Starting phenix.real_space_refine on Sun Aug 24 03:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjt_62375/08_2025/9kjt_62375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjt_62375/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kjt_62375/08_2025/9kjt_62375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjt_62375/08_2025/9kjt_62375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kjt_62375/08_2025/9kjt_62375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjt_62375/08_2025/9kjt_62375.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.16, per 1000 atoms: 0.25 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: 1.60 Conformation dependent library (CDL) restraints added in 741.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.65 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: 3.26 Time building geometry restraints manager: 1.98 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: 0.02 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.920 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- 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 : 16.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG B 206 TYR 0.012 0.001 TYR C 699 PHE 0.013 0.001 PHE A 650 TRP 0.006 0.002 TRP C 184 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00596 (16677) covalent geometry : angle 0.65850 (22572) hydrogen bonds : bond 0.20304 ( 911) hydrogen bonds : angle 7.97201 ( 2532) *********************** 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 : 0.703 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: 0.1181 time to fit residues: 12.2505 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 : 0.647 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** ** A 714 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.061478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.041200 restraints weight = 103496.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.042455 restraints weight = 65420.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.043317 restraints weight = 48339.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.043921 restraints weight = 39462.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.044229 restraints weight = 34235.248| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16677 Z= 0.153 Angle : 0.534 8.795 22572 Z= 0.285 Chirality : 0.044 0.174 2634 Planarity : 0.004 0.030 2931 Dihedral : 3.851 37.561 2296 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.66 % Allowed : 21.74 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.19), residues: 2124 helix: 2.27 (0.19), residues: 750 sheet: 0.91 (0.24), residues: 498 loop : -0.53 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 206 TYR 0.012 0.001 TYR A 296 PHE 0.013 0.001 PHE A 650 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00316 (16677) covalent geometry : angle 0.53368 (22572) hydrogen bonds : bond 0.05693 ( 911) hydrogen bonds : angle 5.44872 ( 2532) *********************** 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 92 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.9190 (OUTLIER) cc_final: 0.8863 (t60) REVERT: A 424 MET cc_start: 0.8282 (ppp) cc_final: 0.7699 (ppp) REVERT: B 376 MET cc_start: 0.8700 (mmm) cc_final: 0.8441 (mmp) REVERT: B 424 MET cc_start: 0.7687 (tmm) cc_final: 0.7366 (tmm) REVERT: C 209 MET cc_start: 0.8740 (mmm) cc_final: 0.8522 (mmm) outliers start: 30 outliers final: 10 residues processed: 88 average time/residue: 0.1373 time to fit residues: 19.0241 Evaluate side-chains 71 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 CYS 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 119 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 137 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 155 ASN B 243 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 392 GLN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.061574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041818 restraints weight = 104351.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.043024 restraints weight = 65380.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.043884 restraints weight = 48528.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.044505 restraints weight = 39256.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.044939 restraints weight = 33776.102| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16677 Z= 0.193 Angle : 0.539 8.700 22572 Z= 0.278 Chirality : 0.043 0.151 2634 Planarity : 0.003 0.032 2931 Dihedral : 3.888 38.307 2294 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.93 % Allowed : 21.85 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 2124 helix: 2.07 (0.19), residues: 758 sheet: 0.84 (0.24), residues: 498 loop : -0.49 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.014 0.001 TYR B 334 PHE 0.015 0.001 PHE A 650 TRP 0.003 0.001 TRP C 184 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00416 (16677) covalent geometry : angle 0.53869 (22572) hydrogen bonds : bond 0.04584 ( 911) hydrogen bonds : angle 5.01263 ( 2532) *********************** 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 97 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.659 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: 0.9526 (OUTLIER) cc_final: 0.9309 (m) REVERT: A 184 TRP cc_start: 0.9206 (OUTLIER) cc_final: 0.8873 (t60) REVERT: A 209 MET cc_start: 0.8935 (mmm) cc_final: 0.8622 (mmm) REVERT: A 292 MET cc_start: 0.9286 (tmm) cc_final: 0.8974 (tmm) REVERT: A 424 MET cc_start: 0.8241 (ppp) cc_final: 0.7450 (ppp) REVERT: A 543 MET cc_start: 0.9217 (ppp) cc_final: 0.8437 (ppp) REVERT: B 209 MET cc_start: 0.8872 (mmm) cc_final: 0.8643 (mmm) REVERT: B 376 MET cc_start: 0.8696 (mmm) cc_final: 0.8473 (mmp) REVERT: B 424 MET cc_start: 0.7581 (tmm) cc_final: 0.7101 (tmm) REVERT: C 81 MET cc_start: 0.8856 (tmm) cc_final: 0.8455 (tmm) REVERT: C 184 TRP cc_start: 0.9258 (OUTLIER) cc_final: 0.7514 (t60) REVERT: C 209 MET cc_start: 0.8815 (mmm) cc_final: 0.8516 (mmm) REVERT: C 323 GLN cc_start: 0.9577 (OUTLIER) cc_final: 0.9359 (mp10) REVERT: C 485 MET cc_start: 0.9192 (mmp) cc_final: 0.8922 (mmp) REVERT: C 543 MET cc_start: 0.9029 (ppp) cc_final: 0.8127 (ppp) outliers start: 35 outliers final: 17 residues processed: 94 average time/residue: 0.1427 time to fit residues: 20.8788 Evaluate side-chains 81 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 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 184 TRP Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 619 LYS 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 81 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 426 HIS ** 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 = 0.3348 r_free = 0.3348 target = 0.061120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.036115 restraints weight = 100813.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.036972 restraints weight = 73872.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.037335 restraints weight = 55511.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.038020 restraints weight = 48585.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.038196 restraints weight = 43641.193| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16677 Z= 0.249 Angle : 0.570 9.060 22572 Z= 0.292 Chirality : 0.042 0.145 2634 Planarity : 0.004 0.034 2931 Dihedral : 3.971 39.525 2294 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.15 % Allowed : 21.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 2124 helix: 1.97 (0.19), residues: 757 sheet: 0.76 (0.24), residues: 498 loop : -0.52 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.014 0.001 TYR B 334 PHE 0.022 0.001 PHE A 650 TRP 0.004 0.001 TRP C 184 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00533 (16677) covalent geometry : angle 0.57035 (22572) hydrogen bonds : bond 0.04360 ( 911) hydrogen bonds : angle 4.91238 ( 2532) *********************** 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 116 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 59 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9318 (m) REVERT: A 184 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8997 (t60) REVERT: A 209 MET cc_start: 0.9059 (mmm) cc_final: 0.8821 (mmm) REVERT: A 285 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9213 (ptpp) REVERT: A 292 MET cc_start: 0.9233 (tmm) cc_final: 0.8908 (tmm) REVERT: A 424 MET cc_start: 0.8256 (ppp) cc_final: 0.7504 (ppp) REVERT: B 376 MET cc_start: 0.8712 (mmm) cc_final: 0.8497 (mmp) REVERT: B 424 MET cc_start: 0.7601 (tmm) cc_final: 0.7140 (tmm) REVERT: B 543 MET cc_start: 0.9019 (ppp) cc_final: 0.8107 (ppp) REVERT: C 44 MET cc_start: 0.5876 (pmm) cc_final: 0.5676 (ppp) REVERT: C 184 TRP cc_start: 0.9275 (OUTLIER) cc_final: 0.7869 (t60) REVERT: C 209 MET cc_start: 0.8891 (mmm) cc_final: 0.8543 (mmm) REVERT: C 323 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9356 (mp10) REVERT: C 543 MET cc_start: 0.9051 (ppp) cc_final: 0.8805 (ppp) outliers start: 57 outliers final: 32 residues processed: 114 average time/residue: 0.1307 time to fit residues: 23.5143 Evaluate side-chains 96 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 179 LEU 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 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 278 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR 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 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 Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 619 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 105 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.061581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.041972 restraints weight = 104540.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.043193 restraints weight = 66080.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044045 restraints weight = 48754.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.044591 restraints weight = 39594.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045034 restraints weight = 34505.154| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16677 Z= 0.210 Angle : 0.552 9.507 22572 Z= 0.282 Chirality : 0.043 0.156 2634 Planarity : 0.003 0.034 2931 Dihedral : 3.957 39.796 2294 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.98 % Allowed : 22.30 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 2124 helix: 2.02 (0.19), residues: 763 sheet: 0.73 (0.24), residues: 494 loop : -0.48 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.014 0.001 TYR B 334 PHE 0.018 0.001 PHE A 650 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00452 (16677) covalent geometry : angle 0.55241 (22572) hydrogen bonds : bond 0.04192 ( 911) hydrogen bonds : angle 4.78068 ( 2532) *********************** 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 115 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 61 time to evaluate : 0.700 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: 0.9502 (OUTLIER) cc_final: 0.9272 (m) REVERT: A 184 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.8976 (t60) REVERT: A 209 MET cc_start: 0.9124 (mmm) cc_final: 0.8840 (mmm) REVERT: A 292 MET cc_start: 0.9285 (tmm) cc_final: 0.8938 (tmm) REVERT: A 424 MET cc_start: 0.8293 (ppp) cc_final: 0.7578 (ppp) REVERT: A 543 MET cc_start: 0.9318 (ppp) cc_final: 0.8380 (ppp) REVERT: B 376 MET cc_start: 0.8716 (mmm) cc_final: 0.8505 (mmp) REVERT: B 424 MET cc_start: 0.7575 (tmm) cc_final: 0.7053 (tmm) REVERT: B 543 MET cc_start: 0.8975 (ppp) cc_final: 0.7979 (ppp) REVERT: C 44 MET cc_start: 0.5818 (pmm) cc_final: 0.5573 (ppp) REVERT: C 81 MET cc_start: 0.8815 (tmm) cc_final: 0.8468 (tmm) REVERT: C 184 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.7917 (t60) REVERT: C 209 MET cc_start: 0.8896 (mmm) cc_final: 0.8493 (mmm) REVERT: C 323 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9362 (mp10) REVERT: C 543 MET cc_start: 0.9104 (ppp) cc_final: 0.8144 (ppp) outliers start: 54 outliers final: 37 residues processed: 112 average time/residue: 0.1352 time to fit residues: 23.7805 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 : 0.682 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 213 THR 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 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 748 SER Chi-restraints excluded: chain B residue 72 VAL 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 469 THR 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 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 188 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 619 LYS Chi-restraints excluded: chain C residue 669 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7783 > 50: distance: 59 - 77: 15.950 distance: 63 - 84: 25.055 distance: 68 - 93: 10.348 distance: 71 - 77: 13.451 distance: 72 - 102: 23.178 distance: 77 - 78: 7.272 distance: 78 - 79: 12.212 distance: 78 - 81: 15.808 distance: 79 - 80: 29.731 distance: 79 - 84: 14.069 distance: 80 - 109: 12.438 distance: 81 - 82: 25.764 distance: 81 - 83: 19.980 distance: 85 - 86: 14.689 distance: 85 - 88: 6.196 distance: 86 - 87: 18.912 distance: 86 - 93: 17.254 distance: 88 - 89: 3.323 distance: 89 - 90: 15.734 distance: 90 - 91: 11.910 distance: 91 - 92: 7.338 distance: 93 - 94: 3.815 distance: 94 - 95: 3.429 distance: 94 - 97: 14.560 distance: 95 - 96: 5.451 distance: 95 - 102: 30.667 distance: 97 - 98: 20.345 distance: 98 - 99: 9.443 distance: 99 - 100: 11.389 distance: 99 - 101: 11.663 distance: 102 - 103: 24.179 distance: 103 - 104: 19.595 distance: 103 - 106: 13.337 distance: 104 - 105: 5.545 distance: 104 - 109: 40.120 distance: 106 - 107: 40.166 distance: 106 - 108: 31.751 distance: 109 - 110: 47.233 distance: 110 - 111: 18.700 distance: 111 - 112: 27.239 distance: 111 - 113: 29.085 distance: 113 - 114: 10.929 distance: 114 - 115: 19.915 distance: 114 - 117: 38.992 distance: 115 - 116: 22.484 distance: 115 - 120: 16.836 distance: 117 - 118: 18.287 distance: 117 - 119: 13.613 distance: 120 - 121: 11.004 distance: 121 - 122: 11.332 distance: 121 - 124: 9.824 distance: 122 - 123: 24.914 distance: 122 - 127: 21.150 distance: 124 - 125: 8.964 distance: 124 - 126: 13.755 distance: 127 - 128: 26.498 distance: 128 - 129: 19.884 distance: 128 - 131: 20.502 distance: 129 - 130: 26.394 distance: 129 - 136: 25.161 distance: 131 - 132: 14.819 distance: 132 - 133: 6.186 distance: 133 - 134: 19.137 distance: 134 - 135: 28.126 distance: 136 - 137: 21.504 distance: 137 - 138: 33.594 distance: 137 - 140: 32.093 distance: 138 - 139: 34.501 distance: 138 - 147: 17.617 distance: 140 - 141: 20.122 distance: 141 - 142: 19.385 distance: 142 - 143: 5.865 distance: 143 - 144: 9.647 distance: 144 - 145: 7.841 distance: 144 - 146: 6.781 distance: 147 - 148: 21.888 distance: 148 - 149: 7.321 distance: 148 - 151: 21.115 distance: 149 - 154: 34.354 distance: 151 - 152: 31.402 distance: 151 - 153: 42.801