Starting phenix.real_space_refine on Thu Jul 2 20:29:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8u_19011/07_2026/8r8u_19011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8u_19011/07_2026/8r8u_19011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r8u_19011/07_2026/8r8u_19011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8u_19011/07_2026/8r8u_19011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r8u_19011/07_2026/8r8u_19011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8u_19011/07_2026/8r8u_19011.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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 10 9.91 5 S 74 5.16 5 C 6462 2.51 5 N 1706 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4944 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 585} Chain breaks: 4 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4944 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 585} Chain breaks: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 0 Ad-hoc single atom residues: {' CA': 5} Chain breaks: 5 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 0 Ad-hoc single atom residues: {' CA': 5} Chain breaks: 5 Time building chain proxies: 2.63, per 1000 atoms: 0.26 Number of scatterers: 10140 At special positions: 0 Unit cell: (99.75, 141.55, 73.15, 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 10 19.99 S 74 16.00 O 1888 8.00 N 1706 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 374.1 milliseconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 26 sheets defined 22.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.128A pdb=" N ASP A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.642A pdb=" N ASP A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.837A pdb=" N GLU A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.536A pdb=" N ASP A 405 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 406 " --> pdb=" O GLY A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 406' Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 558 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.127A pdb=" N ASP B 168 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.642A pdb=" N ASP B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.837A pdb=" N GLU B 351 " --> pdb=" O TRP B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 351' Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.536A pdb=" N ASP B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 406' Processing helix chain 'B' and resid 444 through 454 Processing helix chain 'B' and resid 471 through 474 Processing helix chain 'B' and resid 494 through 507 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 558 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 611 through 621 Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 657 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.851A pdb=" N THR A 5 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 28 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 25 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 76 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 5.969A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 39 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A 68 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 5.969A pdb=" N THR A 15 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR A 111 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 17 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 113 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS A 19 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 115 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.531A pdb=" N ALA A 148 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 271 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 286 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 269 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER A 288 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 267 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 265 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 337 removed outlier: 3.574A pdb=" N LYS A 333 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 359 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 removed outlier: 6.442A pdb=" N ILE A 428 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 462 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 430 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 removed outlier: 8.149A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 592 removed outlier: 5.842A pdb=" N LEU A 596 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 630 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A 598 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 5.851A pdb=" N THR B 5 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 28 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE B 7 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 25 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL B 76 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 20 removed outlier: 5.970A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 39 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP B 68 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 20 removed outlier: 5.970A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 213 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.532A pdb=" N ALA B 148 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 271 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 286 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 269 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 288 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 267 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B 290 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 265 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU B 199 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 333 through 337 removed outlier: 3.574A pdb=" N LYS B 333 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 359 Processing sheet with id=AC2, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.442A pdb=" N ILE B 428 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 462 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 430 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 480 removed outlier: 8.148A pdb=" N ILE B 565 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 489 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 567 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B 491 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 513 through 514 Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 573 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 removed outlier: 5.841A pdb=" N LEU B 596 " --> pdb=" O THR B 628 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 630 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE B 598 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 605 through 606 344 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3292 1.34 - 1.46: 2108 1.46 - 1.58: 4868 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10376 Sorted by residual: bond pdb=" N ARG B 650 " pdb=" CA ARG B 650 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.37e+00 bond pdb=" N ARG A 650 " pdb=" CA ARG A 650 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.37e+00 bond pdb=" N ARG B 495 " pdb=" CA ARG B 495 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.05e+00 bond pdb=" N ARG A 495 " pdb=" CA ARG A 495 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.05e+00 bond pdb=" N ARG B 488 " pdb=" CA ARG B 488 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.26e-02 6.30e+03 4.40e+00 ... (remaining 10371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 13445 0.98 - 1.95: 469 1.95 - 2.93: 125 2.93 - 3.90: 27 3.90 - 4.88: 8 Bond angle restraints: 14074 Sorted by residual: angle pdb=" CA ARG A 123 " pdb=" C ARG A 123 " pdb=" O ARG A 123 " ideal model delta sigma weight residual 121.28 118.04 3.24 1.19e+00 7.06e-01 7.41e+00 angle pdb=" CA ARG B 123 " pdb=" C ARG B 123 " pdb=" O ARG B 123 " ideal model delta sigma weight residual 121.28 118.04 3.24 1.19e+00 7.06e-01 7.41e+00 angle pdb=" CA ARG A 650 " pdb=" C ARG A 650 " pdb=" O ARG A 650 " ideal model delta sigma weight residual 120.43 117.61 2.82 1.09e+00 8.42e-01 6.69e+00 angle pdb=" CA ARG B 495 " pdb=" C ARG B 495 " pdb=" O ARG B 495 " ideal model delta sigma weight residual 120.82 118.12 2.70 1.05e+00 9.07e-01 6.59e+00 angle pdb=" CA ARG B 650 " pdb=" C ARG B 650 " pdb=" O ARG B 650 " ideal model delta sigma weight residual 120.43 117.63 2.80 1.09e+00 8.42e-01 6.58e+00 ... (remaining 14069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 5372 16.11 - 32.21: 598 32.21 - 48.32: 192 48.32 - 64.43: 86 64.43 - 80.53: 10 Dihedral angle restraints: 6258 sinusoidal: 2552 harmonic: 3706 Sorted by residual: dihedral pdb=" CA PHE B 407 " pdb=" C PHE B 407 " pdb=" N GLY B 408 " pdb=" CA GLY B 408 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 407 " pdb=" C PHE A 407 " pdb=" N GLY A 408 " pdb=" CA GLY A 408 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP B 405 " pdb=" CB ASP B 405 " pdb=" CG ASP B 405 " pdb=" OD1 ASP B 405 " ideal model delta sinusoidal sigma weight residual -30.00 -86.39 56.39 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 912 0.028 - 0.057: 382 0.057 - 0.085: 118 0.085 - 0.113: 115 0.113 - 0.141: 35 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL B 203 " pdb=" N VAL B 203 " pdb=" C VAL B 203 " pdb=" CB VAL B 203 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1559 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 449 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" CG ASP B 449 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP B 449 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 449 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 449 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" CG ASP A 449 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 449 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 449 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 488 " 0.147 9.50e-02 1.11e+02 6.60e-02 2.70e+00 pdb=" NE ARG B 488 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 488 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 488 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 488 " 0.006 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 32 2.41 - 3.04: 5637 3.04 - 3.66: 14068 3.66 - 4.28: 22381 4.28 - 4.90: 39446 Nonbonded interactions: 81564 Sorted by model distance: nonbonded pdb=" CA UNK C 0 " pdb=" SG CYS C 12 " model vdw 1.792 3.830 nonbonded pdb=" CA UNK D 0 " pdb=" SG CYS D 12 " model vdw 1.792 3.830 nonbonded pdb=" OH TYR A 435 " pdb=" OE2 GLU B 281 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 281 " pdb=" OH TYR B 435 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 84 " pdb=" OG1 THR B 111 " model vdw 2.254 3.040 ... (remaining 81559 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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 : 0.002 0.028 10376 Z= 0.120 Angle : 0.481 4.875 14074 Z= 0.267 Chirality : 0.044 0.141 1562 Planarity : 0.005 0.066 1818 Dihedral : 16.319 80.534 3854 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 21.37 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1256 helix: 0.82 (0.36), residues: 218 sheet: 1.06 (0.26), residues: 402 loop : -0.47 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 488 TYR 0.010 0.001 TYR B 391 PHE 0.011 0.001 PHE B 583 TRP 0.010 0.001 TRP B 347 HIS 0.002 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (10376) covalent geometry : angle 0.48108 / 0.27 (14074) hydrogen bonds : bond 0.12840 / 8.87 ( 344) hydrogen bonds : angle 5.15727 / 3.49 ( 888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1098 time to fit residues: 23.2727 Evaluate side-chains 143 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.097212 restraints weight = 11424.575| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.78 r_work: 0.2784 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10376 Z= 0.185 Angle : 0.549 5.734 14074 Z= 0.288 Chirality : 0.047 0.139 1562 Planarity : 0.005 0.038 1818 Dihedral : 4.277 20.992 1358 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.63 % Allowed : 18.65 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1256 helix: 1.09 (0.37), residues: 206 sheet: 0.89 (0.26), residues: 410 loop : -0.44 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.011 0.001 TYR A 391 PHE 0.014 0.002 PHE B 583 TRP 0.007 0.001 TRP A 659 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (10376) covalent geometry : angle 0.54862 / 0.29 (14074) hydrogen bonds : bond 0.04667 / 3.17 ( 344) hydrogen bonds : angle 4.89799 / 3.33 ( 888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.348 Fit side-chains REVERT: A 19 CYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7958 (m) REVERT: B 19 CYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7969 (m) outliers start: 30 outliers final: 24 residues processed: 175 average time/residue: 0.0892 time to fit residues: 22.5031 Evaluate side-chains 179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.099527 restraints weight = 11419.059| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.84 r_work: 0.2797 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10376 Z= 0.110 Angle : 0.474 4.856 14074 Z= 0.250 Chirality : 0.044 0.131 1562 Planarity : 0.004 0.037 1818 Dihedral : 4.045 19.907 1358 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.45 % Allowed : 19.26 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1256 helix: 1.21 (0.38), residues: 206 sheet: 0.99 (0.26), residues: 410 loop : -0.39 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.011 0.001 TYR B 391 PHE 0.011 0.001 PHE A 583 TRP 0.007 0.001 TRP A 347 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (10376) covalent geometry : angle 0.47424 / 0.25 (14074) hydrogen bonds : bond 0.03840 / 2.61 ( 344) hydrogen bonds : angle 4.67725 / 3.17 ( 888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.282 Fit side-chains REVERT: A 19 CYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7980 (m) REVERT: A 274 THR cc_start: 0.8888 (m) cc_final: 0.8498 (p) REVERT: A 570 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8403 (mp) REVERT: B 19 CYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7981 (m) REVERT: B 274 THR cc_start: 0.8884 (m) cc_final: 0.8492 (p) REVERT: B 570 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8402 (mp) REVERT: B 626 GLN cc_start: 0.8622 (mt0) cc_final: 0.8221 (mt0) outliers start: 28 outliers final: 14 residues processed: 173 average time/residue: 0.0796 time to fit residues: 20.0661 Evaluate side-chains 164 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097970 restraints weight = 11498.738| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.81 r_work: 0.2775 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10376 Z= 0.137 Angle : 0.505 7.467 14074 Z= 0.262 Chirality : 0.045 0.134 1562 Planarity : 0.004 0.038 1818 Dihedral : 4.132 20.472 1358 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.06 % Allowed : 19.61 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1256 helix: 1.12 (0.37), residues: 206 sheet: 0.97 (0.26), residues: 410 loop : -0.39 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.011 0.001 TYR A 391 PHE 0.013 0.001 PHE A 583 TRP 0.007 0.001 TRP A 347 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (10376) covalent geometry : angle 0.50475 / 0.26 (14074) hydrogen bonds : bond 0.03974 / 2.71 ( 344) hydrogen bonds : angle 4.68997 / 3.18 ( 888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.417 Fit side-chains REVERT: A 19 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8017 (m) REVERT: A 274 THR cc_start: 0.8779 (m) cc_final: 0.8465 (p) REVERT: A 626 GLN cc_start: 0.8628 (mt0) cc_final: 0.8226 (mt0) REVERT: B 19 CYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8002 (m) REVERT: B 237 TYR cc_start: 0.9159 (m-80) cc_final: 0.8955 (m-80) REVERT: B 274 THR cc_start: 0.8780 (m) cc_final: 0.8477 (p) REVERT: B 626 GLN cc_start: 0.8626 (mt0) cc_final: 0.8224 (mt0) outliers start: 35 outliers final: 27 residues processed: 174 average time/residue: 0.0805 time to fit residues: 20.2956 Evaluate side-chains 174 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 122 optimal weight: 0.0370 chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.100186 restraints weight = 11389.069| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.73 r_work: 0.2801 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10376 Z= 0.112 Angle : 0.481 6.545 14074 Z= 0.251 Chirality : 0.045 0.133 1562 Planarity : 0.004 0.037 1818 Dihedral : 4.036 19.973 1358 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.50 % Allowed : 19.35 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1256 helix: 1.17 (0.37), residues: 206 sheet: 1.03 (0.26), residues: 410 loop : -0.37 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.011 0.001 TYR B 391 PHE 0.011 0.001 PHE A 583 TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (10376) covalent geometry : angle 0.48082 / 0.25 (14074) hydrogen bonds : bond 0.03712 / 2.53 ( 344) hydrogen bonds : angle 4.62394 / 3.13 ( 888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.295 Fit side-chains REVERT: A 19 CYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8034 (m) REVERT: A 274 THR cc_start: 0.8734 (m) cc_final: 0.8494 (p) REVERT: A 570 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 626 GLN cc_start: 0.8625 (mt0) cc_final: 0.8240 (mt0) REVERT: B 19 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8016 (m) REVERT: B 274 THR cc_start: 0.8724 (m) cc_final: 0.8458 (p) REVERT: B 570 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 626 GLN cc_start: 0.8632 (mt0) cc_final: 0.8248 (mt0) outliers start: 40 outliers final: 29 residues processed: 174 average time/residue: 0.0812 time to fit residues: 20.1763 Evaluate side-chains 177 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.131752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.099826 restraints weight = 11531.519| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.81 r_work: 0.2813 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10376 Z= 0.105 Angle : 0.471 6.057 14074 Z= 0.246 Chirality : 0.044 0.136 1562 Planarity : 0.004 0.037 1818 Dihedral : 3.964 19.827 1358 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.06 % Allowed : 20.23 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1256 helix: 1.21 (0.37), residues: 206 sheet: 1.02 (0.26), residues: 410 loop : -0.36 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.010 0.001 TYR B 391 PHE 0.012 0.001 PHE A 583 TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.10 (10376) covalent geometry : angle 0.47078 / 0.25 (14074) hydrogen bonds : bond 0.03581 / 2.44 ( 344) hydrogen bonds : angle 4.59187 / 3.11 ( 888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.373 Fit side-chains REVERT: A 19 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 570 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 626 GLN cc_start: 0.8611 (mt0) cc_final: 0.8217 (mt0) REVERT: B 19 CYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7970 (m) REVERT: B 570 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (mp) REVERT: B 626 GLN cc_start: 0.8621 (mt0) cc_final: 0.8232 (mt0) outliers start: 35 outliers final: 28 residues processed: 174 average time/residue: 0.0831 time to fit residues: 21.1049 Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.128040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.096600 restraints weight = 11483.411| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.81 r_work: 0.2749 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10376 Z= 0.189 Angle : 0.552 6.953 14074 Z= 0.287 Chirality : 0.047 0.143 1562 Planarity : 0.005 0.038 1818 Dihedral : 4.319 21.172 1358 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.12 % Allowed : 19.26 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1256 helix: 0.98 (0.37), residues: 206 sheet: 0.91 (0.26), residues: 410 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.011 0.001 TYR A 391 PHE 0.014 0.002 PHE A 583 TRP 0.007 0.001 TRP B 347 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 (10376) covalent geometry : angle 0.55188 / 0.29 (14074) hydrogen bonds : bond 0.04342 / 2.95 ( 344) hydrogen bonds : angle 4.79518 / 3.25 ( 888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.258 Fit side-chains REVERT: A 19 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 378 GLU cc_start: 0.7174 (mp0) cc_final: 0.6971 (mp0) REVERT: A 626 GLN cc_start: 0.8636 (mt0) cc_final: 0.8244 (mt0) REVERT: B 19 CYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7995 (m) REVERT: B 378 GLU cc_start: 0.7170 (mp0) cc_final: 0.6967 (mp0) REVERT: B 626 GLN cc_start: 0.8636 (mt0) cc_final: 0.8242 (mt0) outliers start: 47 outliers final: 39 residues processed: 177 average time/residue: 0.0831 time to fit residues: 21.2486 Evaluate side-chains 182 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 0.0040 chunk 53 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.130332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098965 restraints weight = 11407.569| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.74 r_work: 0.2808 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10376 Z= 0.115 Angle : 0.486 6.014 14074 Z= 0.255 Chirality : 0.045 0.141 1562 Planarity : 0.004 0.037 1818 Dihedral : 4.099 20.530 1358 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.42 % Allowed : 19.96 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1256 helix: 1.09 (0.38), residues: 206 sheet: 0.97 (0.26), residues: 410 loop : -0.40 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.011 0.001 TYR B 391 PHE 0.011 0.001 PHE B 583 TRP 0.008 0.001 TRP B 347 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10376) covalent geometry : angle 0.48606 / 0.25 (14074) hydrogen bonds : bond 0.03716 / 2.53 ( 344) hydrogen bonds : angle 4.64652 / 3.14 ( 888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.306 Fit side-chains REVERT: A 19 CYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7999 (m) REVERT: A 378 GLU cc_start: 0.7036 (mp0) cc_final: 0.6822 (mp0) REVERT: A 570 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 626 GLN cc_start: 0.8612 (mt0) cc_final: 0.8223 (mt0) REVERT: B 19 CYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7939 (m) REVERT: B 80 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7911 (mtp) REVERT: B 570 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8371 (mp) REVERT: B 626 GLN cc_start: 0.8618 (mt0) cc_final: 0.8228 (mt0) outliers start: 39 outliers final: 33 residues processed: 171 average time/residue: 0.0765 time to fit residues: 19.2043 Evaluate side-chains 180 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 0.0010 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.096322 restraints weight = 11481.283| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.80 r_work: 0.2745 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10376 Z= 0.194 Angle : 0.561 6.774 14074 Z= 0.293 Chirality : 0.048 0.145 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.371 21.249 1358 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.85 % Allowed : 20.40 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1256 helix: 0.86 (0.37), residues: 206 sheet: 0.89 (0.26), residues: 410 loop : -0.51 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.011 0.001 TYR B 391 PHE 0.014 0.002 PHE B 583 TRP 0.007 0.001 TRP A 347 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.19 (10376) covalent geometry : angle 0.56116 / 0.29 (14074) hydrogen bonds : bond 0.04388 / 2.99 ( 344) hydrogen bonds : angle 4.83325 / 3.27 ( 888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.300 Fit side-chains REVERT: A 19 CYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7959 (m) REVERT: A 378 GLU cc_start: 0.7169 (mp0) cc_final: 0.6954 (mp0) REVERT: A 626 GLN cc_start: 0.8659 (mt0) cc_final: 0.8271 (mt0) REVERT: B 19 CYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7961 (m) REVERT: B 80 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7992 (mtp) REVERT: B 378 GLU cc_start: 0.7161 (mp0) cc_final: 0.6945 (mp0) REVERT: B 626 GLN cc_start: 0.8663 (mt0) cc_final: 0.8272 (mt0) outliers start: 44 outliers final: 40 residues processed: 174 average time/residue: 0.0852 time to fit residues: 21.3129 Evaluate side-chains 184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 80 optimal weight: 0.0980 chunk 40 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100269 restraints weight = 11342.519| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.73 r_work: 0.2830 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10376 Z= 0.098 Angle : 0.474 5.780 14074 Z= 0.250 Chirality : 0.044 0.140 1562 Planarity : 0.004 0.037 1818 Dihedral : 4.013 19.800 1358 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.50 % Allowed : 20.75 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1256 helix: 1.03 (0.37), residues: 206 sheet: 1.03 (0.26), residues: 410 loop : -0.40 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.010 0.001 TYR B 391 PHE 0.011 0.001 PHE A 583 TRP 0.008 0.001 TRP A 347 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (10376) covalent geometry : angle 0.47384 / 0.25 (14074) hydrogen bonds : bond 0.03509 / 2.39 ( 344) hydrogen bonds : angle 4.60480 / 3.11 ( 888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.245 Fit side-chains REVERT: A 19 CYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7971 (m) REVERT: A 278 GLU cc_start: 0.8063 (pm20) cc_final: 0.7835 (pm20) REVERT: A 626 GLN cc_start: 0.8609 (mt0) cc_final: 0.8222 (mt0) REVERT: B 19 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 80 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7830 (mtp) REVERT: B 626 GLN cc_start: 0.8615 (mt0) cc_final: 0.8231 (mt0) outliers start: 40 outliers final: 32 residues processed: 171 average time/residue: 0.0909 time to fit residues: 22.1435 Evaluate side-chains 180 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 611 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.095033 restraints weight = 11502.283| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.80 r_work: 0.2731 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10376 Z= 0.249 Angle : 0.618 7.070 14074 Z= 0.320 Chirality : 0.050 0.147 1562 Planarity : 0.005 0.038 1818 Dihedral : 4.547 21.708 1358 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.59 % Allowed : 20.32 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.24), residues: 1256 helix: 0.70 (0.37), residues: 206 sheet: 0.85 (0.26), residues: 410 loop : -0.52 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 383 TYR 0.012 0.001 TYR B 391 PHE 0.015 0.002 PHE A 583 TRP 0.007 0.002 TRP A 347 HIS 0.007 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.25 (10376) covalent geometry : angle 0.61799 / 0.32 (14074) hydrogen bonds : bond 0.04779 / 3.24 ( 344) hydrogen bonds : angle 4.90335 / 3.32 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.50 seconds wall clock time: 40 minutes 35.75 seconds (2435.75 seconds total)