PHE F 248 TYR 0.011 0.001 TYR E 438 ARG 0.001 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 1218) hydrogen bonds : angle 4.32419 ( 3213) covalent geometry : bond 0.00254 (28308) covalent geometry : angle 0.46137 (38388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 3.303 Fit side-chains REVERT: A 378 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 589 GLU cc_start: 0.8586 (tp30) cc_final: 0.8136 (tp30) REVERT: A 593 TYR cc_start: 0.8800 (m-80) cc_final: 0.8408 (m-80) REVERT: B 589 GLU cc_start: 0.8677 (tp30) cc_final: 0.8119 (tp30) REVERT: B 593 TYR cc_start: 0.8873 (m-80) cc_final: 0.8374 (m-10) REVERT: C 317 ASP cc_start: 0.8529 (m-30) cc_final: 0.8298 (m-30) REVERT: C 330 LYS cc_start: 0.7654 (tmtm) cc_final: 0.7419 (tmtm) REVERT: C 589 GLU cc_start: 0.8631 (tp30) cc_final: 0.7990 (tp30) REVERT: D 589 GLU cc_start: 0.8622 (tp30) cc_final: 0.8174 (tp30) REVERT: D 593 TYR cc_start: 0.8765 (m-80) cc_final: 0.8297 (m-10) REVERT: E 589 GLU cc_start: 0.8662 (tp30) cc_final: 0.8182 (tp30) REVERT: E 593 TYR cc_start: 0.8947 (m-80) cc_final: 0.8658 (m-10) REVERT: F 378 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8542 (tp) REVERT: F 589 GLU cc_start: 0.8634 (tp30) cc_final: 0.8174 (tp30) REVERT: F 593 TYR cc_start: 0.8760 (m-80) cc_final: 0.8237 (m-10) REVERT: G 330 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6797 (tptp) REVERT: G 378 LEU cc_start: 0.8800 (pt) cc_final: 0.8564 (tp) REVERT: G 589 GLU cc_start: 0.8612 (tp30) cc_final: 0.8057 (tp30) REVERT: G 593 TYR cc_start: 0.8870 (m-80) cc_final: 0.8393 (m-10) outliers start: 62 outliers final: 33 residues processed: 214 average time/residue: 1.2727 time to fit residues: 324.3313 Evaluate side-chains 205 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 330 LYS Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 362 ASN B 559 ASN B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 559 ASN F 590 GLN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061077 restraints weight = 43796.961| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.28 r_work: 0.2586 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28308 Z= 0.157 Angle : 0.479 5.129 38388 Z= 0.267 Chirality : 0.044 0.146 4361 Planarity : 0.004 0.039 4998 Dihedral : 4.814 47.058 3819 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.93 % Allowed : 13.87 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 3549 helix: 0.60 (0.25), residues: 441 sheet: 2.29 (0.13), residues: 1148 loop : -0.99 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 631 HIS 0.003 0.001 HIS D 358 PHE 0.019 0.001 PHE A 248 TYR 0.015 0.001 TYR F 438 ARG 0.001 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 1218) hydrogen bonds : angle 4.35231 ( 3213) covalent geometry : bond 0.00364 (28308) covalent geometry : angle 0.47912 (38388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 3.132 Fit side-chains REVERT: A 378 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 589 GLU cc_start: 0.8604 (tp30) cc_final: 0.8101 (tp30) REVERT: A 593 TYR cc_start: 0.8817 (m-80) cc_final: 0.8325 (m-10) REVERT: B 589 GLU cc_start: 0.8675 (tp30) cc_final: 0.7998 (tp30) REVERT: B 593 TYR cc_start: 0.8869 (m-80) cc_final: 0.8268 (m-10) REVERT: C 317 ASP cc_start: 0.8536 (m-30) cc_final: 0.8330 (m-30) REVERT: C 589 GLU cc_start: 0.8629 (tp30) cc_final: 0.7978 (tp30) REVERT: C 593 TYR cc_start: 0.8690 (m-80) cc_final: 0.8128 (m-80) REVERT: D 258 SER cc_start: 0.9416 (OUTLIER) cc_final: 0.9184 (p) REVERT: D 589 GLU cc_start: 0.8631 (tp30) cc_final: 0.8161 (tp30) REVERT: D 593 TYR cc_start: 0.8770 (m-80) cc_final: 0.8267 (m-10) REVERT: E 589 GLU cc_start: 0.8650 (tp30) cc_final: 0.8131 (tp30) REVERT: E 593 TYR cc_start: 0.8945 (m-80) cc_final: 0.8620 (m-10) REVERT: F 378 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8587 (tp) REVERT: F 589 GLU cc_start: 0.8637 (tp30) cc_final: 0.8229 (tp30) REVERT: F 593 TYR cc_start: 0.8763 (m-80) cc_final: 0.8304 (m-10) REVERT: G 330 LYS cc_start: 0.7404 (tptp) cc_final: 0.7160 (tptp) REVERT: G 378 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8582 (tp) REVERT: G 589 GLU cc_start: 0.8628 (tp30) cc_final: 0.8067 (tp30) REVERT: G 593 TYR cc_start: 0.8872 (m-80) cc_final: 0.8403 (m-10) outliers start: 61 outliers final: 38 residues processed: 207 average time/residue: 1.2905 time to fit residues: 317.4620 Evaluate side-chains 217 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 110 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 252 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 559 ASN B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 559 ASN F 590 GLN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061720 restraints weight = 43678.931| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.27 r_work: 0.2600 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28308 Z= 0.132 Angle : 0.465 4.996 38388 Z= 0.259 Chirality : 0.044 0.145 4361 Planarity : 0.003 0.039 4998 Dihedral : 4.731 45.776 3819 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 3549 helix: 0.62 (0.25), residues: 441 sheet: 2.31 (0.14), residues: 1148 loop : -0.98 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 631 HIS 0.001 0.001 HIS F 313 PHE 0.018 0.001 PHE F 248 TYR 0.013 0.001 TYR E 438 ARG 0.001 0.000 ARG G 393 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 1218) hydrogen bonds : angle 4.27305 ( 3213) covalent geometry : bond 0.00303 (28308) covalent geometry : angle 0.46514 (38388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 3.324 Fit side-chains REVERT: A 589 GLU cc_start: 0.8611 (tp30) cc_final: 0.8043 (tp30) REVERT: A 593 TYR cc_start: 0.8821 (m-80) cc_final: 0.8238 (m-10) REVERT: B 589 GLU cc_start: 0.8646 (tp30) cc_final: 0.7940 (tp30) REVERT: B 593 TYR cc_start: 0.8878 (m-80) cc_final: 0.8248 (m-10) REVERT: C 589 GLU cc_start: 0.8621 (tp30) cc_final: 0.8265 (tp30) REVERT: C 593 TYR cc_start: 0.8705 (m-80) cc_final: 0.8370 (m-80) REVERT: D 589 GLU cc_start: 0.8641 (tp30) cc_final: 0.8154 (tp30) REVERT: D 593 TYR cc_start: 0.8772 (m-80) cc_final: 0.8250 (m-10) REVERT: E 589 GLU cc_start: 0.8664 (tp30) cc_final: 0.8116 (tp30) REVERT: E 593 TYR cc_start: 0.8968 (m-80) cc_final: 0.8632 (m-10) REVERT: F 378 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8603 (tp) REVERT: F 589 GLU cc_start: 0.8648 (tp30) cc_final: 0.8216 (tp30) REVERT: F 593 TYR cc_start: 0.8774 (m-80) cc_final: 0.8289 (m-10) REVERT: G 589 GLU cc_start: 0.8648 (tp30) cc_final: 0.8056 (tp30) REVERT: G 593 TYR cc_start: 0.8879 (m-80) cc_final: 0.8386 (m-10) outliers start: 56 outliers final: 38 residues processed: 208 average time/residue: 1.3054 time to fit residues: 323.4207 Evaluate side-chains 205 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 255 optimal weight: 0.0570 chunk 139 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 304 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 559 ASN F 590 GLN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.062046 restraints weight = 43859.048| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.28 r_work: 0.2607 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28308 Z= 0.121 Angle : 0.458 4.935 38388 Z= 0.255 Chirality : 0.044 0.145 4361 Planarity : 0.003 0.038 4998 Dihedral : 4.605 24.326 3817 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.71 % Allowed : 14.29 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 3549 helix: 0.64 (0.25), residues: 441 sheet: 2.30 (0.14), residues: 1148 loop : -0.97 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 631 HIS 0.005 0.001 HIS D 358 PHE 0.017 0.001 PHE F 248 TYR 0.012 0.001 TYR E 438 ARG 0.001 0.000 ARG E 667 Details of bonding type rmsd hydrogen bonds : bond 0.02752 ( 1218) hydrogen bonds : angle 4.20754 ( 3213) covalent geometry : bond 0.00278 (28308) covalent geometry : angle 0.45843 (38388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 3.148 Fit side-chains REVERT: A 589 GLU cc_start: 0.8610 (tp30) cc_final: 0.8019 (tp30) REVERT: A 593 TYR cc_start: 0.8840 (m-80) cc_final: 0.8241 (m-10) REVERT: B 378 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 589 GLU cc_start: 0.8645 (tp30) cc_final: 0.7964 (tp30) REVERT: B 593 TYR cc_start: 0.8898 (m-80) cc_final: 0.8340 (m-10) REVERT: C 589 GLU cc_start: 0.8631 (tp30) cc_final: 0.8124 (tp30) REVERT: D 258 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.9154 (p) REVERT: D 589 GLU cc_start: 0.8650 (tp30) cc_final: 0.8104 (tp30) REVERT: D 593 TYR cc_start: 0.8779 (m-80) cc_final: 0.8256 (m-10) REVERT: E 378 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8634 (tp) REVERT: E 589 GLU cc_start: 0.8666 (tp30) cc_final: 0.8103 (tp30) REVERT: E 593 TYR cc_start: 0.8961 (m-80) cc_final: 0.8599 (m-10) REVERT: F 378 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8643 (tp) REVERT: F 589 GLU cc_start: 0.8659 (tp30) cc_final: 0.8218 (tp30) REVERT: F 593 TYR cc_start: 0.8790 (m-80) cc_final: 0.8297 (m-10) REVERT: G 589 GLU cc_start: 0.8630 (tp30) cc_final: 0.7972 (tp30) REVERT: G 593 TYR cc_start: 0.8886 (m-80) cc_final: 0.8319 (m-10) outliers start: 54 outliers final: 34 residues processed: 202 average time/residue: 1.3123 time to fit residues: 313.5749 Evaluate side-chains 205 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 338 optimal weight: 0.3980 chunk 172 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 277 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 270 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 348 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 559 ASN B 590 GLN C 318 GLN C 362 ASN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 559 ASN F 590 GLN G 318 GLN G 362 ASN G 559 ASN G 590 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062947 restraints weight = 43624.017| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.26 r_work: 0.2629 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28308 Z= 0.102 Angle : 0.445 4.998 38388 Z= 0.247 Chirality : 0.043 0.144 4361 Planarity : 0.003 0.038 4998 Dihedral : 4.474 24.038 3817 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.30 % Allowed : 14.66 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 3549 helix: 0.68 (0.25), residues: 441 sheet: 2.37 (0.14), residues: 1197 loop : -1.00 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 631 HIS 0.002 0.001 HIS D 358 PHE 0.015 0.001 PHE G 248 TYR 0.011 0.001 TYR C 593 ARG 0.001 0.000 ARG B 667 Details of bonding type rmsd hydrogen bonds : bond 0.02592 ( 1218) hydrogen bonds : angle 4.11293 ( 3213) covalent geometry : bond 0.00232 (28308) covalent geometry : angle 0.44499 (38388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 3.133 Fit side-chains REVERT: A 589 GLU cc_start: 0.8615 (tp30) cc_final: 0.8015 (tp30) REVERT: A 593 TYR cc_start: 0.8845 (m-80) cc_final: 0.8244 (m-10) REVERT: B 378 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8604 (tp) REVERT: B 589 GLU cc_start: 0.8630 (tp30) cc_final: 0.7938 (tp30) REVERT: B 593 TYR cc_start: 0.8895 (m-80) cc_final: 0.8328 (m-10) REVERT: C 589 GLU cc_start: 0.8642 (tp30) cc_final: 0.7926 (tp30) REVERT: C 593 TYR cc_start: 0.8713 (m-80) cc_final: 0.8069 (m-80) REVERT: D 258 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9145 (p) REVERT: D 330 LYS cc_start: 0.7543 (tmtm) cc_final: 0.7317 (tmtm) REVERT: D 589 GLU cc_start: 0.8661 (tp30) cc_final: 0.8116 (tp30) REVERT: D 593 TYR cc_start: 0.8774 (m-80) cc_final: 0.8246 (m-10) REVERT: E 378 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (tp) REVERT: E 589 GLU cc_start: 0.8664 (tp30) cc_final: 0.8104 (tp30) REVERT: E 593 TYR cc_start: 0.8962 (m-80) cc_final: 0.8593 (m-10) REVERT: F 589 GLU cc_start: 0.8655 (tp30) cc_final: 0.8204 (tp30) REVERT: F 593 TYR cc_start: 0.8787 (m-80) cc_final: 0.8286 (m-10) REVERT: G 589 GLU cc_start: 0.8617 (tp30) cc_final: 0.7959 (tp30) REVERT: G 593 TYR cc_start: 0.8885 (m-80) cc_final: 0.8348 (m-10) outliers start: 41 outliers final: 28 residues processed: 197 average time/residue: 1.3705 time to fit residues: 321.5149 Evaluate side-chains 199 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 158 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 102 optimal weight: 0.0470 chunk 17 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 338 optimal weight: 0.0270 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 559 ASN F 590 GLN G 318 GLN G 362 ASN G 559 ASN G 590 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.062641 restraints weight = 43522.258| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.25 r_work: 0.2622 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28308 Z= 0.114 Angle : 0.450 5.165 38388 Z= 0.250 Chirality : 0.043 0.143 4361 Planarity : 0.003 0.037 4998 Dihedral : 4.497 23.970 3817 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.11 % Allowed : 14.95 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 3549 helix: 0.68 (0.25), residues: 441 sheet: 2.30 (0.14), residues: 1134 loop : -0.95 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 631 HIS 0.002 0.001 HIS D 358 PHE 0.016 0.001 PHE G 248 TYR 0.012 0.001 TYR E 438 ARG 0.001 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.02641 ( 1218) hydrogen bonds : angle 4.10550 ( 3213) covalent geometry : bond 0.00260 (28308) covalent geometry : angle 0.45049 (38388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 3.551 Fit side-chains REVERT: A 589 GLU cc_start: 0.8614 (tp30) cc_final: 0.8006 (tp30) REVERT: A 593 TYR cc_start: 0.8838 (m-80) cc_final: 0.8230 (m-10) REVERT: B 378 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8554 (tt) REVERT: B 589 GLU cc_start: 0.8628 (tp30) cc_final: 0.7893 (tp30) REVERT: B 593 TYR cc_start: 0.8892 (m-80) cc_final: 0.8302 (m-80) REVERT: C 589 GLU cc_start: 0.8637 (tp30) cc_final: 0.8134 (tp30) REVERT: D 258 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.9146 (p) REVERT: D 589 GLU cc_start: 0.8660 (tp30) cc_final: 0.8101 (tp30) REVERT: D 593 TYR cc_start: 0.8774 (m-80) cc_final: 0.8246 (m-10) REVERT: E 378 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8633 (tp) REVERT: E 589 GLU cc_start: 0.8663 (tp30) cc_final: 0.8096 (tp30) REVERT: E 593 TYR cc_start: 0.8954 (m-80) cc_final: 0.8628 (m-10) REVERT: F 589 GLU cc_start: 0.8656 (tp30) cc_final: 0.8204 (tp30) REVERT: F 593 TYR cc_start: 0.8789 (m-80) cc_final: 0.8286 (m-10) REVERT: G 589 GLU cc_start: 0.8636 (tp30) cc_final: 0.7960 (tp30) REVERT: G 593 TYR cc_start: 0.8884 (m-80) cc_final: 0.8341 (m-10) outliers start: 35 outliers final: 24 residues processed: 190 average time/residue: 1.4289 time to fit residues: 317.8349 Evaluate side-chains 195 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 355 optimal weight: 30.0000 chunk 264 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 326 optimal weight: 0.0670 chunk 164 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 337 optimal weight: 0.5980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 559 ASN B 590 GLN C 318 GLN C 362 ASN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 362 ASN F 559 ASN F 590 GLN G 318 GLN G 362 ASN G 559 ASN G 590 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.062921 restraints weight = 43663.057| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.29 r_work: 0.2629 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28308 Z= 0.106 Angle : 0.445 4.959 38388 Z= 0.247 Chirality : 0.043 0.143 4361 Planarity : 0.003 0.037 4998 Dihedral : 4.448 23.897 3817 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.14 % Allowed : 14.98 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 3549 helix: 0.69 (0.25), residues: 441 sheet: 2.29 (0.14), residues: 1134 loop : -0.94 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 631 HIS 0.002 0.001 HIS A 313 PHE 0.015 0.001 PHE A 248 TYR 0.012 0.001 TYR C 593 ARG 0.001 0.000 ARG C 667 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 1218) hydrogen bonds : angle 4.06597 ( 3213) covalent geometry : bond 0.00241 (28308) covalent geometry : angle 0.44464 (38388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27676.08 seconds wall clock time: 477 minutes 25.26 seconds (28645.26 seconds total)