Starting phenix.real_space_refine on Tue Jun 24 00:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrm_39544/06_2025/8yrm_39544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrm_39544/06_2025/8yrm_39544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yrm_39544/06_2025/8yrm_39544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrm_39544/06_2025/8yrm_39544.map" model { file = "/net/cci-nas-00/data/ceres_data/8yrm_39544/06_2025/8yrm_39544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrm_39544/06_2025/8yrm_39544.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 42 5.16 5 C 17367 2.51 5 N 4550 2.21 5 O 5880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27853 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3977 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 491} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 12.31, per 1000 atoms: 0.44 Number of scatterers: 27853 At special positions: 0 Unit cell: (176.85, 172.8, 161.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 42 16.00 O 5880 8.00 N 4550 7.00 C 17367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 3.8 seconds 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 78 sheets defined 15.7% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 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: 12.66 Time building geometry restraints manager: 8.32 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: 0.26 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.720 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 63.200 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 28308 Z= 0.488 Angle : 1.042 6.120 38388 Z= 0.682 Chirality : 0.071 0.307 4361 Planarity : 0.007 0.135 4998 Dihedral : 15.561 79.674 10528 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.28 % Rotamer: Outliers : 0.88 % Allowed : 13.05 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3549 helix: -0.45 (0.24), residues: 441 sheet: 1.99 (0.15), residues: 1197 loop : -1.22 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 502 HIS 0.004 0.002 HIS C 313 PHE 0.026 0.004 PHE A 248 TYR 0.031 0.004 TYR C 273 ARG 0.011 0.002 ARG F 457 Details of bonding type rmsd hydrogen bonds : bond 0.19256 ( 1218) hydrogen bonds : angle 7.78017 ( 3213) covalent geometry : bond 0.00822 (28308) covalent geometry : angle 1.04157 (38388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 3.429 Fit side-chains REVERT: A 593 TYR cc_start: 0.8767 (m-80) cc_final: 0.8497 (m-10) REVERT: B 593 TYR cc_start: 0.8761 (m-80) cc_final: 0.8483 (m-10) REVERT: C 589 GLU cc_start: 0.8702 (tp30) cc_final: 0.8496 (tp30) REVERT: D 589 GLU cc_start: 0.8700 (tp30) cc_final: 0.8472 (tp30) REVERT: D 593 TYR cc_start: 0.8697 (m-80) cc_final: 0.8385 (m-80) REVERT: F 589 GLU cc_start: 0.8687 (tp30) cc_final: 0.8402 (tp30) outliers start: 28 outliers final: 21 residues processed: 210 average time/residue: 1.5069 time to fit residues: 368.6785 Evaluate side-chains 187 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 557 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 279 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 324 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 362 ASN A 500 ASN A 508 GLN B 318 GLN B 362 ASN B 500 ASN B 508 GLN B 590 GLN C 318 GLN C 362 ASN C 500 ASN C 508 GLN D 318 GLN D 362 ASN D 508 GLN D 590 GLN E 318 GLN E 362 ASN E 508 GLN E 590 GLN F 318 GLN F 362 ASN F 508 GLN F 590 GLN G 500 ASN G 508 GLN G 590 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.062697 restraints weight = 43559.578| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.23 r_work: 0.2624 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 28308 Z= 0.112 Angle : 0.505 5.364 38388 Z= 0.283 Chirality : 0.045 0.152 4361 Planarity : 0.003 0.033 4998 Dihedral : 5.296 52.817 3849 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.55 % Allowed : 12.55 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 3549 helix: 0.46 (0.25), residues: 441 sheet: 2.29 (0.14), residues: 1197 loop : -1.16 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 244 HIS 0.002 0.001 HIS E 313 PHE 0.013 0.001 PHE F 248 TYR 0.009 0.001 TYR F 438 ARG 0.001 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1218) hydrogen bonds : angle 5.08218 ( 3213) covalent geometry : bond 0.00247 (28308) covalent geometry : angle 0.50546 (38388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 2.995 Fit side-chains REVERT: A 378 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8426 (tt) REVERT: A 589 GLU cc_start: 0.8459 (tp30) cc_final: 0.8241 (tp30) REVERT: A 593 TYR cc_start: 0.8647 (m-80) cc_final: 0.8339 (m-10) REVERT: B 589 GLU cc_start: 0.8577 (tp30) cc_final: 0.8361 (tp30) REVERT: B 593 TYR cc_start: 0.8722 (m-80) cc_final: 0.8451 (m-10) REVERT: C 317 ASP cc_start: 0.8538 (m-30) cc_final: 0.8283 (m-30) REVERT: C 589 GLU cc_start: 0.8512 (tp30) cc_final: 0.8013 (tp30) REVERT: D 589 GLU cc_start: 0.8504 (tp30) cc_final: 0.8239 (tp30) REVERT: D 593 TYR cc_start: 0.8621 (m-80) cc_final: 0.8299 (m-80) REVERT: E 317 ASP cc_start: 0.8463 (m-30) cc_final: 0.8260 (m-30) REVERT: E 589 GLU cc_start: 0.8562 (tp30) cc_final: 0.8261 (tp30) REVERT: F 330 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7444 (tmtm) REVERT: F 589 GLU cc_start: 0.8515 (tp30) cc_final: 0.8233 (tp30) REVERT: F 593 TYR cc_start: 0.8600 (m-80) cc_final: 0.8229 (m-10) REVERT: G 330 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6834 (tptp) REVERT: G 589 GLU cc_start: 0.8499 (tp30) cc_final: 0.8185 (tp30) REVERT: G 593 TYR cc_start: 0.8733 (m-80) cc_final: 0.8443 (m-10) outliers start: 49 outliers final: 22 residues processed: 224 average time/residue: 1.2668 time to fit residues: 339.2799 Evaluate side-chains 201 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 330 LYS Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 330 LYS Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 196 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 325 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 324 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 318 GLN A 367 GLN A 559 ASN A 590 GLN B 318 GLN B 367 GLN B 559 ASN C 318 GLN C 367 GLN C 559 ASN C 590 GLN D 318 GLN D 367 GLN D 500 ASN D 559 ASN D 590 GLN E 318 GLN E 367 GLN E 500 ASN E 559 ASN E 590 GLN F 311 ASN F 318 GLN F 367 GLN F 500 ASN F 559 ASN F 590 GLN G 318 GLN G 367 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059310 restraints weight = 43740.274| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.28 r_work: 0.2552 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28308 Z= 0.229 Angle : 0.537 5.467 38388 Z= 0.300 Chirality : 0.046 0.158 4361 Planarity : 0.004 0.043 4998 Dihedral : 5.201 52.163 3821 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.96 % Allowed : 12.80 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 3549 helix: 0.42 (0.25), residues: 441 sheet: 2.12 (0.14), residues: 1162 loop : -1.07 (0.12), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 631 HIS 0.002 0.001 HIS E 358 PHE 0.023 0.002 PHE G 248 TYR 0.017 0.001 TYR C 438 ARG 0.002 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 1218) hydrogen bonds : angle 4.88702 ( 3213) covalent geometry : bond 0.00533 (28308) covalent geometry : angle 0.53738 (38388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 176 time to evaluate : 3.278 Fit side-chains REVERT: A 589 GLU cc_start: 0.8529 (tp30) cc_final: 0.8238 (tp30) REVERT: A 593 TYR cc_start: 0.8740 (m-80) cc_final: 0.8427 (m-80) REVERT: B 589 GLU cc_start: 0.8622 (tp30) cc_final: 0.8235 (tp30) REVERT: B 593 TYR cc_start: 0.8819 (m-80) cc_final: 0.8437 (m-80) REVERT: C 589 GLU cc_start: 0.8562 (tp30) cc_final: 0.8009 (tp30) REVERT: D 589 GLU cc_start: 0.8577 (tp30) cc_final: 0.8170 (tp30) REVERT: D 593 TYR cc_start: 0.8705 (m-80) cc_final: 0.8239 (m-80) REVERT: E 589 GLU cc_start: 0.8618 (tp30) cc_final: 0.8310 (tp30) REVERT: F 589 GLU cc_start: 0.8569 (tp30) cc_final: 0.8026 (tp30) REVERT: G 330 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6812 (tptp) REVERT: G 589 GLU cc_start: 0.8568 (tp30) cc_final: 0.8241 (tp30) REVERT: G 593 TYR cc_start: 0.8818 (m-80) cc_final: 0.8516 (m-80) outliers start: 62 outliers final: 29 residues processed: 213 average time/residue: 1.2828 time to fit residues: 324.7885 Evaluate side-chains 200 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 3.227 ------------------------------------------------------------------------------- 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 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 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 645 VAL Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 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 451 MET Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 127 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 356 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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 311 ASN 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 = 0.3584 r_free = 0.3584 target = 0.112811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.058265 restraints weight = 44270.628| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.26 r_work: 0.2500 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 28308 Z= 0.296 Angle : 0.565 5.809 38388 Z= 0.315 Chirality : 0.048 0.178 4361 Planarity : 0.004 0.049 4998 Dihedral : 5.410 52.666 3819 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.21 % Allowed : 13.12 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 3549 helix: 0.33 (0.25), residues: 441 sheet: 1.98 (0.14), residues: 1162 loop : -1.10 (0.12), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 631 HIS 0.002 0.001 HIS A 358 PHE 0.026 0.002 PHE F 248 TYR 0.018 0.002 TYR F 438 ARG 0.002 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1218) hydrogen bonds : angle 4.87220 ( 3213) covalent geometry : bond 0.00693 (28308) covalent geometry : angle 0.56527 (38388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 3.451 Fit side-chains REVERT: A 589 GLU cc_start: 0.8560 (tp30) cc_final: 0.8222 (tp30) REVERT: A 593 TYR cc_start: 0.8765 (m-80) cc_final: 0.8434 (m-80) REVERT: B 589 GLU cc_start: 0.8656 (tp30) cc_final: 0.8121 (tp30) REVERT: B 593 TYR cc_start: 0.8851 (m-80) cc_final: 0.8367 (m-80) REVERT: C 589 GLU cc_start: 0.8569 (tp30) cc_final: 0.7958 (tp30) REVERT: C 593 TYR cc_start: 0.8684 (m-80) cc_final: 0.8163 (m-80) REVERT: D 589 GLU cc_start: 0.8595 (tp30) cc_final: 0.8232 (tp30) REVERT: D 593 TYR cc_start: 0.8727 (m-80) cc_final: 0.8347 (m-80) REVERT: E 589 GLU cc_start: 0.8647 (tp30) cc_final: 0.8204 (tp30) REVERT: E 593 TYR cc_start: 0.8979 (m-10) cc_final: 0.8747 (m-10) REVERT: F 589 GLU cc_start: 0.8580 (tp30) cc_final: 0.8075 (tp30) REVERT: G 330 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6978 (tptp) REVERT: G 589 GLU cc_start: 0.8581 (tp30) cc_final: 0.8116 (tp30) outliers start: 70 outliers final: 34 residues processed: 218 average time/residue: 1.2728 time to fit residues: 335.6784 Evaluate side-chains 209 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 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 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 D residue 655 ILE 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 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 332 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 110 optimal weight: 0.8980 chunk 291 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 306 optimal weight: 0.0070 chunk 293 optimal weight: 0.0070 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 328 ASN E 559 ASN E 590 GLN E 734 ASN F 318 GLN F 559 ASN G 318 GLN G 559 ASN G 590 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.063102 restraints weight = 43672.771| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.26 r_work: 0.2637 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28308 Z= 0.097 Angle : 0.460 5.131 38388 Z= 0.256 Chirality : 0.044 0.150 4361 Planarity : 0.004 0.047 4998 Dihedral : 4.672 47.989 3819 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.83 % Allowed : 13.62 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.13), residues: 3549 helix: 0.63 (0.25), residues: 441 sheet: 2.34 (0.14), residues: 1197 loop : -1.07 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 631 HIS 0.003 0.001 HIS D 358 PHE 0.014 0.001 PHE F 248 TYR 0.009 0.001 TYR E 593 ARG 0.001 0.000 ARG D 527 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 1218) hydrogen bonds : angle 4.31132 ( 3213) covalent geometry : bond 0.00213 (28308) covalent geometry : angle 0.45977 (38388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 3.205 Fit side-chains REVERT: A 378 LEU cc_start: 0.8746 (pt) cc_final: 0.8536 (tp) REVERT: A 589 GLU cc_start: 0.8586 (tp30) cc_final: 0.8031 (tp30) REVERT: A 593 TYR cc_start: 0.8838 (m-80) cc_final: 0.8279 (m-10) REVERT: B 589 GLU cc_start: 0.8660 (tp30) cc_final: 0.8107 (tp30) REVERT: B 593 TYR cc_start: 0.8870 (m-80) cc_final: 0.8386 (m-80) REVERT: C 317 ASP cc_start: 0.8537 (m-30) cc_final: 0.8292 (m-30) REVERT: C 378 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8518 (tp) REVERT: C 589 GLU cc_start: 0.8624 (tp30) cc_final: 0.8255 (tp30) REVERT: C 593 TYR cc_start: 0.8734 (m-80) cc_final: 0.8345 (m-80) REVERT: D 589 GLU cc_start: 0.8623 (tp30) cc_final: 0.8140 (tp30) REVERT: D 593 TYR cc_start: 0.8770 (m-80) cc_final: 0.8234 (m-10) REVERT: E 330 LYS cc_start: 0.7790 (tttm) cc_final: 0.7304 (tptp) REVERT: E 589 GLU cc_start: 0.8679 (tp30) cc_final: 0.8120 (tp30) REVERT: E 593 TYR cc_start: 0.9006 (m-10) cc_final: 0.8710 (m-10) REVERT: F 378 LEU cc_start: 0.8787 (pt) cc_final: 0.8582 (tp) REVERT: F 589 GLU cc_start: 0.8611 (tp30) cc_final: 0.8062 (tp30) REVERT: F 593 TYR cc_start: 0.8710 (m-80) cc_final: 0.8191 (m-80) REVERT: G 330 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.7074 (tptp) REVERT: G 378 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8484 (tp) REVERT: G 589 GLU cc_start: 0.8590 (tp30) cc_final: 0.7963 (tp30) outliers start: 58 outliers final: 31 residues processed: 215 average time/residue: 1.3609 time to fit residues: 347.9874 Evaluate side-chains 201 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 3.464 ------------------------------------------------------------------------------- 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 A residue 655 ILE 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 645 VAL Chi-restraints excluded: chain B residue 655 ILE 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 C residue 684 THR Chi-restraints excluded: chain D residue 363 SER 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 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 330 LYS Chi-restraints excluded: chain G residue 332 ASP Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 362 ASN B 559 ASN B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 362 ASN F 559 ASN 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 = 0.3615 r_free = 0.3615 target = 0.114807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.060893 restraints weight = 43804.959| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.25 r_work: 0.2583 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28308 Z= 0.155 Angle : 0.483 5.230 38388 Z= 0.269 Chirality : 0.044 0.146 4361 Planarity : 0.004 0.043 4998 Dihedral : 4.860 47.812 3819 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.52 % Allowed : 13.91 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 3549 helix: 0.66 (0.26), residues: 441 sheet: 2.39 (0.14), residues: 1162 loop : -1.02 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 631 HIS 0.002 0.001 HIS D 358 PHE 0.020 0.001 PHE F 248 TYR 0.016 0.001 TYR F 438 ARG 0.001 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 1218) hydrogen bonds : angle 4.36983 ( 3213) covalent geometry : bond 0.00356 (28308) covalent geometry : angle 0.48300 (38388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 3.454 Fit side-chains REVERT: A 378 LEU cc_start: 0.8780 (pt) cc_final: 0.8551 (tp) REVERT: A 589 GLU cc_start: 0.8598 (tp30) cc_final: 0.8057 (tp30) REVERT: A 593 TYR cc_start: 0.8818 (m-80) cc_final: 0.8255 (m-10) REVERT: B 589 GLU cc_start: 0.8649 (tp30) cc_final: 0.7994 (tp30) REVERT: B 593 TYR cc_start: 0.8871 (m-80) cc_final: 0.8272 (m-10) REVERT: C 317 ASP cc_start: 0.8536 (m-30) cc_final: 0.8310 (m-30) REVERT: C 378 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8516 (tp) REVERT: C 589 GLU cc_start: 0.8630 (tp30) cc_final: 0.8133 (tp30) REVERT: D 589 GLU cc_start: 0.8623 (tp30) cc_final: 0.8039 (tp30) REVERT: D 593 TYR cc_start: 0.8769 (m-80) cc_final: 0.8177 (m-10) REVERT: E 330 LYS cc_start: 0.7759 (tttm) cc_final: 0.7264 (tptp) REVERT: E 589 GLU cc_start: 0.8653 (tp30) cc_final: 0.8042 (tp30) REVERT: E 593 TYR cc_start: 0.8996 (m-10) cc_final: 0.8649 (m-10) REVERT: F 378 LEU cc_start: 0.8826 (pt) cc_final: 0.8572 (tp) REVERT: F 589 GLU cc_start: 0.8598 (tp30) cc_final: 0.8041 (tp30) REVERT: G 330 LYS cc_start: 0.7287 (tptp) cc_final: 0.6859 (tptp) REVERT: G 589 GLU cc_start: 0.8578 (tp30) cc_final: 0.7925 (tp30) outliers start: 48 outliers final: 31 residues processed: 201 average time/residue: 1.3936 time to fit residues: 330.6375 Evaluate side-chains 200 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 3.037 ------------------------------------------------------------------------------- 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 378 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 378 LEU 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 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 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 479 THR Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 110 optimal weight: 3.9990 chunk 126 optimal weight: 0.0980 chunk 117 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.116828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.063730 restraints weight = 43712.953| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.27 r_work: 0.2652 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28308 Z= 0.092 Angle : 0.444 4.819 38388 Z= 0.246 Chirality : 0.043 0.147 4361 Planarity : 0.003 0.040 4998 Dihedral : 4.484 42.013 3819 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.58 % Allowed : 13.97 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 3549 helix: 0.70 (0.25), residues: 441 sheet: 2.41 (0.13), residues: 1197 loop : -0.99 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 631 HIS 0.003 0.001 HIS G 358 PHE 0.015 0.001 PHE F 248 TYR 0.010 0.001 TYR C 593 ARG 0.001 0.000 ARG D 667 Details of bonding type rmsd hydrogen bonds : bond 0.02498 ( 1218) hydrogen bonds : angle 4.11579 ( 3213) covalent geometry : bond 0.00207 (28308) covalent geometry : angle 0.44365 (38388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 2.950 Fit side-chains REVERT: A 589 GLU cc_start: 0.8610 (tp30) cc_final: 0.8021 (tp30) REVERT: A 593 TYR cc_start: 0.8840 (m-80) cc_final: 0.8251 (m-10) REVERT: B 378 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8603 (tp) REVERT: B 589 GLU cc_start: 0.8630 (tp30) cc_final: 0.7862 (tp30) REVERT: B 593 TYR cc_start: 0.8896 (m-80) cc_final: 0.8248 (m-80) REVERT: C 331 THR cc_start: 0.7386 (OUTLIER) cc_final: 0.7139 (t) REVERT: C 589 GLU cc_start: 0.8659 (tp30) cc_final: 0.8005 (tp30) REVERT: C 593 TYR cc_start: 0.8752 (m-80) cc_final: 0.8120 (m-80) REVERT: D 589 GLU cc_start: 0.8650 (tp30) cc_final: 0.8070 (tp30) REVERT: D 593 TYR cc_start: 0.8773 (m-80) cc_final: 0.8203 (m-10) REVERT: E 330 LYS cc_start: 0.7779 (tttm) cc_final: 0.7269 (tptp) REVERT: E 378 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8620 (tp) REVERT: E 589 GLU cc_start: 0.8696 (tp30) cc_final: 0.8091 (tp30) REVERT: E 593 TYR cc_start: 0.9019 (m-10) cc_final: 0.8704 (m-10) REVERT: F 330 LYS cc_start: 0.7561 (tmtm) cc_final: 0.6652 (tptp) REVERT: F 589 GLU cc_start: 0.8646 (tp30) cc_final: 0.8167 (tp30) REVERT: F 593 TYR cc_start: 0.8727 (m-80) cc_final: 0.8220 (m-80) REVERT: F 695 ASP cc_start: 0.7668 (t70) cc_final: 0.6985 (t0) REVERT: G 330 LYS cc_start: 0.7327 (tptp) cc_final: 0.6897 (tptp) REVERT: G 378 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8498 (tp) REVERT: G 589 GLU cc_start: 0.8614 (tp30) cc_final: 0.7868 (tp30) outliers start: 50 outliers final: 24 residues processed: 212 average time/residue: 1.5458 time to fit residues: 389.8208 Evaluate side-chains 200 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 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 378 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 331 THR 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 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 645 VAL Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 645 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 255 optimal weight: 0.0980 chunk 139 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 304 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 362 ASN D 559 ASN D 590 GLN E 318 GLN E 362 ASN E 559 ASN E 590 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.063101 restraints weight = 43887.110| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.28 r_work: 0.2632 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1741 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 : 0.447 4.701 38388 Z= 0.249 Chirality : 0.043 0.144 4361 Planarity : 0.003 0.037 4998 Dihedral : 4.450 23.792 3817 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.98 % Allowed : 14.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 3549 helix: 0.74 (0.25), residues: 441 sheet: 2.33 (0.14), residues: 1134 loop : -0.93 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 631 HIS 0.002 0.001 HIS D 313 PHE 0.016 0.001 PHE F 248 TYR 0.012 0.001 TYR E 438 ARG 0.002 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02579 ( 1218) hydrogen bonds : angle 4.07702 ( 3213) covalent geometry : bond 0.00237 (28308) covalent geometry : angle 0.44676 (38388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 2.929 Fit side-chains REVERT: A 589 GLU cc_start: 0.8613 (tp30) cc_final: 0.8012 (tp30) REVERT: A 593 TYR cc_start: 0.8841 (m-80) cc_final: 0.8236 (m-10) REVERT: B 378 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 589 GLU cc_start: 0.8614 (tp30) cc_final: 0.7855 (tp30) REVERT: B 593 TYR cc_start: 0.8884 (m-80) cc_final: 0.8237 (m-10) REVERT: C 589 GLU cc_start: 0.8637 (tp30) cc_final: 0.8087 (tp30) REVERT: C 593 TYR cc_start: 0.8734 (m-80) cc_final: 0.8237 (m-80) REVERT: D 589 GLU cc_start: 0.8649 (tp30) cc_final: 0.8069 (tp30) REVERT: D 593 TYR cc_start: 0.8770 (m-80) cc_final: 0.8193 (m-10) REVERT: E 330 LYS cc_start: 0.7761 (tttm) cc_final: 0.7333 (tptp) REVERT: E 589 GLU cc_start: 0.8689 (tp30) cc_final: 0.8046 (tp30) REVERT: E 593 TYR cc_start: 0.9013 (m-10) cc_final: 0.8683 (m-10) REVERT: F 330 LYS cc_start: 0.7304 (tmtm) cc_final: 0.6825 (tptp) REVERT: F 589 GLU cc_start: 0.8615 (tp30) cc_final: 0.8209 (tp30) REVERT: F 593 TYR cc_start: 0.8683 (m-80) cc_final: 0.8257 (m-80) REVERT: F 695 ASP cc_start: 0.7630 (t70) cc_final: 0.6976 (t0) REVERT: G 378 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8493 (tp) REVERT: G 589 GLU cc_start: 0.8599 (tp30) cc_final: 0.7963 (tp30) REVERT: G 593 TYR cc_start: 0.8822 (m-80) cc_final: 0.8336 (m-80) outliers start: 31 outliers final: 19 residues processed: 189 average time/residue: 1.3749 time to fit residues: 304.8002 Evaluate side-chains 191 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 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 491 SER Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 338 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 277 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 348 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 559 ASN B 590 GLN C 318 GLN C 362 ASN C 559 ASN C 590 GLN D 318 GLN D 559 ASN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN F 590 GLN G 318 GLN G 362 ASN 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 = 0.3641 r_free = 0.3641 target = 0.116415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.063244 restraints weight = 43700.280| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.26 r_work: 0.2636 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28308 Z= 0.103 Angle : 0.444 4.576 38388 Z= 0.247 Chirality : 0.043 0.145 4361 Planarity : 0.003 0.038 4998 Dihedral : 4.417 23.931 3817 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.98 % Allowed : 14.73 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 3549 helix: 0.73 (0.25), residues: 441 sheet: 2.35 (0.13), residues: 1148 loop : -0.92 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 631 HIS 0.002 0.001 HIS F 313 PHE 0.015 0.001 PHE F 248 TYR 0.011 0.001 TYR E 438 ARG 0.001 0.000 ARG D 527 Details of bonding type rmsd hydrogen bonds : bond 0.02544 ( 1218) hydrogen bonds : angle 4.04468 ( 3213) covalent geometry : bond 0.00236 (28308) covalent geometry : angle 0.44411 (38388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 3.104 Fit side-chains REVERT: A 589 GLU cc_start: 0.8612 (tp30) cc_final: 0.8005 (tp30) REVERT: A 593 TYR cc_start: 0.8839 (m-80) cc_final: 0.8227 (m-10) REVERT: B 378 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8602 (tp) REVERT: B 589 GLU cc_start: 0.8606 (tp30) cc_final: 0.7824 (tp30) REVERT: B 593 TYR cc_start: 0.8882 (m-80) cc_final: 0.8209 (m-80) REVERT: C 589 GLU cc_start: 0.8635 (tp30) cc_final: 0.8121 (tp30) REVERT: C 593 TYR cc_start: 0.8743 (m-80) cc_final: 0.8184 (m-80) REVERT: C 695 ASP cc_start: 0.7914 (t70) cc_final: 0.7656 (t70) REVERT: D 330 LYS cc_start: 0.7587 (tmtm) cc_final: 0.7377 (tmtm) REVERT: D 589 GLU cc_start: 0.8653 (tp30) cc_final: 0.8109 (tp30) REVERT: D 593 TYR cc_start: 0.8767 (m-80) cc_final: 0.8235 (m-10) REVERT: E 330 LYS cc_start: 0.7772 (tttm) cc_final: 0.7336 (tptp) REVERT: E 378 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8632 (tp) REVERT: E 589 GLU cc_start: 0.8684 (tp30) cc_final: 0.8046 (tp30) REVERT: E 593 TYR cc_start: 0.9022 (m-10) cc_final: 0.8684 (m-10) REVERT: F 330 LYS cc_start: 0.7218 (tmtm) cc_final: 0.6785 (tptp) REVERT: F 589 GLU cc_start: 0.8602 (tp30) cc_final: 0.8191 (tp30) REVERT: F 593 TYR cc_start: 0.8718 (m-80) cc_final: 0.8285 (m-80) REVERT: F 695 ASP cc_start: 0.7594 (t70) cc_final: 0.6933 (t0) REVERT: G 378 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8573 (tp) REVERT: G 589 GLU cc_start: 0.8580 (tp30) cc_final: 0.7907 (tp30) REVERT: G 593 TYR cc_start: 0.8798 (m-80) cc_final: 0.8280 (m-80) outliers start: 31 outliers final: 17 residues processed: 190 average time/residue: 1.4529 time to fit residues: 328.7273 Evaluate side-chains 191 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 332 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 491 SER Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 378 LEU 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 158 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 327 optimal weight: 0.5980 chunk 338 optimal weight: 0.0970 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A 590 GLN B 318 GLN B 590 GLN C 318 GLN C 559 ASN C 590 GLN D 318 GLN D 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 559 ASN F 590 GLN G 318 GLN G 590 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.062514 restraints weight = 43601.181| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.26 r_work: 0.2620 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28308 Z= 0.121 Angle : 0.454 4.707 38388 Z= 0.252 Chirality : 0.043 0.145 4361 Planarity : 0.003 0.037 4998 Dihedral : 4.494 24.033 3817 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.85 % Allowed : 14.95 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 3549 helix: 0.72 (0.25), residues: 441 sheet: 2.34 (0.13), residues: 1148 loop : -0.93 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 631 HIS 0.002 0.001 HIS F 313 PHE 0.017 0.001 PHE F 248 TYR 0.013 0.001 TYR E 438 ARG 0.001 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.02646 ( 1218) hydrogen bonds : angle 4.07594 ( 3213) covalent geometry : bond 0.00280 (28308) covalent geometry : angle 0.45365 (38388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 3.354 Fit side-chains REVERT: A 589 GLU cc_start: 0.8615 (tp30) cc_final: 0.8056 (tp30) REVERT: A 593 TYR cc_start: 0.8835 (m-80) cc_final: 0.8277 (m-10) REVERT: B 378 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8550 (tt) REVERT: B 589 GLU cc_start: 0.8610 (tp30) cc_final: 0.7925 (tp30) REVERT: B 593 TYR cc_start: 0.8884 (m-80) cc_final: 0.8313 (m-10) REVERT: C 589 GLU cc_start: 0.8637 (tp30) cc_final: 0.8265 (tp30) REVERT: C 593 TYR cc_start: 0.8756 (m-80) cc_final: 0.8388 (m-80) REVERT: C 695 ASP cc_start: 0.7905 (t70) cc_final: 0.7668 (t70) REVERT: D 589 GLU cc_start: 0.8653 (tp30) cc_final: 0.8109 (tp30) REVERT: D 593 TYR cc_start: 0.8775 (m-80) cc_final: 0.8240 (m-10) REVERT: E 330 LYS cc_start: 0.7774 (tttm) cc_final: 0.7328 (tptp) REVERT: E 378 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8622 (tp) REVERT: E 589 GLU cc_start: 0.8693 (tp30) cc_final: 0.8067 (tp30) REVERT: E 593 TYR cc_start: 0.9026 (m-10) cc_final: 0.8689 (m-10) REVERT: F 330 LYS cc_start: 0.7202 (tmtm) cc_final: 0.6992 (tptp) REVERT: F 589 GLU cc_start: 0.8604 (tp30) cc_final: 0.8183 (tp30) REVERT: F 593 TYR cc_start: 0.8716 (m-80) cc_final: 0.8272 (m-80) REVERT: F 695 ASP cc_start: 0.7583 (t70) cc_final: 0.6915 (t0) REVERT: G 589 GLU cc_start: 0.8576 (tp30) cc_final: 0.7893 (tp30) REVERT: G 593 TYR cc_start: 0.8809 (m-80) cc_final: 0.8283 (m-80) outliers start: 27 outliers final: 19 residues processed: 184 average time/residue: 1.4671 time to fit residues: 316.8068 Evaluate side-chains 192 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain 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 491 SER Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 326 optimal weight: 0.4980 chunk 164 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 559 ASN B 590 GLN C 318 GLN C 362 ASN C 559 ASN C 590 GLN D 318 GLN D 590 GLN E 318 GLN E 559 ASN E 590 GLN F 318 GLN 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 = 0.3631 r_free = 0.3631 target = 0.115764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.062204 restraints weight = 43694.921| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.26 r_work: 0.2612 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1724 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= 0.127 Angle : 0.457 4.769 38388 Z= 0.254 Chirality : 0.044 0.145 4361 Planarity : 0.003 0.038 4998 Dihedral : 4.533 24.146 3817 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.04 % Allowed : 14.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 3549 helix: 0.70 (0.25), residues: 441 sheet: 2.32 (0.13), residues: 1148 loop : -0.94 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 631 HIS 0.002 0.001 HIS F 313 PHE 0.017 0.001 PHE G 248 TYR 0.013 0.001 TYR E 438 ARG 0.001 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 1218) hydrogen bonds : angle 4.09933 ( 3213) covalent geometry : bond 0.00292 (28308) covalent geometry : angle 0.45706 (38388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30961.22 seconds wall clock time: 533 minutes 12.78 seconds (31992.78 seconds total)