Starting phenix.real_space_refine on Sun Dec 29 08:05:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8u_19011/12_2024/8r8u_19011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8u_19011/12_2024/8r8u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r8u_19011/12_2024/8r8u_19011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8u_19011/12_2024/8r8u_19011.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8u_19011/12_2024/8r8u_19011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8u_19011/12_2024/8r8u_19011.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.37, per 1000 atoms: 0.63 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.63 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: 3.98 Time building geometry restraints manager: 2.79 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: 0.00 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: 1.880 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.170 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.790 ------------------------------------------------------------------------------- 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= 0.152 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (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 TRP 0.010 0.001 TRP B 347 HIS 0.002 0.001 HIS A 236 PHE 0.011 0.001 PHE B 583 TYR 0.010 0.001 TYR B 391 ARG 0.003 0.000 ARG B 488 *********************** 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 : 1.253 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2638 time to fit residues: 55.3493 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 : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10376 Z= 0.215 Angle : 0.497 4.881 14074 Z= 0.261 Chirality : 0.045 0.135 1562 Planarity : 0.004 0.037 1818 Dihedral : 4.037 19.928 1358 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.84 % Allowed : 19.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1256 helix: 1.23 (0.37), residues: 206 sheet: 0.97 (0.26), residues: 410 loop : -0.36 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 659 HIS 0.004 0.001 HIS B 202 PHE 0.013 0.001 PHE B 583 TYR 0.010 0.001 TYR A 391 ARG 0.004 0.000 ARG A 372 *********************** 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 179 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.242 Fit side-chains REVERT: A 19 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7917 (m) REVERT: B 19 CYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7922 (m) outliers start: 21 outliers final: 15 residues processed: 170 average time/residue: 0.2396 time to fit residues: 58.1529 Evaluate side-chains 170 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10376 Z= 0.304 Angle : 0.545 6.009 14074 Z= 0.284 Chirality : 0.047 0.138 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.333 21.260 1358 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.33 % Allowed : 18.74 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1256 helix: 1.02 (0.37), residues: 206 sheet: 0.89 (0.26), residues: 410 loop : -0.46 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.002 PHE A 583 TYR 0.011 0.001 TYR A 391 ARG 0.005 0.000 ARG B 372 *********************** 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 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.238 Fit side-chains REVERT: A 19 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7973 (m) REVERT: B 19 CYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7970 (m) outliers start: 38 outliers final: 28 residues processed: 174 average time/residue: 0.2246 time to fit residues: 55.6699 Evaluate side-chains 178 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 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 91 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 ILE 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 113 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0984 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= 0.293 Angle : 0.537 5.888 14074 Z= 0.280 Chirality : 0.047 0.135 1562 Planarity : 0.005 0.040 1818 Dihedral : 4.360 21.421 1358 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.47 % Allowed : 18.74 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1256 helix: 0.96 (0.37), residues: 206 sheet: 0.89 (0.26), residues: 410 loop : -0.50 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.001 PHE B 475 TYR 0.012 0.001 TYR B 391 ARG 0.004 0.000 ARG B 383 *********************** 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 202 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 1.187 Fit side-chains REVERT: A 19 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7998 (m) REVERT: A 626 GLN cc_start: 0.8532 (mt0) cc_final: 0.8138 (mt0) REVERT: B 19 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8001 (m) REVERT: B 626 GLN cc_start: 0.8535 (mt0) cc_final: 0.8143 (mt0) outliers start: 51 outliers final: 40 residues processed: 184 average time/residue: 0.2204 time to fit residues: 58.3178 Evaluate side-chains 187 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 198 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0919 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= 0.203 Angle : 0.495 6.385 14074 Z= 0.259 Chirality : 0.045 0.134 1562 Planarity : 0.005 0.039 1818 Dihedral : 4.182 20.627 1358 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.24 % Allowed : 19.96 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1256 helix: 1.05 (0.37), residues: 206 sheet: 0.97 (0.26), residues: 410 loop : -0.44 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.001 PHE B 475 TYR 0.011 0.001 TYR B 391 ARG 0.004 0.000 ARG A 383 *********************** 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 188 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.121 Fit side-chains REVERT: A 19 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7963 (m) REVERT: A 274 THR cc_start: 0.8823 (m) cc_final: 0.8509 (p) REVERT: A 626 GLN cc_start: 0.8527 (mt0) cc_final: 0.8137 (mt0) REVERT: B 19 CYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7961 (m) REVERT: B 626 GLN cc_start: 0.8529 (mt0) cc_final: 0.8141 (mt0) outliers start: 37 outliers final: 31 residues processed: 172 average time/residue: 0.2352 time to fit residues: 56.7177 Evaluate side-chains 178 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 198 THR 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 269 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 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 434 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10376 Z= 0.388 Angle : 0.590 7.703 14074 Z= 0.305 Chirality : 0.048 0.143 1562 Planarity : 0.005 0.042 1818 Dihedral : 4.526 21.721 1358 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.55 % Allowed : 19.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1256 helix: 0.78 (0.37), residues: 206 sheet: 0.88 (0.26), residues: 410 loop : -0.58 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 347 HIS 0.006 0.001 HIS B 202 PHE 0.015 0.002 PHE B 583 TYR 0.012 0.001 TYR B 391 ARG 0.005 0.000 ARG B 383 *********************** 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 200 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.045 Fit side-chains REVERT: A 19 CYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8004 (m) REVERT: A 274 THR cc_start: 0.8845 (m) cc_final: 0.8481 (p) REVERT: A 626 GLN cc_start: 0.8575 (mt0) cc_final: 0.8187 (mt0) REVERT: B 19 CYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8006 (m) REVERT: B 626 GLN cc_start: 0.8578 (mt0) cc_final: 0.8190 (mt0) outliers start: 52 outliers final: 44 residues processed: 188 average time/residue: 0.2323 time to fit residues: 63.0642 Evaluate side-chains 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 THR 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 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 91 LYS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 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 413 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 611 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0973 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= 0.173 Angle : 0.485 6.572 14074 Z= 0.254 Chirality : 0.044 0.133 1562 Planarity : 0.005 0.044 1818 Dihedral : 4.180 20.672 1358 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.24 % Allowed : 20.23 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1256 helix: 1.03 (0.38), residues: 206 sheet: 0.95 (0.26), residues: 410 loop : -0.48 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE B 475 TYR 0.011 0.001 TYR B 391 ARG 0.004 0.000 ARG A 383 *********************** 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 182 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.099 Fit side-chains REVERT: A 19 CYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7955 (m) REVERT: A 274 THR cc_start: 0.8810 (m) cc_final: 0.8544 (p) REVERT: A 626 GLN cc_start: 0.8549 (mt0) cc_final: 0.8167 (mt0) REVERT: B 19 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7965 (m) REVERT: B 274 THR cc_start: 0.8808 (m) cc_final: 0.8547 (p) REVERT: B 626 GLN cc_start: 0.8549 (mt0) cc_final: 0.8169 (mt0) outliers start: 37 outliers final: 28 residues processed: 169 average time/residue: 0.2200 time to fit residues: 53.0824 Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 198 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 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 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 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10376 Z= 0.255 Angle : 0.527 6.948 14074 Z= 0.274 Chirality : 0.046 0.137 1562 Planarity : 0.005 0.045 1818 Dihedral : 4.283 20.880 1358 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.68 % Allowed : 19.79 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1256 helix: 0.93 (0.37), residues: 206 sheet: 0.95 (0.26), residues: 410 loop : -0.49 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.004 0.001 HIS B 202 PHE 0.013 0.001 PHE B 583 TYR 0.011 0.001 TYR B 391 ARG 0.005 0.000 ARG B 383 *********************** 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 191 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.750 Fit side-chains REVERT: A 19 CYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7979 (m) REVERT: A 274 THR cc_start: 0.8828 (m) cc_final: 0.8534 (p) REVERT: A 626 GLN cc_start: 0.8555 (mt0) cc_final: 0.8178 (mt0) REVERT: B 19 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 274 THR cc_start: 0.8802 (m) cc_final: 0.8511 (p) REVERT: B 626 GLN cc_start: 0.8531 (mt0) cc_final: 0.8148 (mt0) outliers start: 42 outliers final: 39 residues processed: 178 average time/residue: 0.2565 time to fit residues: 65.3324 Evaluate side-chains 190 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 THR 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 281 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 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 91 LYS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 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 113 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.0000 chunk 119 optimal weight: 0.2980 overall best weight: 0.3362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0930 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= 0.132 Angle : 0.460 6.060 14074 Z= 0.241 Chirality : 0.044 0.133 1562 Planarity : 0.004 0.046 1818 Dihedral : 3.925 18.997 1358 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.24 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1256 helix: 1.09 (0.37), residues: 206 sheet: 1.07 (0.26), residues: 410 loop : -0.38 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 659 HIS 0.002 0.000 HIS A 202 PHE 0.010 0.001 PHE A 475 TYR 0.010 0.001 TYR B 391 ARG 0.005 0.000 ARG A 383 *********************** 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 184 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.199 Fit side-chains REVERT: A 19 CYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 80 MET cc_start: 0.8093 (mtp) cc_final: 0.7865 (mtp) REVERT: A 274 THR cc_start: 0.8675 (m) cc_final: 0.8455 (p) REVERT: A 626 GLN cc_start: 0.8513 (mt0) cc_final: 0.8131 (mt0) REVERT: B 19 CYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7937 (m) REVERT: B 274 THR cc_start: 0.8675 (m) cc_final: 0.8459 (p) REVERT: B 626 GLN cc_start: 0.8513 (mt0) cc_final: 0.8132 (mt0) outliers start: 37 outliers final: 26 residues processed: 169 average time/residue: 0.2385 time to fit residues: 56.7024 Evaluate side-chains 168 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 434 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain 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 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS 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 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10376 Z= 0.194 Angle : 0.493 6.383 14074 Z= 0.258 Chirality : 0.045 0.132 1562 Planarity : 0.005 0.047 1818 Dihedral : 4.022 19.641 1358 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.98 % Allowed : 20.58 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1256 helix: 0.78 (0.37), residues: 218 sheet: 1.16 (0.26), residues: 406 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE B 475 TYR 0.011 0.001 TYR B 391 ARG 0.005 0.000 ARG A 383 ********************** 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 177 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.166 Fit side-chains REVERT: A 626 GLN cc_start: 0.8512 (mt0) cc_final: 0.8128 (mt0) REVERT: B 19 CYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7881 (m) REVERT: B 626 GLN cc_start: 0.8512 (mt0) cc_final: 0.8126 (mt0) outliers start: 34 outliers final: 31 residues processed: 167 average time/residue: 0.2287 time to fit residues: 54.7637 Evaluate side-chains 174 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 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 251 VAL 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 432 ASP 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 251 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 534 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.130360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.099112 restraints weight = 11320.309| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.77 r_work: 0.2800 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1026 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= 0.176 Angle : 0.487 6.264 14074 Z= 0.255 Chirality : 0.044 0.132 1562 Planarity : 0.004 0.046 1818 Dihedral : 4.010 19.560 1358 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.98 % Allowed : 20.23 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1256 helix: 1.04 (0.38), residues: 206 sheet: 1.08 (0.26), residues: 410 loop : -0.39 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 347 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE B 583 TYR 0.010 0.001 TYR B 391 ARG 0.005 0.000 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.65 seconds wall clock time: 42 minutes 38.53 seconds (2558.53 seconds total)