Starting phenix.real_space_refine on Sat Aug 23 06:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8u_19011/08_2025/8r8u_19011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8u_19011/08_2025/8r8u_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_19011/08_2025/8r8u_19011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8u_19011/08_2025/8r8u_19011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r8u_19011/08_2025/8r8u_19011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8u_19011/08_2025/8r8u_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.91, per 1000 atoms: 0.19 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: 0.83 Conformation dependent library (CDL) restraints added in 377.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.31 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: 1.30 Time building geometry restraints manager: 1.11 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 aren 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 covalent geometry : bond 0.00229 (10376) covalent geometry : angle 0.48108 (14074) hydrogen bonds : bond 0.12840 ( 344) hydrogen bonds : angle 5.15727 ( 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 : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0915 time to fit residues: 19.4114 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 : 0.274 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.0570 chunk 51 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3369 r_free = 0.3369 target = 0.131149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100254 restraints weight = 11310.200| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.67 r_work: 0.2818 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0566 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 : 0.478 4.850 14074 Z= 0.252 Chirality : 0.044 0.135 1562 Planarity : 0.004 0.037 1818 Dihedral : 3.945 19.314 1358 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.58 % Allowed : 19.79 % 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 aren not related in a simple way. whole: 0.55 (0.24), residues: 1256 helix: 1.28 (0.37), residues: 206 sheet: 1.01 (0.26), residues: 410 loop : -0.33 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 383 TYR 0.009 0.001 TYR A 391 PHE 0.012 0.001 PHE B 583 TRP 0.007 0.001 TRP A 659 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00276 (10376) covalent geometry : angle 0.47796 (14074) hydrogen bonds : bond 0.04073 ( 344) hydrogen bonds : angle 4.75166 ( 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 177 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.256 Fit side-chains REVERT: A 19 CYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7947 (m) REVERT: B 19 CYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7942 (m) outliers start: 18 outliers final: 8 residues processed: 171 average time/residue: 0.0865 time to fit residues: 20.9034 Evaluate side-chains 163 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 334 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: 1.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097424 restraints weight = 11390.668| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.83 r_work: 0.2768 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10376 Z= 0.147 Angle : 0.514 7.312 14074 Z= 0.267 Chirality : 0.046 0.136 1562 Planarity : 0.004 0.038 1818 Dihedral : 4.150 20.691 1358 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.80 % Allowed : 18.83 % Favored : 78.37 % 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 aren not related in a simple way. whole: 0.44 (0.24), residues: 1256 helix: 1.15 (0.37), residues: 206 sheet: 0.94 (0.26), residues: 410 loop : -0.40 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.010 0.001 TYR A 391 PHE 0.012 0.001 PHE B 583 TRP 0.007 0.001 TRP A 347 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00368 (10376) covalent geometry : angle 0.51428 (14074) hydrogen bonds : bond 0.04187 ( 344) hydrogen bonds : angle 4.76815 ( 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 188 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.281 Fit side-chains REVERT: A 19 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7968 (m) REVERT: A 80 MET cc_start: 0.8114 (mtp) cc_final: 0.7911 (mtp) REVERT: A 369 ASP cc_start: 0.8268 (t70) cc_final: 0.8061 (t70) REVERT: B 19 CYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7981 (m) REVERT: B 80 MET cc_start: 0.8111 (mtp) cc_final: 0.7908 (mtp) REVERT: B 369 ASP cc_start: 0.8273 (t70) cc_final: 0.8061 (t70) outliers start: 32 outliers final: 25 residues processed: 176 average time/residue: 0.0783 time to fit residues: 19.9696 Evaluate side-chains 180 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 281 GLU 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 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 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 281 GLU 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 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: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095554 restraints weight = 11513.547| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.76 r_work: 0.2772 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1016 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= 0.196 Angle : 0.562 7.498 14074 Z= 0.291 Chirality : 0.048 0.139 1562 Planarity : 0.005 0.040 1818 Dihedral : 4.428 21.788 1358 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.12 % Allowed : 18.56 % 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 aren not related in a simple way. whole: 0.27 (0.24), residues: 1256 helix: 0.96 (0.37), residues: 206 sheet: 0.87 (0.26), residues: 410 loop : -0.51 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.012 0.001 TYR B 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 covalent geometry : bond 0.00499 (10376) covalent geometry : angle 0.56176 (14074) hydrogen bonds : bond 0.04593 ( 344) hydrogen bonds : angle 4.91631 ( 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 204 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.351 Fit side-chains REVERT: A 19 CYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7978 (m) REVERT: A 80 MET cc_start: 0.8179 (mtp) cc_final: 0.7870 (mtp) REVERT: A 237 TYR cc_start: 0.9134 (m-80) cc_final: 0.8928 (m-80) REVERT: A 626 GLN cc_start: 0.8586 (mt0) cc_final: 0.8180 (mt0) REVERT: B 19 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8010 (m) REVERT: B 237 TYR cc_start: 0.9131 (m-80) cc_final: 0.8926 (m-80) REVERT: B 626 GLN cc_start: 0.8582 (mt0) cc_final: 0.8175 (mt0) outliers start: 47 outliers final: 36 residues processed: 183 average time/residue: 0.0806 time to fit residues: 21.0887 Evaluate side-chains 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 336 ILE 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 91 LYS 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 378 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3348 r_free = 0.3348 target = 0.129512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097546 restraints weight = 11381.410| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.84 r_work: 0.2760 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0951 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= 0.128 Angle : 0.498 6.404 14074 Z= 0.260 Chirality : 0.045 0.134 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.204 21.026 1358 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.42 % Allowed : 19.88 % 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 aren not related in a simple way. whole: 0.37 (0.24), residues: 1256 helix: 1.05 (0.37), residues: 206 sheet: 0.94 (0.26), residues: 410 loop : -0.45 (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 A 391 PHE 0.012 0.001 PHE A 475 TRP 0.007 0.001 TRP A 659 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00317 (10376) covalent geometry : angle 0.49845 (14074) hydrogen bonds : bond 0.03997 ( 344) hydrogen bonds : angle 4.77495 ( 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 194 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.443 Fit side-chains REVERT: A 19 CYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7951 (m) REVERT: A 80 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7772 (mtp) REVERT: A 626 GLN cc_start: 0.8592 (mt0) cc_final: 0.8188 (mt0) REVERT: B 19 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 80 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7778 (mtp) REVERT: B 626 GLN cc_start: 0.8593 (mt0) cc_final: 0.8191 (mt0) outliers start: 39 outliers final: 30 residues processed: 175 average time/residue: 0.1050 time to fit residues: 25.7783 Evaluate side-chains 183 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 80 MET 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 413 SER Chi-restraints excluded: chain A residue 429 LEU 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 80 MET Chi-restraints excluded: chain B residue 91 LYS 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 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 429 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 90 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.129750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.097950 restraints weight = 11512.622| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.83 r_work: 0.2778 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0924 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= 0.118 Angle : 0.486 6.029 14074 Z= 0.254 Chirality : 0.045 0.133 1562 Planarity : 0.004 0.039 1818 Dihedral : 4.105 20.632 1358 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.33 % Allowed : 20.58 % 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 aren not related in a simple way. whole: 0.42 (0.24), residues: 1256 helix: 1.11 (0.37), residues: 206 sheet: 0.97 (0.26), residues: 410 loop : -0.42 (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 A 391 PHE 0.011 0.001 PHE A 583 TRP 0.008 0.001 TRP B 347 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00288 (10376) covalent geometry : angle 0.48635 (14074) hydrogen bonds : bond 0.03830 ( 344) hydrogen bonds : angle 4.71081 ( 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 186 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.357 Fit side-chains REVERT: A 19 CYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7917 (m) REVERT: A 80 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7781 (mtp) REVERT: A 274 THR cc_start: 0.8697 (m) cc_final: 0.8442 (p) REVERT: A 626 GLN cc_start: 0.8620 (mt0) cc_final: 0.8225 (mt0) REVERT: B 19 CYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7926 (m) REVERT: B 80 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7775 (mtp) REVERT: B 274 THR cc_start: 0.8707 (m) cc_final: 0.8447 (p) REVERT: B 626 GLN cc_start: 0.8616 (mt0) cc_final: 0.8221 (mt0) outliers start: 38 outliers final: 29 residues processed: 169 average time/residue: 0.0937 time to fit residues: 22.3870 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 : 0.337 ------------------------------------------------------------------------------- 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 80 MET 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 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 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 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 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 413 SER 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: 3.9990 chunk 38 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.127212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.095680 restraints weight = 11486.161| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.79 r_work: 0.2748 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10376 Z= 0.179 Angle : 0.544 6.586 14074 Z= 0.283 Chirality : 0.047 0.136 1562 Planarity : 0.005 0.040 1818 Dihedral : 4.340 21.209 1358 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.12 % Allowed : 19.70 % Favored : 76.18 % 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 aren not related in a simple way. whole: 0.28 (0.24), residues: 1256 helix: 0.93 (0.37), residues: 206 sheet: 0.91 (0.26), residues: 410 loop : -0.52 (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 A 583 TRP 0.007 0.001 TRP A 347 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00454 (10376) covalent geometry : angle 0.54426 (14074) hydrogen bonds : bond 0.04374 ( 344) hydrogen bonds : angle 4.84608 ( 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 200 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.437 Fit side-chains REVERT: A 19 CYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7972 (m) REVERT: A 80 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7825 (mtp) REVERT: A 274 THR cc_start: 0.8817 (m) cc_final: 0.8480 (p) REVERT: A 626 GLN cc_start: 0.8659 (mt0) cc_final: 0.8277 (mt0) REVERT: B 19 CYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7968 (m) REVERT: B 80 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: B 274 THR cc_start: 0.8784 (m) cc_final: 0.8454 (p) REVERT: B 626 GLN cc_start: 0.8659 (mt0) cc_final: 0.8276 (mt0) outliers start: 47 outliers final: 42 residues processed: 181 average time/residue: 0.1046 time to fit residues: 27.1736 Evaluate side-chains 194 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 80 MET 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 269 ILE 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 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 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 336 ILE Chi-restraints excluded: chain B residue 378 GLU 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 552 LEU 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: 2.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.127353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.095863 restraints weight = 11441.599| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.79 r_work: 0.2755 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10376 Z= 0.166 Angle : 0.532 6.396 14074 Z= 0.277 Chirality : 0.046 0.135 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.333 21.072 1358 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.20 % Allowed : 19.53 % Favored : 76.27 % 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 aren not related in a simple way. whole: 0.28 (0.24), residues: 1256 helix: 0.91 (0.37), residues: 206 sheet: 0.94 (0.26), residues: 410 loop : -0.54 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 383 TYR 0.011 0.001 TYR B 391 PHE 0.013 0.001 PHE B 583 TRP 0.008 0.001 TRP B 347 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00419 (10376) covalent geometry : angle 0.53153 (14074) hydrogen bonds : bond 0.04276 ( 344) hydrogen bonds : angle 4.83354 ( 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 198 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.422 Fit side-chains REVERT: A 19 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7946 (m) REVERT: A 80 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7815 (mtp) REVERT: A 274 THR cc_start: 0.8847 (m) cc_final: 0.8500 (p) REVERT: A 626 GLN cc_start: 0.8655 (mt0) cc_final: 0.8270 (mt0) REVERT: B 19 CYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7946 (m) REVERT: B 80 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: B 274 THR cc_start: 0.8835 (m) cc_final: 0.8496 (p) REVERT: B 626 GLN cc_start: 0.8654 (mt0) cc_final: 0.8269 (mt0) outliers start: 48 outliers final: 41 residues processed: 180 average time/residue: 0.1022 time to fit residues: 26.4189 Evaluate side-chains 193 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 80 MET 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 269 ILE 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 552 LEU Chi-restraints excluded: chain A residue 570 LEU 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 269 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 GLU 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 552 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 611 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3345 r_free = 0.3345 target = 0.129365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.097966 restraints weight = 11415.959| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.79 r_work: 0.2774 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1005 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 : 0.491 5.785 14074 Z= 0.257 Chirality : 0.045 0.133 1562 Planarity : 0.004 0.039 1818 Dihedral : 4.122 20.263 1358 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.50 % Allowed : 20.14 % Favored : 76.36 % 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 aren not related in a simple way. whole: 0.40 (0.24), residues: 1256 helix: 1.03 (0.37), residues: 206 sheet: 1.01 (0.26), residues: 410 loop : -0.46 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 383 TYR 0.011 0.001 TYR A 391 PHE 0.011 0.001 PHE B 475 TRP 0.008 0.001 TRP B 347 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00280 (10376) covalent geometry : angle 0.49072 (14074) hydrogen bonds : bond 0.03797 ( 344) hydrogen bonds : angle 4.71162 ( 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 190 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.481 Fit side-chains REVERT: A 19 CYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7906 (m) REVERT: A 80 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7729 (mtp) REVERT: A 274 THR cc_start: 0.8788 (m) cc_final: 0.8504 (p) REVERT: A 626 GLN cc_start: 0.8612 (mt0) cc_final: 0.8224 (mt0) REVERT: A 634 PHE cc_start: 0.8771 (m-80) cc_final: 0.8528 (m-80) REVERT: B 19 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7904 (m) REVERT: B 80 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: B 274 THR cc_start: 0.8760 (m) cc_final: 0.8489 (p) REVERT: B 626 GLN cc_start: 0.8619 (mt0) cc_final: 0.8234 (mt0) outliers start: 40 outliers final: 34 residues processed: 173 average time/residue: 0.1076 time to fit residues: 26.6975 Evaluate side-chains 184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 80 MET 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 269 ILE 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 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 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 378 GLU 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: 6.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 44 optimal weight: 0.0370 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3362 r_free = 0.3362 target = 0.130905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.098953 restraints weight = 11298.752| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.79 r_work: 0.2803 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0950 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= 0.092 Angle : 0.464 5.486 14074 Z= 0.244 Chirality : 0.044 0.131 1562 Planarity : 0.004 0.039 1818 Dihedral : 3.926 19.209 1358 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.89 % Allowed : 21.19 % Favored : 75.92 % 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 aren not related in a simple way. whole: 0.51 (0.24), residues: 1256 helix: 1.07 (0.37), residues: 206 sheet: 1.12 (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 B 383 TYR 0.010 0.001 TYR B 391 PHE 0.010 0.001 PHE A 583 TRP 0.009 0.001 TRP A 347 HIS 0.002 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00215 (10376) covalent geometry : angle 0.46352 (14074) hydrogen bonds : bond 0.03450 ( 344) hydrogen bonds : angle 4.59850 ( 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 185 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.423 Fit side-chains REVERT: A 19 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7874 (m) REVERT: A 274 THR cc_start: 0.8688 (m) cc_final: 0.8481 (p) REVERT: A 626 GLN cc_start: 0.8595 (mt0) cc_final: 0.8208 (mt0) REVERT: A 634 PHE cc_start: 0.8861 (m-80) cc_final: 0.8613 (m-80) REVERT: B 19 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7865 (m) REVERT: B 626 GLN cc_start: 0.8609 (mt0) cc_final: 0.8223 (mt0) outliers start: 33 outliers final: 27 residues processed: 168 average time/residue: 0.1192 time to fit residues: 27.5225 Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 260 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR 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 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 534 THR 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: 7.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.096894 restraints weight = 11485.405| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.73 r_work: 0.2752 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10376 Z= 0.176 Angle : 0.546 6.367 14074 Z= 0.286 Chirality : 0.047 0.135 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.265 20.886 1358 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.15 % Allowed : 20.23 % 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 aren not related in a simple way. whole: 0.31 (0.24), residues: 1256 helix: 0.66 (0.37), residues: 218 sheet: 1.09 (0.26), residues: 406 loop : -0.53 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 383 TYR 0.010 0.001 TYR B 391 PHE 0.013 0.001 PHE B 583 TRP 0.008 0.001 TRP A 347 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00445 (10376) covalent geometry : angle 0.54633 (14074) hydrogen bonds : bond 0.04313 ( 344) hydrogen bonds : angle 4.77824 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.16 seconds wall clock time: 45 minutes 3.89 seconds (2703.89 seconds total)