Starting phenix.real_space_refine on Thu Jun 19 04:35:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iw0_60937/06_2025/9iw0_60937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iw0_60937/06_2025/9iw0_60937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iw0_60937/06_2025/9iw0_60937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iw0_60937/06_2025/9iw0_60937.map" model { file = "/net/cci-nas-00/data/ceres_data/9iw0_60937/06_2025/9iw0_60937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iw0_60937/06_2025/9iw0_60937.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 111 5.16 5 C 14046 2.51 5 N 3735 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22122 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7374 Classifications: {'peptide': 927} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 866} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 18.72, per 1000 atoms: 0.85 Number of scatterers: 22122 At special positions: 0 Unit cell: (117.5, 120, 133.75, 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 111 16.00 O 4230 8.00 N 3735 7.00 C 14046 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: 5.21 Conformation dependent library (CDL) restraints added in 2.9 seconds 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5178 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 46 sheets defined 20.1% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.518A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.568A pdb=" N GLY B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.084A pdb=" N MET B 338 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 518 through 523 removed outlier: 4.145A pdb=" N ASN B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 removed outlier: 3.803A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 615 through 627 Processing helix chain 'B' and resid 628 through 632 removed outlier: 4.032A pdb=" N ASP B 632 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 785 through 790 removed outlier: 4.121A pdb=" N ASN B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 814 Processing helix chain 'B' and resid 879 through 883 Processing helix chain 'B' and resid 884 through 889 Processing helix chain 'A' and resid 7 through 13 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.518A pdb=" N TYR A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.568A pdb=" N GLY A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 310 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.084A pdb=" N MET A 338 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.145A pdb=" N ASN A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.803A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 628 through 632 removed outlier: 4.032A pdb=" N ASP A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 785 through 790 removed outlier: 4.121A pdb=" N ASN A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 879 through 883 Processing helix chain 'A' and resid 884 through 889 Processing helix chain 'C' and resid 7 through 13 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.518A pdb=" N TYR C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 24' Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 304 through 310 removed outlier: 3.568A pdb=" N GLY C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 310 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.085A pdb=" N MET C 338 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 388 through 393 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 518 through 523 removed outlier: 4.145A pdb=" N ASN C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 543 removed outlier: 3.803A pdb=" N LEU C 542 " --> pdb=" O ARG C 538 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 543 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'C' and resid 615 through 627 Processing helix chain 'C' and resid 628 through 632 removed outlier: 4.033A pdb=" N ASP C 632 " --> pdb=" O ASP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 706 through 708 No H-bonds generated for 'chain 'C' and resid 706 through 708' Processing helix chain 'C' and resid 754 through 767 Processing helix chain 'C' and resid 785 through 790 removed outlier: 4.121A pdb=" N ASN C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 814 Processing helix chain 'C' and resid 879 through 883 Processing helix chain 'C' and resid 884 through 889 Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.603A pdb=" N ILE B 600 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP B 108 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE B 602 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 106 " --> pdb=" O PHE B 602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS B 209 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 443 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 153 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS B 209 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 210 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR B 281 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY B 212 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU B 283 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA B 214 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 278 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N MET B 261 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL A 424 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE B 263 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.907A pdb=" N ILE B 183 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 296 removed outlier: 6.285A pdb=" N GLN B 311 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AB1, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.541A pdb=" N TRP B 516 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 409 removed outlier: 4.120A pdb=" N ASN B 405 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN C 405 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 405 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 432 through 434 removed outlier: 6.846A pdb=" N GLU B 443 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA C 155 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 445 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS C 209 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 432 through 434 removed outlier: 4.076A pdb=" N PHE C 263 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL B 424 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N MET C 261 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 278 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 210 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR C 281 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY C 212 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU C 283 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 214 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS C 209 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 633 through 636 removed outlier: 3.732A pdb=" N GLN B 633 " --> pdb=" O VAL B 920 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 641 through 648 removed outlier: 4.416A pdb=" N GLY B 669 " --> pdb=" O GLU B 913 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER B 661 " --> pdb=" O HIS B 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS B 891 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 712 " --> pdb=" O GLU B 898 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER B 661 " --> pdb=" O HIS B 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS B 891 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 712 " --> pdb=" O GLU B 898 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 791 through 798 Processing sheet with id=AC1, first strand: chain 'A' and resid 65 through 68 removed outlier: 5.603A pdb=" N ILE A 600 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP A 108 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE A 602 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 106 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AC3, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AC4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AC5, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS A 209 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU C 443 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 153 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS A 209 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE A 210 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR A 281 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 212 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU A 283 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 214 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 278 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N MET A 261 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL C 424 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 263 " --> pdb=" O ILE C 422 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.907A pdb=" N ILE A 183 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 292 through 296 removed outlier: 6.285A pdb=" N GLN A 311 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AD1, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.540A pdb=" N TRP A 516 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 633 through 636 removed outlier: 3.732A pdb=" N GLN A 633 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 641 through 648 removed outlier: 4.416A pdb=" N GLY A 669 " --> pdb=" O GLU A 913 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER A 661 " --> pdb=" O HIS A 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A 891 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 712 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER A 661 " --> pdb=" O HIS A 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A 891 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 712 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 791 through 798 Processing sheet with id=AD7, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.603A pdb=" N ILE C 600 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP C 108 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 602 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 106 " --> pdb=" O PHE C 602 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AD9, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AE1, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.907A pdb=" N ILE C 183 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 292 through 296 removed outlier: 6.285A pdb=" N GLN C 311 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 322 Processing sheet with id=AE5, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.540A pdb=" N TRP C 516 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.732A pdb=" N GLN C 633 " --> pdb=" O VAL C 920 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 641 through 648 removed outlier: 4.416A pdb=" N GLY C 669 " --> pdb=" O GLU C 913 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER C 661 " --> pdb=" O HIS C 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS C 891 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 712 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER C 661 " --> pdb=" O HIS C 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS C 891 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 712 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 791 through 798 701 hydrogen bonds defined for protein. 1788 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: 9.70 Time building geometry restraints manager: 6.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5661 1.33 - 1.45: 4650 1.45 - 1.57: 12204 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 22725 Sorted by residual: bond pdb=" CA PRO C 481 " pdb=" C PRO C 481 " ideal model delta sigma weight residual 1.514 1.537 -0.022 5.50e-03 3.31e+04 1.63e+01 bond pdb=" CA PRO B 481 " pdb=" C PRO B 481 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" CA PRO A 481 " pdb=" C PRO A 481 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.55e+01 bond pdb=" N VAL A 721 " pdb=" CA VAL A 721 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N VAL C 721 " pdb=" CA VAL C 721 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.17e-02 7.31e+03 1.18e+01 ... (remaining 22720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 30281 2.24 - 4.48: 608 4.48 - 6.72: 50 6.72 - 8.97: 9 8.97 - 11.21: 6 Bond angle restraints: 30954 Sorted by residual: angle pdb=" N ASN A 437 " pdb=" CA ASN A 437 " pdb=" C ASN A 437 " ideal model delta sigma weight residual 113.30 102.09 11.21 1.34e+00 5.57e-01 7.00e+01 angle pdb=" N ASN B 437 " pdb=" CA ASN B 437 " pdb=" C ASN B 437 " ideal model delta sigma weight residual 113.30 102.12 11.18 1.34e+00 5.57e-01 6.97e+01 angle pdb=" N ASN C 437 " pdb=" CA ASN C 437 " pdb=" C ASN C 437 " ideal model delta sigma weight residual 113.30 102.12 11.18 1.34e+00 5.57e-01 6.96e+01 angle pdb=" C ASN A 150 " pdb=" CA ASN A 150 " pdb=" CB ASN A 150 " ideal model delta sigma weight residual 110.22 119.51 -9.29 1.67e+00 3.59e-01 3.09e+01 angle pdb=" C ASN C 150 " pdb=" CA ASN C 150 " pdb=" CB ASN C 150 " ideal model delta sigma weight residual 110.22 119.50 -9.28 1.67e+00 3.59e-01 3.09e+01 ... (remaining 30949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 11403 16.77 - 33.54: 1517 33.54 - 50.32: 409 50.32 - 67.09: 105 67.09 - 83.86: 27 Dihedral angle restraints: 13461 sinusoidal: 5343 harmonic: 8118 Sorted by residual: dihedral pdb=" N THR B 148 " pdb=" C THR B 148 " pdb=" CA THR B 148 " pdb=" CB THR B 148 " ideal model delta harmonic sigma weight residual 123.40 133.84 -10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CA THR A 148 " pdb=" CB THR A 148 " ideal model delta harmonic sigma weight residual 123.40 133.84 -10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N THR C 148 " pdb=" C THR C 148 " pdb=" CA THR C 148 " pdb=" CB THR C 148 " ideal model delta harmonic sigma weight residual 123.40 133.83 -10.43 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 13458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2938 0.084 - 0.169: 336 0.169 - 0.253: 14 0.253 - 0.337: 3 0.337 - 0.422: 3 Chirality restraints: 3294 Sorted by residual: chirality pdb=" CA THR B 148 " pdb=" N THR B 148 " pdb=" C THR B 148 " pdb=" CB THR B 148 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR A 148 " pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CB THR A 148 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR C 148 " pdb=" N THR C 148 " pdb=" C THR C 148 " pdb=" CB THR C 148 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 3291 not shown) Planarity restraints: 4089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 434 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C LYS C 434 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS C 434 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP C 435 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 434 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C LYS A 434 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS A 434 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 435 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 434 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C LYS B 434 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS B 434 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP B 435 " 0.013 2.00e-02 2.50e+03 ... (remaining 4086 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2210 2.74 - 3.28: 21242 3.28 - 3.82: 37548 3.82 - 4.36: 46868 4.36 - 4.90: 79170 Nonbonded interactions: 187038 Sorted by model distance: nonbonded pdb=" OG1 THR B 58 " pdb=" O MET B 614 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 58 " pdb=" O MET A 614 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 58 " pdb=" O MET C 614 " model vdw 2.204 3.040 nonbonded pdb=" N GLU A 208 " pdb=" OE1 GLU A 208 " model vdw 2.218 3.120 nonbonded pdb=" N GLU C 208 " pdb=" OE1 GLU C 208 " model vdw 2.218 3.120 ... (remaining 187033 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 58.420 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.005 0.040 22725 Z= 0.274 Angle : 0.722 11.208 30954 Z= 0.434 Chirality : 0.052 0.422 3294 Planarity : 0.005 0.053 4089 Dihedral : 16.703 83.860 8283 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.33 % Favored : 95.45 % Rotamer: Outliers : 1.54 % Allowed : 23.87 % Favored : 74.60 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 6.67 % 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: -0.85 (0.15), residues: 2769 helix: 0.22 (0.30), residues: 327 sheet: 0.14 (0.20), residues: 585 loop : -0.98 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 723 HIS 0.007 0.001 HIS C 708 PHE 0.011 0.001 PHE C 667 TYR 0.025 0.002 TYR A 23 ARG 0.010 0.001 ARG C 668 Details of bonding type rmsd hydrogen bonds : bond 0.23756 ( 623) hydrogen bonds : angle 9.07879 ( 1788) covalent geometry : bond 0.00486 (22725) covalent geometry : angle 0.72221 (30954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 587 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8006 (tppp) cc_final: 0.7749 (tppp) REVERT: B 190 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7737 (mm-40) REVERT: B 490 THR cc_start: 0.7768 (p) cc_final: 0.7563 (m) REVERT: B 823 TYR cc_start: 0.8670 (t80) cc_final: 0.8377 (t80) REVERT: A 14 HIS cc_start: 0.8079 (m-70) cc_final: 0.7694 (m-70) REVERT: A 22 GLU cc_start: 0.6825 (mp0) cc_final: 0.6490 (mp0) REVERT: A 23 TYR cc_start: 0.8176 (p90) cc_final: 0.7968 (p90) REVERT: A 33 ARG cc_start: 0.6736 (mtm180) cc_final: 0.6427 (mtm180) REVERT: A 84 TYR cc_start: 0.7765 (m-80) cc_final: 0.7432 (m-80) REVERT: A 88 VAL cc_start: 0.8465 (t) cc_final: 0.8125 (m) REVERT: A 181 LYS cc_start: 0.8045 (tptp) cc_final: 0.7720 (mptp) REVERT: A 190 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7491 (mm-40) REVERT: A 221 MET cc_start: 0.8056 (mtt) cc_final: 0.7664 (mtp) REVERT: A 288 GLU cc_start: 0.7352 (pt0) cc_final: 0.7150 (pt0) REVERT: A 372 ASP cc_start: 0.8031 (t0) cc_final: 0.7787 (t0) REVERT: A 612 PHE cc_start: 0.8579 (t80) cc_final: 0.8144 (t80) REVERT: A 614 MET cc_start: 0.7134 (ttm) cc_final: 0.6901 (ttm) REVERT: A 663 ASN cc_start: 0.8325 (t0) cc_final: 0.7995 (t0) REVERT: A 678 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7805 (tttm) REVERT: A 692 VAL cc_start: 0.8432 (m) cc_final: 0.8085 (t) REVERT: A 723 TRP cc_start: 0.8354 (t60) cc_final: 0.8130 (t60) REVERT: A 727 ASP cc_start: 0.8020 (t0) cc_final: 0.7475 (t0) REVERT: A 774 TYR cc_start: 0.8206 (p90) cc_final: 0.7901 (p90) REVERT: A 864 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7339 (mtp-110) REVERT: C 22 GLU cc_start: 0.7161 (mp0) cc_final: 0.6848 (mp0) REVERT: C 49 THR cc_start: 0.8102 (m) cc_final: 0.7861 (p) REVERT: C 81 LYS cc_start: 0.8257 (tppp) cc_final: 0.7887 (tptt) REVERT: C 92 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7140 (mtt-85) REVERT: C 137 VAL cc_start: 0.8147 (t) cc_final: 0.7832 (p) REVERT: C 161 ASN cc_start: 0.8343 (t0) cc_final: 0.8087 (t0) REVERT: C 190 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7164 (mm-40) REVERT: C 294 VAL cc_start: 0.8586 (t) cc_final: 0.8283 (p) REVERT: C 330 MET cc_start: 0.8104 (mtp) cc_final: 0.7835 (mtt) REVERT: C 443 GLU cc_start: 0.7592 (pt0) cc_final: 0.7076 (pm20) REVERT: C 540 MET cc_start: 0.8498 (mtt) cc_final: 0.8246 (mtt) REVERT: C 570 SER cc_start: 0.8060 (m) cc_final: 0.7415 (p) REVERT: C 604 SER cc_start: 0.8339 (m) cc_final: 0.8037 (p) REVERT: C 622 LEU cc_start: 0.7854 (tp) cc_final: 0.7563 (tp) REVERT: C 623 GLU cc_start: 0.7082 (pm20) cc_final: 0.6679 (mp0) REVERT: C 629 ASP cc_start: 0.7455 (t0) cc_final: 0.6882 (m-30) REVERT: C 630 THR cc_start: 0.8425 (p) cc_final: 0.8089 (p) REVERT: C 716 MET cc_start: 0.7529 (tpp) cc_final: 0.7180 (mpp) REVERT: C 727 ASP cc_start: 0.7929 (t0) cc_final: 0.7263 (t0) REVERT: C 747 ASN cc_start: 0.8281 (m-40) cc_final: 0.7968 (m-40) REVERT: C 752 ASN cc_start: 0.7869 (p0) cc_final: 0.7632 (p0) REVERT: C 762 MET cc_start: 0.8448 (mmp) cc_final: 0.8098 (mmt) REVERT: C 811 LEU cc_start: 0.8451 (tp) cc_final: 0.8229 (tp) REVERT: C 864 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7205 (mtm-85) outliers start: 37 outliers final: 15 residues processed: 610 average time/residue: 0.3918 time to fit residues: 352.0642 Evaluate side-chains 576 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 557 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 935 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.4725 > 50: distance: 48 - 53: 23.474 distance: 53 - 54: 30.428 distance: 54 - 55: 51.668 distance: 54 - 57: 56.479 distance: 55 - 56: 30.859 distance: 55 - 62: 34.387 distance: 57 - 58: 41.132 distance: 58 - 59: 35.211 distance: 59 - 60: 35.293 distance: 59 - 61: 42.125 distance: 62 - 63: 17.812 distance: 63 - 64: 14.807 distance: 63 - 66: 38.297 distance: 64 - 65: 26.940 distance: 64 - 70: 44.235 distance: 66 - 67: 35.972 distance: 67 - 68: 25.905 distance: 67 - 69: 33.969 distance: 70 - 76: 50.583 distance: 71 - 72: 38.623 distance: 71 - 74: 40.579 distance: 72 - 73: 41.270 distance: 72 - 77: 29.529 distance: 74 - 75: 10.919 distance: 75 - 76: 39.791 distance: 77 - 78: 15.241 distance: 78 - 79: 38.134 distance: 78 - 81: 6.149 distance: 79 - 80: 21.124 distance: 79 - 85: 36.927 distance: 80 - 178: 26.350 distance: 81 - 82: 27.468 distance: 82 - 84: 45.110 distance: 85 - 86: 16.118 distance: 86 - 87: 15.129 distance: 86 - 89: 4.056 distance: 87 - 88: 11.899 distance: 87 - 97: 36.537 distance: 89 - 90: 5.014 distance: 90 - 91: 9.878 distance: 90 - 92: 13.041 distance: 91 - 93: 5.896 distance: 93 - 95: 13.986 distance: 94 - 95: 11.447 distance: 95 - 96: 25.739 distance: 97 - 98: 18.053 distance: 97 - 167: 16.752 distance: 98 - 99: 16.020 distance: 98 - 101: 20.242 distance: 99 - 100: 18.575 distance: 99 - 103: 31.055 distance: 100 - 164: 28.136 distance: 101 - 102: 31.647 distance: 103 - 104: 33.828 distance: 103 - 219: 25.710 distance: 104 - 105: 33.244 distance: 104 - 107: 12.733 distance: 105 - 106: 20.107 distance: 105 - 114: 47.832 distance: 106 - 216: 37.047 distance: 107 - 108: 10.055 distance: 108 - 109: 3.713 distance: 108 - 110: 23.282 distance: 109 - 111: 26.686 distance: 110 - 112: 15.254 distance: 111 - 113: 30.573 distance: 112 - 113: 12.011 distance: 114 - 115: 21.123 distance: 114 - 120: 13.521 distance: 115 - 116: 22.358 distance: 115 - 118: 3.263 distance: 116 - 117: 3.282 distance: 116 - 121: 12.834 distance: 118 - 119: 25.750 distance: 119 - 120: 32.541 distance: 121 - 122: 20.355 distance: 122 - 123: 25.500 distance: 122 - 125: 8.448 distance: 123 - 124: 5.305 distance: 123 - 129: 24.705 distance: 125 - 126: 8.028 distance: 126 - 127: 12.326 distance: 126 - 128: 9.963 distance: 129 - 130: 5.281 distance: 130 - 131: 30.526 distance: 130 - 133: 15.936 distance: 131 - 132: 19.609 distance: 131 - 137: 16.282 distance: 133 - 134: 19.157 distance: 134 - 135: 12.937 distance: 134 - 136: 12.230