Starting phenix.real_space_refine on Sun May 18 05:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjt_62375/05_2025/9kjt_62375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjt_62375/05_2025/9kjt_62375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kjt_62375/05_2025/9kjt_62375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjt_62375/05_2025/9kjt_62375.map" model { file = "/net/cci-nas-00/data/ceres_data/9kjt_62375/05_2025/9kjt_62375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjt_62375/05_2025/9kjt_62375.cif" } resolution = 3.84 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= 0.002 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10359 2.51 5 N 2820 2.21 5 O 3162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16413 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5471 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675} Chain: "B" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5471 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675} Chain: "C" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5471 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675} Time building chain proxies: 9.89, per 1000 atoms: 0.60 Number of scatterers: 16413 At special positions: 0 Unit cell: (107.9, 108.73, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3162 8.00 N 2820 7.00 C 10359 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: 4.00 Conformation dependent library (CDL) restraints added in 1.9 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 15 sheets defined 40.9% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 237 through 267 removed outlier: 3.808A pdb=" N PHE A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 6.479A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.672A pdb=" N ILE A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.580A pdb=" N THR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 499 Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.622A pdb=" N VAL A 571 " --> pdb=" O PRO A 567 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 593 " --> pdb=" O MET A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 622 removed outlier: 3.930A pdb=" N ALA A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 653 through 671 removed outlier: 3.975A pdb=" N ASP A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 749 through 752 Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 165 through 179 Processing helix chain 'B' and resid 205 through 210 removed outlier: 4.242A pdb=" N SER B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.905A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 6.116A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 Processing helix chain 'B' and resid 332 through 356 Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.624A pdb=" N ILE B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.788A pdb=" N THR B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 499 Processing helix chain 'B' and resid 534 through 541 Processing helix chain 'B' and resid 567 through 593 removed outlier: 3.667A pdb=" N VAL B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 593 " --> pdb=" O MET B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.339A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 653 through 671 removed outlier: 4.350A pdb=" N ASP B 671 " --> pdb=" O ILE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.660A pdb=" N PHE C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 5.463A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 Processing helix chain 'C' and resid 332 through 356 Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.784A pdb=" N ILE C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 removed outlier: 4.105A pdb=" N THR C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 499 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.727A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 593 " --> pdb=" O MET C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.181A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 653 through 668 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 749 through 753 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.602A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP A 149 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 3.594A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 228 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA A 221 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE A 226 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR A 550 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 526 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.232A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET A 424 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER A 474 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS A 426 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 476 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU A 428 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLU A 478 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'A' and resid 705 through 708 removed outlier: 6.679A pdb=" N LYS A 697 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 686 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 734 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 748 " --> pdb=" O LYS A 734 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG A 746 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG A 738 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG A 744 " --> pdb=" O ARG A 738 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.504A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.871A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.543A pdb=" N GLY B 382 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AB1, first strand: chain 'B' and resid 705 through 708 removed outlier: 7.671A pdb=" N GLY B 693 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE B 689 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET B 695 " --> pdb=" O THR B 687 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 734 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 51 removed outlier: 6.544A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG C 103 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.612A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET C 228 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA C 221 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE C 226 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR C 550 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 370 through 374 removed outlier: 3.584A pdb=" N GLY C 382 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET C 424 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER C 474 " --> pdb=" O MET C 424 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS C 426 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL C 476 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 428 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU C 478 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 606 through 611 Processing sheet with id=AB6, first strand: chain 'C' and resid 705 through 708 removed outlier: 6.956A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE C 689 " --> pdb=" O GLY C 693 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET C 695 " --> pdb=" O THR C 687 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2532 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: 5.47 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5496 1.34 - 1.46: 3349 1.46 - 1.58: 7709 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 16677 Sorted by residual: bond pdb=" CA PHE A 545 " pdb=" CB PHE A 545 " ideal model delta sigma weight residual 1.526 1.495 0.032 1.70e-02 3.46e+03 3.45e+00 bond pdb=" C ALA B 651 " pdb=" N PRO B 652 " ideal model delta sigma weight residual 1.336 1.315 0.021 1.20e-02 6.94e+03 2.95e+00 bond pdb=" C PRO C 90 " pdb=" N SER C 91 " ideal model delta sigma weight residual 1.339 1.260 0.079 5.57e-02 3.22e+02 2.01e+00 bond pdb=" C MET A 96 " pdb=" N PRO A 97 " ideal model delta sigma weight residual 1.339 1.292 0.047 3.40e-02 8.65e+02 1.93e+00 bond pdb=" C MET B 96 " pdb=" N PRO B 97 " ideal model delta sigma weight residual 1.340 1.302 0.038 2.76e-02 1.31e+03 1.90e+00 ... (remaining 16672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 22268 2.36 - 4.73: 256 4.73 - 7.09: 38 7.09 - 9.46: 7 9.46 - 11.82: 3 Bond angle restraints: 22572 Sorted by residual: angle pdb=" CB MET C 657 " pdb=" CG MET C 657 " pdb=" SD MET C 657 " ideal model delta sigma weight residual 112.70 124.52 -11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 123.30 -10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 657 " pdb=" CG MET A 657 " pdb=" SD MET A 657 " ideal model delta sigma weight residual 112.70 122.47 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " ideal model delta sigma weight residual 112.70 122.04 -9.34 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CB MET B 228 " pdb=" CG MET B 228 " pdb=" SD MET B 228 " ideal model delta sigma weight residual 112.70 121.83 -9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 22567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8978 17.88 - 35.77: 985 35.77 - 53.65: 222 53.65 - 71.53: 48 71.53 - 89.42: 45 Dihedral angle restraints: 10278 sinusoidal: 4131 harmonic: 6147 Sorted by residual: dihedral pdb=" CA LYS A 718 " pdb=" C LYS A 718 " pdb=" N HIS A 719 " pdb=" CA HIS A 719 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP C 518 " pdb=" CB ASP C 518 " pdb=" CG ASP C 518 " pdb=" OD1 ASP C 518 " ideal model delta sinusoidal sigma weight residual -30.00 -87.88 57.88 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP B 135 " pdb=" CB ASP B 135 " pdb=" CG ASP B 135 " pdb=" OD1 ASP B 135 " ideal model delta sinusoidal sigma weight residual -30.00 -87.58 57.58 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1735 0.034 - 0.067: 574 0.067 - 0.101: 256 0.101 - 0.134: 62 0.134 - 0.168: 7 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CB THR A 205 " pdb=" CA THR A 205 " pdb=" OG1 THR A 205 " pdb=" CG2 THR A 205 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB THR C 703 " pdb=" CA THR C 703 " pdb=" OG1 THR C 703 " pdb=" CG2 THR C 703 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CB THR B 665 " pdb=" CA THR B 665 " pdb=" OG1 THR B 665 " pdb=" CG2 THR B 665 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 2631 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 683 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C THR C 683 " 0.024 2.00e-02 2.50e+03 pdb=" O THR C 683 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA C 684 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 203 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO B 204 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 221 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 222 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 222 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 222 " -0.018 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2034 2.74 - 3.28: 17653 3.28 - 3.82: 28072 3.82 - 4.36: 32174 4.36 - 4.90: 54336 Nonbonded interactions: 134269 Sorted by model distance: nonbonded pdb=" O ILE A 283 " pdb=" OG1 THR A 287 " model vdw 2.198 3.040 nonbonded pdb=" OG SER C 60 " pdb=" O SER C 70 " model vdw 2.204 3.040 nonbonded pdb=" N GLU A 520 " pdb=" OE1 GLU A 520 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR B 78 " pdb=" OD1 ASP B 160 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLN B 387 " pdb=" NE2 GLN B 392 " model vdw 2.209 3.120 ... (remaining 134264 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.090 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.006 0.079 16677 Z= 0.285 Angle : 0.659 11.824 22572 Z= 0.325 Chirality : 0.042 0.168 2634 Planarity : 0.003 0.034 2931 Dihedral : 16.584 89.419 6318 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.11 % Allowed : 24.06 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.01 (0.19), residues: 2124 helix: 1.91 (0.19), residues: 748 sheet: 0.86 (0.24), residues: 507 loop : -0.52 (0.23), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 184 HIS 0.007 0.001 HIS A 426 PHE 0.013 0.001 PHE A 650 TYR 0.012 0.001 TYR C 699 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.20304 ( 911) hydrogen bonds : angle 7.97201 ( 2532) covalent geometry : bond 0.00596 (16677) covalent geometry : angle 0.65850 (22572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.9297 (OUTLIER) cc_final: 0.8915 (t60) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.2607 time to fit residues: 26.6804 Evaluate side-chains 60 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN C 392 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034891 restraints weight = 100054.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.036038 restraints weight = 71592.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036487 restraints weight = 57705.213| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16677 Z= 0.262 Angle : 0.599 8.814 22572 Z= 0.315 Chirality : 0.044 0.173 2634 Planarity : 0.004 0.031 2931 Dihedral : 3.994 38.597 2296 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.88 % Allowed : 22.96 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.99 (0.19), residues: 2124 helix: 1.98 (0.19), residues: 756 sheet: 0.88 (0.24), residues: 492 loop : -0.65 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 184 HIS 0.003 0.001 HIS A 708 PHE 0.018 0.001 PHE A 650 TYR 0.012 0.001 TYR C 296 ARG 0.007 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 911) hydrogen bonds : angle 5.56136 ( 2532) covalent geometry : bond 0.00557 (16677) covalent geometry : angle 0.59929 (22572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.9000 (t60) REVERT: A 209 MET cc_start: 0.8779 (mmm) cc_final: 0.8522 (mmm) REVERT: A 424 MET cc_start: 0.8251 (ppp) cc_final: 0.7653 (ppp) REVERT: B 376 MET cc_start: 0.8715 (mmm) cc_final: 0.8466 (mmp) REVERT: B 424 MET cc_start: 0.7748 (tmm) cc_final: 0.7395 (tmm) REVERT: C 184 TRP cc_start: 0.9315 (OUTLIER) cc_final: 0.7523 (t60) REVERT: C 209 MET cc_start: 0.8811 (mmm) cc_final: 0.8582 (mmm) REVERT: C 597 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8764 (mtm-85) outliers start: 34 outliers final: 13 residues processed: 92 average time/residue: 0.2888 time to fit residues: 41.4272 Evaluate side-chains 74 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 597 ARG Chi-restraints excluded: chain C residue 619 LYS Chi-restraints excluded: chain C residue 718 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 178 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 143 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 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 = 0.3381 r_free = 0.3381 target = 0.062001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.041429 restraints weight = 102467.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.042699 restraints weight = 64850.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043569 restraints weight = 48004.350| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16677 Z= 0.109 Angle : 0.502 8.242 22572 Z= 0.261 Chirality : 0.043 0.151 2634 Planarity : 0.003 0.035 2931 Dihedral : 3.855 37.673 2294 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.66 % Allowed : 21.85 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.25 (0.19), residues: 2124 helix: 2.27 (0.19), residues: 752 sheet: 0.85 (0.24), residues: 493 loop : -0.45 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS C 304 PHE 0.011 0.001 PHE A 340 TYR 0.013 0.001 TYR A 296 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 911) hydrogen bonds : angle 4.88136 ( 2532) covalent geometry : bond 0.00225 (16677) covalent geometry : angle 0.50163 (22572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9520 (OUTLIER) cc_final: 0.9294 (m) REVERT: A 184 TRP cc_start: 0.9115 (OUTLIER) cc_final: 0.8798 (t60) REVERT: A 209 MET cc_start: 0.8864 (mmm) cc_final: 0.8529 (mmm) REVERT: A 424 MET cc_start: 0.8335 (ppp) cc_final: 0.7539 (ppp) REVERT: A 543 MET cc_start: 0.9213 (ppp) cc_final: 0.8453 (ppp) REVERT: B 376 MET cc_start: 0.8627 (mmm) cc_final: 0.8411 (mmp) REVERT: B 424 MET cc_start: 0.7592 (tmm) cc_final: 0.7099 (tmm) REVERT: B 702 MET cc_start: 0.1029 (mtt) cc_final: 0.0511 (mtt) REVERT: C 81 MET cc_start: 0.8822 (tmm) cc_final: 0.8442 (tmm) REVERT: C 209 MET cc_start: 0.8845 (mmm) cc_final: 0.8525 (mmm) REVERT: C 323 GLN cc_start: 0.9588 (OUTLIER) cc_final: 0.9367 (mp10) REVERT: C 543 MET cc_start: 0.9033 (ppp) cc_final: 0.8148 (ppp) REVERT: C 745 MET cc_start: -0.6746 (ptp) cc_final: -0.6975 (ptp) outliers start: 30 outliers final: 15 residues processed: 92 average time/residue: 0.2893 time to fit residues: 41.9906 Evaluate side-chains 79 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 718 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.041223 restraints weight = 103720.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.042412 restraints weight = 65468.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.043269 restraints weight = 48732.962| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16677 Z= 0.199 Angle : 0.525 8.847 22572 Z= 0.270 Chirality : 0.042 0.145 2634 Planarity : 0.003 0.034 2931 Dihedral : 3.828 38.508 2294 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.26 % Allowed : 22.02 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.18 (0.19), residues: 2124 helix: 2.21 (0.19), residues: 754 sheet: 0.79 (0.24), residues: 498 loop : -0.48 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 184 HIS 0.003 0.001 HIS A 708 PHE 0.017 0.001 PHE A 650 TYR 0.014 0.001 TYR B 334 ARG 0.005 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 911) hydrogen bonds : angle 4.83049 ( 2532) covalent geometry : bond 0.00429 (16677) covalent geometry : angle 0.52512 (22572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9512 (OUTLIER) cc_final: 0.9288 (m) REVERT: A 184 TRP cc_start: 0.9216 (OUTLIER) cc_final: 0.8920 (t60) REVERT: A 209 MET cc_start: 0.8959 (mmm) cc_final: 0.8600 (mmm) REVERT: A 424 MET cc_start: 0.8220 (ppp) cc_final: 0.7449 (ppp) REVERT: A 543 MET cc_start: 0.9283 (ppp) cc_final: 0.8507 (ppp) REVERT: B 376 MET cc_start: 0.8698 (mmm) cc_final: 0.8480 (mmp) REVERT: B 424 MET cc_start: 0.7580 (tmm) cc_final: 0.7121 (tmm) REVERT: C 81 MET cc_start: 0.8850 (tmm) cc_final: 0.8479 (tmm) REVERT: C 184 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.7530 (t60) REVERT: C 209 MET cc_start: 0.8891 (mmm) cc_final: 0.8539 (mmm) REVERT: C 323 GLN cc_start: 0.9589 (OUTLIER) cc_final: 0.9365 (mp10) REVERT: C 543 MET cc_start: 0.9053 (ppp) cc_final: 0.8103 (ppp) outliers start: 41 outliers final: 27 residues processed: 98 average time/residue: 0.3104 time to fit residues: 48.7960 Evaluate side-chains 91 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 718 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 46 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 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 = 0.3362 r_free = 0.3362 target = 0.061449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.041373 restraints weight = 104739.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.042622 restraints weight = 65699.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.043479 restraints weight = 48232.379| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16677 Z= 0.165 Angle : 0.519 9.601 22572 Z= 0.263 Chirality : 0.042 0.194 2634 Planarity : 0.003 0.036 2931 Dihedral : 3.818 38.799 2294 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.81 % Allowed : 21.96 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.25 (0.19), residues: 2124 helix: 2.27 (0.19), residues: 760 sheet: 0.78 (0.24), residues: 494 loop : -0.43 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 184 HIS 0.003 0.000 HIS A 708 PHE 0.015 0.001 PHE A 650 TYR 0.013 0.001 TYR B 334 ARG 0.005 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 911) hydrogen bonds : angle 4.67526 ( 2532) covalent geometry : bond 0.00355 (16677) covalent geometry : angle 0.51869 (22572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 61 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9272 (m) REVERT: A 184 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.8909 (t60) REVERT: A 209 MET cc_start: 0.9043 (mmm) cc_final: 0.8677 (mmm) REVERT: A 392 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9090 (tt0) REVERT: A 424 MET cc_start: 0.8262 (ppp) cc_final: 0.7557 (ppp) REVERT: A 543 MET cc_start: 0.9271 (ppp) cc_final: 0.8461 (ppp) REVERT: B 376 MET cc_start: 0.8686 (mmm) cc_final: 0.8474 (mmp) REVERT: B 424 MET cc_start: 0.7541 (tmm) cc_final: 0.7040 (tmm) REVERT: C 184 TRP cc_start: 0.9244 (OUTLIER) cc_final: 0.7862 (t60) REVERT: C 209 MET cc_start: 0.8928 (mmm) cc_final: 0.8530 (mmm) REVERT: C 323 GLN cc_start: 0.9586 (OUTLIER) cc_final: 0.9366 (mp10) REVERT: C 543 MET cc_start: 0.9078 (ppp) cc_final: 0.8117 (ppp) outliers start: 51 outliers final: 32 residues processed: 109 average time/residue: 0.2550 time to fit residues: 44.5123 Evaluate side-chains 97 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 408 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 154 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 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 = 0.3365 r_free = 0.3365 target = 0.062006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.042230 restraints weight = 103367.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.043458 restraints weight = 65117.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.044324 restraints weight = 47997.816| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16677 Z= 0.180 Angle : 0.532 10.508 22572 Z= 0.270 Chirality : 0.042 0.152 2634 Planarity : 0.003 0.035 2931 Dihedral : 3.832 39.268 2294 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.81 % Allowed : 22.19 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.26 (0.19), residues: 2124 helix: 2.24 (0.19), residues: 763 sheet: 0.79 (0.24), residues: 494 loop : -0.40 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS A 708 PHE 0.016 0.001 PHE A 650 TYR 0.014 0.001 TYR B 334 ARG 0.008 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 911) hydrogen bonds : angle 4.62500 ( 2532) covalent geometry : bond 0.00387 (16677) covalent geometry : angle 0.53221 (22572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 60 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9271 (m) REVERT: A 184 TRP cc_start: 0.9201 (OUTLIER) cc_final: 0.8806 (t60) REVERT: A 209 MET cc_start: 0.9108 (mmm) cc_final: 0.8730 (mmm) REVERT: A 392 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.9107 (tt0) REVERT: A 424 MET cc_start: 0.8223 (ppp) cc_final: 0.7509 (ppp) REVERT: A 543 MET cc_start: 0.9265 (ppp) cc_final: 0.8424 (ppp) REVERT: B 376 MET cc_start: 0.8700 (mmm) cc_final: 0.8488 (mmp) REVERT: B 424 MET cc_start: 0.7564 (tmm) cc_final: 0.7033 (tmm) REVERT: C 81 MET cc_start: 0.8852 (tmm) cc_final: 0.8521 (tmm) REVERT: C 184 TRP cc_start: 0.9253 (OUTLIER) cc_final: 0.7896 (t60) REVERT: C 209 MET cc_start: 0.8920 (mmm) cc_final: 0.8486 (mmm) REVERT: C 323 GLN cc_start: 0.9574 (OUTLIER) cc_final: 0.9362 (mp10) REVERT: C 543 MET cc_start: 0.9110 (ppp) cc_final: 0.8150 (ppp) outliers start: 51 outliers final: 37 residues processed: 108 average time/residue: 0.2705 time to fit residues: 46.4030 Evaluate side-chains 102 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 669 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 104 optimal weight: 0.5980 chunk 125 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 212 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 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 = 0.3385 r_free = 0.3385 target = 0.062609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.042707 restraints weight = 101952.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.044002 restraints weight = 64048.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.044849 restraints weight = 46997.315| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16677 Z= 0.114 Angle : 0.500 11.120 22572 Z= 0.253 Chirality : 0.043 0.144 2634 Planarity : 0.003 0.038 2931 Dihedral : 3.756 38.736 2294 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.59 % Allowed : 22.52 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.42 (0.19), residues: 2124 helix: 2.43 (0.19), residues: 757 sheet: 0.86 (0.24), residues: 494 loop : -0.32 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 184 HIS 0.003 0.000 HIS A 708 PHE 0.010 0.001 PHE B 340 TYR 0.013 0.001 TYR B 334 ARG 0.006 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 911) hydrogen bonds : angle 4.43451 ( 2532) covalent geometry : bond 0.00246 (16677) covalent geometry : angle 0.50026 (22572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9246 (m) REVERT: A 184 TRP cc_start: 0.9114 (OUTLIER) cc_final: 0.8741 (t60) REVERT: A 209 MET cc_start: 0.9173 (mmm) cc_final: 0.8799 (mmm) REVERT: A 392 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8972 (tt0) REVERT: A 424 MET cc_start: 0.8270 (ppp) cc_final: 0.7564 (ppp) REVERT: A 496 MET cc_start: 0.9422 (tpt) cc_final: 0.9138 (tpt) REVERT: A 543 MET cc_start: 0.9244 (ppp) cc_final: 0.8417 (ppp) REVERT: B 376 MET cc_start: 0.8655 (mmm) cc_final: 0.8442 (mmp) REVERT: B 424 MET cc_start: 0.7446 (tmm) cc_final: 0.6923 (tmm) REVERT: C 81 MET cc_start: 0.8796 (tmm) cc_final: 0.8502 (tmm) REVERT: C 209 MET cc_start: 0.8915 (mmm) cc_final: 0.8465 (mmm) REVERT: C 543 MET cc_start: 0.9075 (ppp) cc_final: 0.8125 (ppp) outliers start: 47 outliers final: 31 residues processed: 108 average time/residue: 0.2442 time to fit residues: 42.8954 Evaluate side-chains 94 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 669 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 65 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 198 optimal weight: 0.0020 chunk 95 optimal weight: 7.9990 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 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 = 0.3352 r_free = 0.3352 target = 0.061301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.041038 restraints weight = 105652.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.042265 restraints weight = 66980.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.043098 restraints weight = 49820.783| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16677 Z= 0.178 Angle : 0.546 12.032 22572 Z= 0.271 Chirality : 0.042 0.145 2634 Planarity : 0.003 0.037 2931 Dihedral : 3.763 39.109 2294 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.37 % Allowed : 23.23 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.36 (0.19), residues: 2124 helix: 2.36 (0.19), residues: 757 sheet: 0.82 (0.24), residues: 494 loop : -0.34 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS A 708 PHE 0.015 0.001 PHE A 650 TYR 0.014 0.001 TYR B 334 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 911) hydrogen bonds : angle 4.49714 ( 2532) covalent geometry : bond 0.00388 (16677) covalent geometry : angle 0.54589 (22572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9495 (OUTLIER) cc_final: 0.9258 (m) REVERT: A 184 TRP cc_start: 0.9182 (OUTLIER) cc_final: 0.8786 (t60) REVERT: A 209 MET cc_start: 0.9188 (mmm) cc_final: 0.8791 (mmm) REVERT: A 392 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9132 (tt0) REVERT: A 424 MET cc_start: 0.8246 (ppp) cc_final: 0.7578 (ppp) REVERT: A 543 MET cc_start: 0.9263 (ppp) cc_final: 0.8418 (ppp) REVERT: B 184 TRP cc_start: 0.9162 (OUTLIER) cc_final: 0.8855 (t60) REVERT: B 376 MET cc_start: 0.8660 (mmm) cc_final: 0.8453 (mmp) REVERT: B 424 MET cc_start: 0.7504 (tmm) cc_final: 0.6963 (tmm) REVERT: C 209 MET cc_start: 0.8961 (mmm) cc_final: 0.8513 (mmm) REVERT: C 543 MET cc_start: 0.9073 (ppp) cc_final: 0.8098 (ppp) outliers start: 43 outliers final: 37 residues processed: 99 average time/residue: 0.2600 time to fit residues: 41.1279 Evaluate side-chains 100 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 184 TRP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 669 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 104 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 243 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.041577 restraints weight = 104630.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.042853 restraints weight = 65890.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.043723 restraints weight = 48765.002| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16677 Z= 0.104 Angle : 0.515 12.363 22572 Z= 0.257 Chirality : 0.043 0.142 2634 Planarity : 0.003 0.039 2931 Dihedral : 3.719 38.541 2294 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.99 % Allowed : 23.73 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.41 (0.19), residues: 2124 helix: 2.35 (0.19), residues: 769 sheet: 0.87 (0.24), residues: 493 loop : -0.31 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 184 HIS 0.003 0.000 HIS A 708 PHE 0.010 0.001 PHE B 340 TYR 0.013 0.001 TYR B 334 ARG 0.004 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 911) hydrogen bonds : angle 4.36377 ( 2532) covalent geometry : bond 0.00230 (16677) covalent geometry : angle 0.51525 (22572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9475 (OUTLIER) cc_final: 0.9235 (m) REVERT: A 184 TRP cc_start: 0.9068 (OUTLIER) cc_final: 0.8678 (t60) REVERT: A 209 MET cc_start: 0.9188 (mmm) cc_final: 0.8791 (mmm) REVERT: A 392 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8979 (mt0) REVERT: A 424 MET cc_start: 0.8305 (ppp) cc_final: 0.7628 (ppp) REVERT: A 543 MET cc_start: 0.9214 (ppp) cc_final: 0.8349 (ppp) REVERT: B 376 MET cc_start: 0.8605 (mmm) cc_final: 0.8401 (mmp) REVERT: B 424 MET cc_start: 0.7474 (tmm) cc_final: 0.6926 (tmm) REVERT: C 44 MET cc_start: 0.6115 (pmm) cc_final: 0.5818 (ptt) REVERT: C 81 MET cc_start: 0.8811 (tmm) cc_final: 0.8536 (tmm) REVERT: C 209 MET cc_start: 0.8945 (mmm) cc_final: 0.8476 (mmm) REVERT: C 543 MET cc_start: 0.9073 (ppp) cc_final: 0.8143 (ppp) outliers start: 36 outliers final: 30 residues processed: 95 average time/residue: 0.2494 time to fit residues: 38.4336 Evaluate side-chains 94 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 670 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 4 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.061435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041520 restraints weight = 104746.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.042760 restraints weight = 66055.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.043585 restraints weight = 48859.209| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16677 Z= 0.212 Angle : 0.580 12.576 22572 Z= 0.286 Chirality : 0.042 0.145 2634 Planarity : 0.003 0.038 2931 Dihedral : 3.775 39.880 2294 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.21 % Allowed : 23.23 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.35 (0.19), residues: 2124 helix: 2.32 (0.19), residues: 757 sheet: 0.85 (0.24), residues: 498 loop : -0.34 (0.23), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS A 708 PHE 0.020 0.001 PHE A 650 TYR 0.014 0.001 TYR B 334 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 911) hydrogen bonds : angle 4.51311 ( 2532) covalent geometry : bond 0.00459 (16677) covalent geometry : angle 0.58044 (22572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9277 (m) REVERT: A 184 TRP cc_start: 0.9207 (OUTLIER) cc_final: 0.8791 (t60) REVERT: A 209 MET cc_start: 0.9179 (mmm) cc_final: 0.8782 (mmm) REVERT: A 392 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9129 (tt0) REVERT: A 424 MET cc_start: 0.8196 (ppp) cc_final: 0.7647 (ppp) REVERT: A 543 MET cc_start: 0.9225 (ppp) cc_final: 0.8863 (ppp) REVERT: B 376 MET cc_start: 0.8713 (mmm) cc_final: 0.8504 (mmp) REVERT: B 424 MET cc_start: 0.7528 (tmm) cc_final: 0.7005 (tmm) REVERT: C 81 MET cc_start: 0.8820 (tmm) cc_final: 0.8507 (tmm) REVERT: C 209 MET cc_start: 0.8951 (mmm) cc_final: 0.8498 (mmm) REVERT: C 485 MET cc_start: 0.9124 (mmp) cc_final: 0.8918 (mmp) REVERT: C 543 MET cc_start: 0.9084 (ppp) cc_final: 0.8094 (ppp) outliers start: 40 outliers final: 35 residues processed: 96 average time/residue: 0.2622 time to fit residues: 40.4673 Evaluate side-chains 97 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 670 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 105 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 141 optimal weight: 40.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.041811 restraints weight = 103359.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.043030 restraints weight = 65045.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.043913 restraints weight = 48083.340| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16677 Z= 0.145 Angle : 0.543 12.808 22572 Z= 0.268 Chirality : 0.042 0.162 2634 Planarity : 0.003 0.038 2931 Dihedral : 3.761 39.874 2294 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.37 % Allowed : 23.18 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.36 (0.19), residues: 2124 helix: 2.29 (0.19), residues: 769 sheet: 0.86 (0.24), residues: 498 loop : -0.33 (0.23), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 184 HIS 0.003 0.000 HIS A 708 PHE 0.013 0.001 PHE A 650 TYR 0.013 0.001 TYR B 334 ARG 0.004 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 911) hydrogen bonds : angle 4.42727 ( 2532) covalent geometry : bond 0.00317 (16677) covalent geometry : angle 0.54281 (22572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.36 seconds wall clock time: 78 minutes 43.21 seconds (4723.21 seconds total)