Starting phenix.real_space_refine on Mon Aug 25 12:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrm_39544/08_2025/8yrm_39544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrm_39544/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yrm_39544/08_2025/8yrm_39544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrm_39544/08_2025/8yrm_39544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yrm_39544/08_2025/8yrm_39544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrm_39544/08_2025/8yrm_39544.map" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 3.60, per 1000 atoms: 0.13 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: 1.65 Conformation dependent library (CDL) restraints added in 843.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.89 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: 4.09 Time building geometry restraints manager: 2.40 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.020 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.050 Set scattering table: 0.110 Process input model: 18.550 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- 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 : 3.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (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 ARG 0.011 0.002 ARG F 457 TYR 0.031 0.004 TYR C 273 PHE 0.026 0.004 PHE A 248 TRP 0.025 0.004 TRP A 502 HIS 0.004 0.002 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00822 (28308) covalent geometry : angle 1.04157 (38388) hydrogen bonds : bond 0.19256 ( 1218) hydrogen bonds : angle 7.78017 ( 3213) *********************** 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 : 0.964 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: 0.6144 time to fit residues: 150.0075 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 : 0.881 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 367 GLN A 500 ASN A 508 GLN A 590 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 500 ASN D 508 GLN D 590 GLN E 318 GLN E 362 ASN E 500 ASN E 508 GLN E 590 GLN F 318 GLN F 362 ASN F 367 GLN F 500 ASN F 508 GLN F 590 GLN G 500 ASN G 508 GLN G 590 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060555 restraints weight = 44016.767| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.27 r_work: 0.2579 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28308 Z= 0.171 Angle : 0.532 5.428 38388 Z= 0.298 Chirality : 0.046 0.153 4361 Planarity : 0.004 0.037 4998 Dihedral : 5.533 53.000 3849 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.61 % Allowed : 12.29 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 3549 helix: 0.40 (0.25), residues: 441 sheet: 2.14 (0.14), residues: 1134 loop : -1.13 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 393 TYR 0.014 0.001 TYR F 438 PHE 0.016 0.001 PHE F 248 TRP 0.006 0.001 TRP C 244 HIS 0.002 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00394 (28308) covalent geometry : angle 0.53214 (38388) hydrogen bonds : bond 0.03824 ( 1218) hydrogen bonds : angle 5.18804 ( 3213) *********************** 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 241 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.873 Fit side-chains REVERT: A 589 GLU cc_start: 0.8469 (tp30) cc_final: 0.8253 (tp30) REVERT: A 593 TYR cc_start: 0.8663 (m-80) cc_final: 0.8351 (m-10) REVERT: B 589 GLU cc_start: 0.8585 (tp30) cc_final: 0.8356 (tp30) REVERT: B 593 TYR cc_start: 0.8734 (m-80) cc_final: 0.8482 (m-80) REVERT: C 317 ASP cc_start: 0.8564 (m-30) cc_final: 0.8299 (m-30) REVERT: C 589 GLU cc_start: 0.8513 (tp30) cc_final: 0.8041 (tp30) REVERT: D 589 GLU cc_start: 0.8506 (tp30) cc_final: 0.8243 (tp30) REVERT: D 593 TYR cc_start: 0.8630 (m-80) cc_final: 0.8317 (m-80) REVERT: E 317 ASP cc_start: 0.8487 (m-30) cc_final: 0.8284 (m-30) REVERT: E 589 GLU cc_start: 0.8571 (tp30) cc_final: 0.8275 (tp30) REVERT: F 330 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7434 (tmtm) REVERT: F 589 GLU cc_start: 0.8523 (tp30) cc_final: 0.8037 (tp30) REVERT: G 330 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6817 (tptp) REVERT: G 589 GLU cc_start: 0.8500 (tp30) cc_final: 0.8199 (tp30) REVERT: G 593 TYR cc_start: 0.8738 (m-80) cc_final: 0.8465 (m-10) outliers start: 51 outliers final: 26 residues processed: 214 average time/residue: 0.5427 time to fit residues: 137.4653 Evaluate side-chains 203 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP 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 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 332 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 645 VAL 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 306 LEU Chi-restraints excluded: chain F residue 330 LYS 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 332 ASP Chi-restraints excluded: chain G residue 479 THR 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 350 optimal weight: 10.0000 chunk 288 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 242 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 559 ASN A 590 GLN B 318 GLN B 559 ASN B 590 GLN C 318 GLN C 559 ASN D 318 GLN D 559 ASN D 590 GLN D 734 ASN 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 = 0.3639 r_free = 0.3639 target = 0.116510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.062877 restraints weight = 43895.095| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.28 r_work: 0.2630 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 28308 Z= 0.108 Angle : 0.467 4.869 38388 Z= 0.260 Chirality : 0.044 0.152 4361 Planarity : 0.003 0.039 4998 Dihedral : 4.736 48.173 3825 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.74 % Allowed : 12.80 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.13), residues: 3549 helix: 0.64 (0.26), residues: 441 sheet: 2.39 (0.14), residues: 1197 loop : -1.06 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 527 TYR 0.010 0.001 TYR F 593 PHE 0.015 0.001 PHE F 248 TRP 0.009 0.001 TRP F 631 HIS 0.002 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00241 (28308) covalent geometry : angle 0.46657 (38388) hydrogen bonds : bond 0.03037 ( 1218) hydrogen bonds : angle 4.54761 ( 3213) *********************** 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 242 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 1.025 Fit side-chains REVERT: A 378 LEU cc_start: 0.8768 (pt) cc_final: 0.8539 (tp) REVERT: A 589 GLU cc_start: 0.8559 (tp30) cc_final: 0.8196 (tp30) REVERT: A 593 TYR cc_start: 0.8744 (m-80) cc_final: 0.8344 (m-10) REVERT: B 589 GLU cc_start: 0.8605 (tp30) cc_final: 0.8187 (tp30) REVERT: B 593 TYR cc_start: 0.8812 (m-80) cc_final: 0.8398 (m-10) REVERT: C 317 ASP cc_start: 0.8543 (m-30) cc_final: 0.8334 (m-30) REVERT: C 589 GLU cc_start: 0.8610 (tp30) cc_final: 0.7999 (tp30) REVERT: D 589 GLU cc_start: 0.8604 (tp30) cc_final: 0.8204 (tp30) REVERT: D 593 TYR cc_start: 0.8706 (m-80) cc_final: 0.8254 (m-10) REVERT: E 589 GLU cc_start: 0.8633 (tp30) cc_final: 0.8193 (tp30) REVERT: E 593 TYR cc_start: 0.8914 (m-80) cc_final: 0.8691 (m-80) REVERT: F 589 GLU cc_start: 0.8605 (tp30) cc_final: 0.8117 (tp30) REVERT: F 593 TYR cc_start: 0.8720 (m-80) cc_final: 0.8119 (m-80) REVERT: G 330 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6799 (tptp) REVERT: G 378 LEU cc_start: 0.8788 (pt) cc_final: 0.8544 (tp) REVERT: G 589 GLU cc_start: 0.8566 (tp30) cc_final: 0.8058 (tp30) REVERT: G 593 TYR cc_start: 0.8829 (m-80) cc_final: 0.8453 (m-10) outliers start: 55 outliers final: 21 residues processed: 218 average time/residue: 0.5576 time to fit residues: 144.2028 Evaluate side-chains 196 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP 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 332 ASP Chi-restraints excluded: chain E residue 378 LEU 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 645 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 309 optimal weight: 0.2980 chunk 348 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN 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 362 ASN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 311 ASN F 318 GLN F 362 ASN F 559 ASN F 590 GLN G 318 GLN 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 = 0.3633 r_free = 0.3633 target = 0.116113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.062469 restraints weight = 43521.096| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.27 r_work: 0.2622 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1450 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= 0.120 Angle : 0.466 5.049 38388 Z= 0.260 Chirality : 0.044 0.156 4361 Planarity : 0.003 0.037 4998 Dihedral : 4.666 45.450 3821 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.86 % Allowed : 13.40 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.13), residues: 3549 helix: 0.67 (0.26), residues: 441 sheet: 2.42 (0.14), residues: 1197 loop : -1.03 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 289 TYR 0.013 0.001 TYR F 438 PHE 0.017 0.001 PHE F 248 TRP 0.010 0.001 TRP G 631 HIS 0.002 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00274 (28308) covalent geometry : angle 0.46617 (38388) hydrogen bonds : bond 0.02931 ( 1218) hydrogen bonds : angle 4.38290 ( 3213) *********************** 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 240 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.764 Fit side-chains REVERT: A 589 GLU cc_start: 0.8580 (tp30) cc_final: 0.8105 (tp30) REVERT: A 593 TYR cc_start: 0.8782 (m-80) cc_final: 0.8276 (m-10) REVERT: B 589 GLU cc_start: 0.8650 (tp30) cc_final: 0.8152 (tp30) REVERT: B 593 TYR cc_start: 0.8860 (m-80) cc_final: 0.8424 (m-10) REVERT: C 589 GLU cc_start: 0.8617 (tp30) cc_final: 0.7985 (tp30) REVERT: D 589 GLU cc_start: 0.8620 (tp30) cc_final: 0.8139 (tp30) REVERT: D 593 TYR cc_start: 0.8740 (m-80) cc_final: 0.8181 (m-10) REVERT: E 589 GLU cc_start: 0.8647 (tp30) cc_final: 0.8215 (tp30) REVERT: E 593 TYR cc_start: 0.8935 (m-80) cc_final: 0.8695 (m-10) REVERT: F 378 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8488 (tt) REVERT: F 589 GLU cc_start: 0.8600 (tp30) cc_final: 0.7986 (tp30) REVERT: F 593 TYR cc_start: 0.8725 (m-80) cc_final: 0.8081 (m-80) REVERT: G 330 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6816 (tptp) REVERT: G 589 GLU cc_start: 0.8589 (tp30) cc_final: 0.8126 (tp30) REVERT: G 593 TYR cc_start: 0.8853 (m-80) cc_final: 0.8446 (m-10) outliers start: 59 outliers final: 28 residues processed: 216 average time/residue: 0.5578 time to fit residues: 142.4694 Evaluate side-chains 203 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP 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 479 THR 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 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 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 645 VAL Chi-restraints excluded: chain E residue 684 THR 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 332 ASP Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 737 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 135 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 352 optimal weight: 0.0870 chunk 260 optimal weight: 2.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- 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 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 318 GLN F 559 ASN F 590 GLN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061101 restraints weight = 43721.116| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.26 r_work: 0.2586 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 28308 Z= 0.161 Angle : 0.481 5.061 38388 Z= 0.269 Chirality : 0.045 0.149 4361 Planarity : 0.004 0.039 4998 Dihedral : 4.768 24.003 3819 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.80 % Allowed : 13.59 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.13), residues: 3549 helix: 0.61 (0.26), residues: 441 sheet: 2.34 (0.14), residues: 1148 loop : -1.00 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 393 TYR 0.015 0.001 TYR F 438 PHE 0.019 0.001 PHE G 248 TRP 0.007 0.001 TRP G 631 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00374 (28308) covalent geometry : angle 0.48069 (38388) hydrogen bonds : bond 0.03085 ( 1218) hydrogen bonds : angle 4.38834 ( 3213) *********************** 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 232 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 1.143 Fit side-chains REVERT: A 589 GLU cc_start: 0.8606 (tp30) cc_final: 0.8150 (tp30) REVERT: A 593 TYR cc_start: 0.8809 (m-80) cc_final: 0.8417 (m-80) REVERT: B 589 GLU cc_start: 0.8689 (tp30) cc_final: 0.8143 (tp30) REVERT: B 593 TYR cc_start: 0.8897 (m-80) cc_final: 0.8409 (m-10) REVERT: C 330 LYS cc_start: 0.7542 (tmtm) cc_final: 0.7292 (tmtm) REVERT: C 589 GLU cc_start: 0.8617 (tp30) cc_final: 0.7998 (tp30) REVERT: D 589 GLU cc_start: 0.8616 (tp30) cc_final: 0.8149 (tp30) REVERT: D 593 TYR cc_start: 0.8760 (m-80) cc_final: 0.8274 (m-10) REVERT: E 589 GLU cc_start: 0.8647 (tp30) cc_final: 0.8147 (tp30) REVERT: E 593 TYR cc_start: 0.8940 (m-80) cc_final: 0.8638 (m-10) REVERT: F 378 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8487 (tt) REVERT: F 589 GLU cc_start: 0.8611 (tp30) cc_final: 0.8169 (tp30) REVERT: F 593 TYR cc_start: 0.8756 (m-80) cc_final: 0.8255 (m-80) REVERT: G 330 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6815 (tptp) REVERT: G 589 GLU cc_start: 0.8612 (tp30) cc_final: 0.8081 (tp30) REVERT: G 593 TYR cc_start: 0.8864 (m-80) cc_final: 0.8412 (m-10) outliers start: 57 outliers final: 30 residues processed: 209 average time/residue: 0.5997 time to fit residues: 148.1990 Evaluate side-chains 205 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP 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 645 VAL 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 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 645 VAL Chi-restraints excluded: chain E residue 684 THR 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 645 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 143 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 566 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 G 318 GLN G 367 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 = 0.3577 r_free = 0.3577 target = 0.112365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.057810 restraints weight = 43949.510| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 2.25 r_work: 0.2491 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 28308 Z= 0.344 Angle : 0.580 5.781 38388 Z= 0.323 Chirality : 0.049 0.173 4361 Planarity : 0.004 0.048 4998 Dihedral : 5.419 29.863 3819 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.05 % Allowed : 13.53 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 3549 helix: 0.37 (0.25), residues: 441 sheet: 2.02 (0.14), residues: 1162 loop : -1.07 (0.12), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 393 TYR 0.020 0.002 TYR D 438 PHE 0.029 0.002 PHE G 248 TRP 0.005 0.001 TRP C 244 HIS 0.002 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00811 (28308) covalent geometry : angle 0.58026 (38388) hydrogen bonds : bond 0.03771 ( 1218) hydrogen bonds : angle 4.77346 ( 3213) *********************** 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 244 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 179 time to evaluate : 1.051 Fit side-chains REVERT: A 361 ASP cc_start: 0.7406 (t0) cc_final: 0.7047 (t0) REVERT: A 589 GLU cc_start: 0.8609 (tp30) cc_final: 0.8136 (tp30) REVERT: B 489 LYS cc_start: 0.8027 (mttp) cc_final: 0.7617 (mttt) REVERT: B 589 GLU cc_start: 0.8667 (tp30) cc_final: 0.8074 (tp30) REVERT: B 593 TYR cc_start: 0.8874 (m-80) cc_final: 0.8398 (m-80) REVERT: C 589 GLU cc_start: 0.8607 (tp30) cc_final: 0.7989 (tp30) REVERT: D 258 SER cc_start: 0.9441 (OUTLIER) cc_final: 0.9240 (p) REVERT: D 489 LYS cc_start: 0.8055 (mttp) cc_final: 0.7630 (mttt) REVERT: D 589 GLU cc_start: 0.8622 (tp30) cc_final: 0.8086 (tp30) REVERT: D 593 TYR cc_start: 0.8764 (m-80) cc_final: 0.8236 (m-10) REVERT: E 330 LYS cc_start: 0.7785 (tttm) cc_final: 0.7316 (tptp) REVERT: E 489 LYS cc_start: 0.8085 (mttp) cc_final: 0.7672 (mttt) REVERT: E 589 GLU cc_start: 0.8626 (tp30) cc_final: 0.8150 (tp30) REVERT: E 593 TYR cc_start: 0.8955 (m-80) cc_final: 0.8684 (m-10) REVERT: F 589 GLU cc_start: 0.8625 (tp30) cc_final: 0.8041 (tp30) REVERT: G 330 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.7081 (tptp) REVERT: G 589 GLU cc_start: 0.8626 (tp30) cc_final: 0.8114 (tp30) REVERT: G 593 TYR cc_start: 0.8891 (m-80) cc_final: 0.8505 (m-80) outliers start: 65 outliers final: 40 residues processed: 221 average time/residue: 0.5736 time to fit residues: 149.5431 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 : 1.100 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 555 SER 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 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 655 ILE 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 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 479 THR Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 306 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 215 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 327 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 328 ASN 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 = 0.3629 r_free = 0.3629 target = 0.115753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.062266 restraints weight = 43383.384| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.26 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: 0.8766 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28308 Z= 0.104 Angle : 0.459 5.138 38388 Z= 0.256 Chirality : 0.044 0.147 4361 Planarity : 0.004 0.044 4998 Dihedral : 4.707 25.348 3819 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.55 % Allowed : 14.19 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.13), residues: 3549 helix: 0.60 (0.25), residues: 441 sheet: 2.31 (0.14), residues: 1197 loop : -1.06 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 289 TYR 0.010 0.001 TYR C 593 PHE 0.016 0.001 PHE F 248 TRP 0.005 0.001 TRP D 631 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00232 (28308) covalent geometry : angle 0.45886 (38388) hydrogen bonds : bond 0.02700 ( 1218) hydrogen bonds : angle 4.26978 ( 3213) *********************** 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 230 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.916 Fit side-chains REVERT: A 589 GLU cc_start: 0.8616 (tp30) cc_final: 0.8023 (tp30) REVERT: A 593 TYR cc_start: 0.8855 (m-80) cc_final: 0.8260 (m-10) REVERT: B 589 GLU cc_start: 0.8634 (tp30) cc_final: 0.7989 (tp30) REVERT: B 593 TYR cc_start: 0.8873 (m-80) cc_final: 0.8288 (m-80) REVERT: C 378 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8456 (tp) REVERT: C 589 GLU cc_start: 0.8655 (tp30) cc_final: 0.7989 (tp30) REVERT: C 593 TYR cc_start: 0.8726 (m-80) cc_final: 0.8141 (m-80) REVERT: D 589 GLU cc_start: 0.8651 (tp30) cc_final: 0.8073 (tp30) REVERT: D 593 TYR cc_start: 0.8798 (m-80) cc_final: 0.8215 (m-10) REVERT: E 330 LYS cc_start: 0.7818 (tttm) cc_final: 0.7324 (tptp) REVERT: E 489 LYS cc_start: 0.7968 (mttp) cc_final: 0.7615 (mttt) REVERT: E 589 GLU cc_start: 0.8667 (tp30) cc_final: 0.8110 (tp30) REVERT: E 593 TYR cc_start: 0.8989 (m-80) cc_final: 0.8658 (m-10) REVERT: F 378 LEU cc_start: 0.8805 (pt) cc_final: 0.8535 (tp) REVERT: F 589 GLU cc_start: 0.8649 (tp30) cc_final: 0.8177 (tp30) REVERT: F 593 TYR cc_start: 0.8730 (m-80) cc_final: 0.8185 (m-80) REVERT: G 589 GLU cc_start: 0.8631 (tp30) cc_final: 0.8076 (tp30) REVERT: G 593 TYR cc_start: 0.8897 (m-80) cc_final: 0.8499 (m-80) outliers start: 49 outliers final: 32 residues processed: 209 average time/residue: 0.5374 time to fit residues: 132.0800 Evaluate side-chains 204 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP 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 378 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL 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 306 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 645 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 207 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 353 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 295 optimal weight: 0.0670 chunk 33 optimal weight: 6.9990 overall best weight: 2.0524 ------------------------------------------------------------------------------- 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 362 ASN 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 = 0.3603 r_free = 0.3603 target = 0.114006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.059928 restraints weight = 43820.265| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.28 r_work: 0.2563 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28308 Z= 0.191 Angle : 0.497 5.248 38388 Z= 0.278 Chirality : 0.045 0.156 4361 Planarity : 0.004 0.044 4998 Dihedral : 4.965 25.679 3819 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.45 % Allowed : 14.22 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 3549 helix: 0.56 (0.25), residues: 441 sheet: 2.18 (0.14), residues: 1134 loop : -1.04 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 393 TYR 0.017 0.001 TYR C 438 PHE 0.022 0.002 PHE A 248 TRP 0.005 0.001 TRP A 244 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00446 (28308) covalent geometry : angle 0.49736 (38388) hydrogen bonds : bond 0.03123 ( 1218) hydrogen bonds : angle 4.40561 ( 3213) *********************** 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: 46 poor density : 176 time to evaluate : 0.976 Fit side-chains REVERT: A 589 GLU cc_start: 0.8626 (tp30) cc_final: 0.8052 (tp30) REVERT: A 593 TYR cc_start: 0.8837 (m-80) cc_final: 0.8244 (m-10) REVERT: B 589 GLU cc_start: 0.8650 (tp30) cc_final: 0.7905 (tp30) REVERT: B 593 TYR cc_start: 0.8871 (m-80) cc_final: 0.8211 (m-80) REVERT: C 378 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 589 GLU cc_start: 0.8626 (tp30) cc_final: 0.8073 (tp30) REVERT: C 593 TYR cc_start: 0.8700 (m-80) cc_final: 0.8180 (m-80) REVERT: D 589 GLU cc_start: 0.8637 (tp30) cc_final: 0.8047 (tp30) REVERT: D 593 TYR cc_start: 0.8793 (m-80) cc_final: 0.8177 (m-10) REVERT: E 330 LYS cc_start: 0.7779 (tttm) cc_final: 0.7358 (tptp) REVERT: E 489 LYS cc_start: 0.7995 (mttp) cc_final: 0.7626 (mttt) REVERT: E 589 GLU cc_start: 0.8657 (tp30) cc_final: 0.8077 (tp30) REVERT: E 593 TYR cc_start: 0.8967 (m-80) cc_final: 0.8600 (m-10) REVERT: F 378 LEU cc_start: 0.8853 (pt) cc_final: 0.8504 (tt) REVERT: F 589 GLU cc_start: 0.8619 (tp30) cc_final: 0.8169 (tp30) REVERT: F 593 TYR cc_start: 0.8704 (m-80) cc_final: 0.8218 (m-80) REVERT: G 589 GLU cc_start: 0.8642 (tp30) cc_final: 0.8032 (tp30) REVERT: G 593 TYR cc_start: 0.8893 (m-80) cc_final: 0.8419 (m-10) outliers start: 46 outliers final: 32 residues processed: 205 average time/residue: 0.5859 time to fit residues: 141.2041 Evaluate side-chains 206 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL 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 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 479 THR 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 331 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 645 VAL 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 276 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 226 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 328 ASN D 559 ASN D 590 GLN E 318 GLN E 328 ASN E 559 ASN E 590 GLN F 318 GLN F 362 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 = 0.3612 r_free = 0.3612 target = 0.114552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.060718 restraints weight = 43695.165| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.27 r_work: 0.2581 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28308 Z= 0.152 Angle : 0.477 5.444 38388 Z= 0.266 Chirality : 0.044 0.145 4361 Planarity : 0.004 0.044 4998 Dihedral : 4.846 25.955 3819 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.30 % Allowed : 14.35 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.13), residues: 3549 helix: 0.57 (0.25), residues: 441 sheet: 2.19 (0.14), residues: 1134 loop : -1.02 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 289 TYR 0.014 0.001 TYR F 438 PHE 0.020 0.001 PHE F 248 TRP 0.005 0.001 TRP A 244 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00350 (28308) covalent geometry : angle 0.47692 (38388) hydrogen bonds : bond 0.02906 ( 1218) hydrogen bonds : angle 4.31487 ( 3213) *********************** 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 215 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 1.168 Fit side-chains REVERT: A 589 GLU cc_start: 0.8611 (tp30) cc_final: 0.8028 (tp30) REVERT: A 593 TYR cc_start: 0.8846 (m-80) cc_final: 0.8273 (m-10) REVERT: B 589 GLU cc_start: 0.8629 (tp30) cc_final: 0.7966 (tp30) REVERT: B 593 TYR cc_start: 0.8861 (m-80) cc_final: 0.8277 (m-10) REVERT: C 378 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8487 (tp) REVERT: C 589 GLU cc_start: 0.8626 (tp30) cc_final: 0.8054 (tp30) REVERT: C 593 TYR cc_start: 0.8712 (m-80) cc_final: 0.8163 (m-80) REVERT: D 589 GLU cc_start: 0.8639 (tp30) cc_final: 0.8055 (tp30) REVERT: D 593 TYR cc_start: 0.8783 (m-80) cc_final: 0.8201 (m-10) REVERT: E 330 LYS cc_start: 0.7796 (tttm) cc_final: 0.7417 (tptp) REVERT: E 489 LYS cc_start: 0.7989 (mttp) cc_final: 0.7621 (mttt) REVERT: E 589 GLU cc_start: 0.8658 (tp30) cc_final: 0.8068 (tp30) REVERT: E 593 TYR cc_start: 0.8959 (m-80) cc_final: 0.8584 (m-10) REVERT: F 378 LEU cc_start: 0.8827 (pt) cc_final: 0.8577 (tp) REVERT: F 589 GLU cc_start: 0.8618 (tp30) cc_final: 0.8164 (tp30) REVERT: F 593 TYR cc_start: 0.8723 (m-80) cc_final: 0.8225 (m-80) REVERT: G 589 GLU cc_start: 0.8620 (tp30) cc_final: 0.7975 (tp30) REVERT: G 593 TYR cc_start: 0.8886 (m-80) cc_final: 0.8344 (m-10) outliers start: 41 outliers final: 32 residues processed: 199 average time/residue: 0.5888 time to fit residues: 137.3452 Evaluate side-chains 206 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 378 LEU 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 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 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 331 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 645 VAL 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 347 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 121 optimal weight: 0.8980 chunk 250 optimal weight: 20.0000 chunk 323 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 277 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.114931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.061173 restraints weight = 43635.869| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.28 r_work: 0.2591 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1611 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= 0.136 Angle : 0.468 5.638 38388 Z= 0.261 Chirality : 0.044 0.145 4361 Planarity : 0.004 0.043 4998 Dihedral : 4.767 25.809 3819 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.14 % Allowed : 14.70 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.13), residues: 3549 helix: 0.61 (0.25), residues: 441 sheet: 2.19 (0.14), residues: 1134 loop : -1.01 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 667 TYR 0.013 0.001 TYR F 438 PHE 0.019 0.001 PHE F 248 TRP 0.004 0.001 TRP A 244 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00312 (28308) covalent geometry : angle 0.46834 (38388) hydrogen bonds : bond 0.02802 ( 1218) hydrogen bonds : angle 4.24866 ( 3213) ********************** 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 208 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.036 Fit side-chains REVERT: A 589 GLU cc_start: 0.8620 (tp30) cc_final: 0.8028 (tp30) REVERT: A 593 TYR cc_start: 0.8846 (m-80) cc_final: 0.8275 (m-10) REVERT: B 589 GLU cc_start: 0.8616 (tp30) cc_final: 0.7843 (tp30) REVERT: B 593 TYR cc_start: 0.8857 (m-80) cc_final: 0.8173 (m-80) REVERT: C 378 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8512 (tp) REVERT: C 589 GLU cc_start: 0.8632 (tp30) cc_final: 0.8051 (tp30) REVERT: C 593 TYR cc_start: 0.8711 (m-80) cc_final: 0.8153 (m-80) REVERT: D 589 GLU cc_start: 0.8649 (tp30) cc_final: 0.8065 (tp30) REVERT: D 593 TYR cc_start: 0.8783 (m-80) cc_final: 0.8203 (m-10) REVERT: E 330 LYS cc_start: 0.7777 (tttm) cc_final: 0.7375 (tptp) REVERT: E 589 GLU cc_start: 0.8654 (tp30) cc_final: 0.8060 (tp30) REVERT: E 593 TYR cc_start: 0.8960 (m-80) cc_final: 0.8582 (m-10) REVERT: F 378 LEU cc_start: 0.8819 (pt) cc_final: 0.8613 (tp) REVERT: F 589 GLU cc_start: 0.8621 (tp30) cc_final: 0.8163 (tp30) REVERT: F 593 TYR cc_start: 0.8744 (m-80) cc_final: 0.8242 (m-80) REVERT: G 589 GLU cc_start: 0.8617 (tp30) cc_final: 0.7966 (tp30) REVERT: G 593 TYR cc_start: 0.8892 (m-80) cc_final: 0.8348 (m-10) outliers start: 36 outliers final: 28 residues processed: 192 average time/residue: 0.6290 time to fit residues: 141.0233 Evaluate side-chains 199 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 479 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 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 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 331 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 645 VAL 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 267 optimal weight: 30.0000 chunk 120 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 318 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 559 ASN B 590 GLN C 318 GLN C 362 ASN C 559 ASN C 590 GLN D 318 GLN D 328 ASN D 362 ASN D 559 ASN D 590 GLN E 318 GLN E 328 ASN E 559 ASN E 590 GLN F 318 GLN F 362 ASN F 590 GLN G 318 GLN G 590 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.059654 restraints weight = 43686.536| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 2.26 r_work: 0.2545 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28308 Z= 0.206 Angle : 0.504 6.362 38388 Z= 0.281 Chirality : 0.045 0.145 4361 Planarity : 0.004 0.044 4998 Dihedral : 5.022 25.986 3819 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.26 % Allowed : 14.60 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.13), residues: 3549 helix: 0.49 (0.25), residues: 441 sheet: 2.14 (0.14), residues: 1134 loop : -1.03 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 393 TYR 0.017 0.001 TYR B 438 PHE 0.022 0.002 PHE A 248 TRP 0.004 0.001 TRP A 244 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00481 (28308) covalent geometry : angle 0.50446 (38388) hydrogen bonds : bond 0.03146 ( 1218) hydrogen bonds : angle 4.41642 ( 3213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12619.85 seconds wall clock time: 214 minutes 53.74 seconds (12893.74 seconds total)