Starting phenix.real_space_refine on Sun Sep 29 17:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/09_2024/6pbx_20294.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/09_2024/6pbx_20294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/09_2024/6pbx_20294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/09_2024/6pbx_20294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/09_2024/6pbx_20294.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbx_20294/09_2024/6pbx_20294.cif" } resolution = 4.0 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= 0.000 sd= 0.002 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 128 5.16 5 C 14880 2.51 5 N 3836 2.21 5 O 4184 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-5461/modules/chem_data/mon_lib" Total number of atoms: 23028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4897 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 860 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 12.42, per 1000 atoms: 0.54 Number of scatterers: 23028 At special positions: 0 Unit cell: (157, 157, 142, 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 128 16.00 O 4184 8.00 N 3836 7.00 C 14880 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: 5.13 Conformation dependent library (CDL) restraints added in 2.8 seconds 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 16 sheets defined 64.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.805A pdb=" N ILE A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 215 through 241 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS A 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.848A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.805A pdb=" N ILE C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 215 through 241 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.635A pdb=" N LYS C 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.693A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 520 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 removed outlier: 3.829A pdb=" N GLU C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.806A pdb=" N ILE E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 215 through 241 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS E 327 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 418 through 435 Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 520 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU E 624 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 692 Processing helix chain 'E' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.804A pdb=" N ILE G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 Processing helix chain 'G' and resid 215 through 241 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 285 through 295 Processing helix chain 'G' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 379 removed outlier: 3.807A pdb=" N LEU G 352 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 418 through 435 Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 520 Processing helix chain 'G' and resid 524 through 532 Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU G 624 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'G' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE D 16 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.598A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.432A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER A 45 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE A 30 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP A 641 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 618 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.398A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 607 through 611 removed outlier: 6.564A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.431A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER C 45 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE C 30 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP C 641 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 618 " --> pdb=" O TYR C 672 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.397A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 607 through 611 removed outlier: 6.564A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.432A pdb=" N LEU E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER E 45 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE E 30 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 125 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 571 through 575 removed outlier: 6.236A pdb=" N ASP E 641 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 618 " --> pdb=" O TYR E 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 587 through 588 removed outlier: 4.397A pdb=" N ALA E 628 " --> pdb=" O VAL E 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 607 through 611 removed outlier: 6.563A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.431A pdb=" N LEU G 32 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER G 45 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE G 30 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 125 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP G 641 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY G 618 " --> pdb=" O TYR G 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 587 through 588 removed outlier: 4.398A pdb=" N ALA G 628 " --> pdb=" O VAL G 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 607 through 611 removed outlier: 6.563A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4236 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: 7.93 Time building geometry restraints manager: 6.06 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: 7379 1.34 - 1.46: 5112 1.46 - 1.58: 10837 1.58 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 23524 Sorted by residual: bond pdb=" C LEU C 195 " pdb=" N PRO C 196 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.52e+00 bond pdb=" C LEU A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.43e+00 bond pdb=" CG1 ILE C 224 " pdb=" CD1 ILE C 224 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" C LEU G 195 " pdb=" N PRO G 196 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.39e+00 bond pdb=" CG1 ILE A 224 " pdb=" CD1 ILE A 224 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.33e+00 ... (remaining 23519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 31343 2.27 - 4.54: 639 4.54 - 6.81: 82 6.81 - 9.07: 28 9.07 - 11.34: 8 Bond angle restraints: 32100 Sorted by residual: angle pdb=" N LEU C 195 " pdb=" CA LEU C 195 " pdb=" C LEU C 195 " ideal model delta sigma weight residual 109.81 119.83 -10.02 2.21e+00 2.05e-01 2.06e+01 angle pdb=" N LEU A 195 " pdb=" CA LEU A 195 " pdb=" C LEU A 195 " ideal model delta sigma weight residual 109.81 119.81 -10.00 2.21e+00 2.05e-01 2.05e+01 angle pdb=" N LEU E 195 " pdb=" CA LEU E 195 " pdb=" C LEU E 195 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" N LEU G 195 " pdb=" CA LEU G 195 " pdb=" C LEU G 195 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" CA PRO G 196 " pdb=" N PRO G 196 " pdb=" CD PRO G 196 " ideal model delta sigma weight residual 112.00 106.68 5.32 1.40e+00 5.10e-01 1.44e+01 ... (remaining 32095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 12216 16.35 - 32.69: 1068 32.69 - 49.04: 284 49.04 - 65.39: 44 65.39 - 81.74: 8 Dihedral angle restraints: 13620 sinusoidal: 4404 harmonic: 9216 Sorted by residual: dihedral pdb=" CA PRO G 502 " pdb=" C PRO G 502 " pdb=" N LYS G 503 " pdb=" CA LYS G 503 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO E 502 " pdb=" C PRO E 502 " pdb=" N LYS E 503 " pdb=" CA LYS E 503 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO A 502 " pdb=" C PRO A 502 " pdb=" N LYS A 503 " pdb=" CA LYS A 503 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2618 0.045 - 0.090: 851 0.090 - 0.134: 253 0.134 - 0.179: 50 0.179 - 0.224: 16 Chirality restraints: 3788 Sorted by residual: chirality pdb=" CB THR E 228 " pdb=" CA THR E 228 " pdb=" OG1 THR E 228 " pdb=" CG2 THR E 228 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR G 228 " pdb=" CA THR G 228 " pdb=" OG1 THR G 228 " pdb=" CG2 THR G 228 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 432 " pdb=" CA THR A 432 " pdb=" OG1 THR A 432 " pdb=" CG2 THR A 432 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3785 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 169 " -0.047 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 170 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 169 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 170 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 169 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO G 170 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 170 " -0.039 5.00e-02 4.00e+02 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6400 2.79 - 3.32: 22457 3.32 - 3.85: 40104 3.85 - 4.37: 43824 4.37 - 4.90: 73821 Nonbonded interactions: 186606 Sorted by model distance: nonbonded pdb=" O VAL E 172 " pdb=" OG SER F 38 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR C 582 " pdb=" OG SER C 590 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 582 " pdb=" OG SER A 590 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR G 582 " pdb=" OG SER G 590 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR E 582 " pdb=" OG SER E 590 " model vdw 2.281 3.040 ... (remaining 186601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.010 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: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 47.820 Find NCS groups from input model: 0.780 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 0.072 23524 Z= 0.394 Angle : 0.825 11.343 32100 Z= 0.454 Chirality : 0.050 0.224 3788 Planarity : 0.006 0.069 4076 Dihedral : 14.043 81.736 7636 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.12), residues: 3088 helix: -2.01 (0.09), residues: 1760 sheet: -2.23 (0.33), residues: 204 loop : -1.70 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 370 HIS 0.010 0.002 HIS G 543 PHE 0.017 0.002 PHE F 68 TYR 0.017 0.002 TYR C 44 ARG 0.016 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9046 (mp0) REVERT: A 102 LYS cc_start: 0.9131 (tttp) cc_final: 0.8925 (ttmt) REVERT: A 468 PHE cc_start: 0.8574 (m-80) cc_final: 0.8372 (m-10) REVERT: A 470 ASN cc_start: 0.9215 (t0) cc_final: 0.9013 (t0) REVERT: A 519 MET cc_start: 0.8441 (ttm) cc_final: 0.7910 (tmm) REVERT: B 32 LEU cc_start: 0.8035 (tp) cc_final: 0.7779 (mt) REVERT: B 123 GLU cc_start: 0.8476 (tp30) cc_final: 0.8270 (tp30) REVERT: B 144 MET cc_start: 0.8239 (tpt) cc_final: 0.7685 (tpt) REVERT: C 59 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9022 (mp0) REVERT: C 99 MET cc_start: 0.8998 (mtp) cc_final: 0.8383 (mtp) REVERT: C 468 PHE cc_start: 0.8455 (m-80) cc_final: 0.8192 (m-10) REVERT: C 470 ASN cc_start: 0.9197 (t0) cc_final: 0.8987 (t0) REVERT: C 519 MET cc_start: 0.8459 (ttm) cc_final: 0.7996 (tmm) REVERT: C 651 GLN cc_start: 0.8796 (mt0) cc_final: 0.8553 (mt0) REVERT: C 652 LYS cc_start: 0.8829 (mttt) cc_final: 0.8618 (mmtm) REVERT: E 59 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9011 (mp0) REVERT: E 99 MET cc_start: 0.8988 (mtp) cc_final: 0.8360 (mtp) REVERT: E 470 ASN cc_start: 0.9164 (t0) cc_final: 0.8935 (t0) REVERT: E 519 MET cc_start: 0.8470 (ttm) cc_final: 0.8031 (tmm) REVERT: E 651 GLN cc_start: 0.8823 (mt0) cc_final: 0.8579 (mt0) REVERT: E 652 LYS cc_start: 0.8827 (mttt) cc_final: 0.8617 (mmtm) REVERT: G 60 VAL cc_start: 0.9278 (t) cc_final: 0.9073 (p) REVERT: G 463 LEU cc_start: 0.9183 (mt) cc_final: 0.8960 (mt) REVERT: G 468 PHE cc_start: 0.8441 (m-80) cc_final: 0.7997 (m-80) REVERT: G 470 ASN cc_start: 0.9256 (t0) cc_final: 0.8894 (t0) REVERT: G 519 MET cc_start: 0.8443 (ttm) cc_final: 0.7842 (tmm) REVERT: D 32 LEU cc_start: 0.8061 (tp) cc_final: 0.7540 (mt) REVERT: D 123 GLU cc_start: 0.8517 (tp30) cc_final: 0.8311 (tp30) REVERT: D 144 MET cc_start: 0.8203 (tpt) cc_final: 0.7661 (tpt) REVERT: F 32 LEU cc_start: 0.8253 (tp) cc_final: 0.8027 (mt) REVERT: F 119 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8155 (tm-30) REVERT: F 123 GLU cc_start: 0.8518 (tp30) cc_final: 0.8313 (mm-30) REVERT: F 139 GLU cc_start: 0.9275 (mp0) cc_final: 0.8798 (pm20) REVERT: F 144 MET cc_start: 0.8165 (tpt) cc_final: 0.7622 (tpt) REVERT: H 139 GLU cc_start: 0.9250 (mp0) cc_final: 0.8787 (pm20) REVERT: H 144 MET cc_start: 0.8137 (tpt) cc_final: 0.7568 (tpt) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.3305 time to fit residues: 253.3351 Evaluate side-chains 329 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.8312 > 50: distance: 1 - 18: 36.604 distance: 5 - 28: 36.666 distance: 10 - 36: 33.513 distance: 13 - 18: 35.191 distance: 18 - 19: 38.962 distance: 19 - 20: 32.358 distance: 20 - 21: 41.356 distance: 20 - 28: 8.170 distance: 22 - 23: 29.430 distance: 23 - 24: 51.199 distance: 23 - 25: 55.265 distance: 24 - 26: 68.103 distance: 25 - 27: 41.632 distance: 26 - 27: 54.039 distance: 28 - 29: 39.845 distance: 29 - 30: 39.899 distance: 29 - 32: 56.232 distance: 30 - 31: 40.689 distance: 32 - 33: 40.433 distance: 33 - 34: 27.605 distance: 33 - 35: 44.778 distance: 36 - 37: 41.113 distance: 37 - 38: 57.281 distance: 38 - 44: 40.344 distance: 39 - 71: 57.432 distance: 41 - 43: 40.312 distance: 45 - 46: 38.720 distance: 45 - 48: 56.586 distance: 46 - 47: 37.913 distance: 47 - 82: 52.916 distance: 48 - 49: 58.022 distance: 50 - 51: 39.699 distance: 51 - 52: 41.691 distance: 52 - 53: 39.931 distance: 52 - 54: 46.090 distance: 55 - 56: 40.606 distance: 56 - 57: 9.826 distance: 56 - 59: 42.024 distance: 57 - 58: 51.108 distance: 57 - 64: 49.373 distance: 59 - 60: 42.613 distance: 60 - 61: 26.736 distance: 61 - 62: 18.740 distance: 62 - 63: 19.889 distance: 65 - 66: 8.190 distance: 65 - 68: 35.288 distance: 66 - 67: 31.330 distance: 66 - 71: 41.437 distance: 68 - 69: 23.842 distance: 68 - 70: 24.385 distance: 71 - 72: 40.356 distance: 72 - 73: 69.239 distance: 72 - 75: 40.101 distance: 73 - 82: 40.943 distance: 75 - 76: 35.086 distance: 76 - 77: 23.930 distance: 76 - 78: 34.668 distance: 77 - 79: 26.223 distance: 79 - 81: 28.678 distance: 80 - 81: 30.441 distance: 82 - 83: 43.471 distance: 83 - 84: 41.697 distance: 83 - 86: 46.602 distance: 84 - 85: 24.757 distance: 84 - 91: 40.693 distance: 87 - 88: 43.181 distance: 88 - 89: 46.161 distance: 89 - 90: 19.812 distance: 92 - 93: 56.969 distance: 93 - 94: 56.677 distance: 93 - 100: 39.520 distance: 95 - 96: 39.763 distance: 96 - 97: 4.365 distance: 97 - 98: 61.831 distance: 97 - 99: 53.434 distance: 100 - 101: 44.707 distance: 101 - 102: 41.459 distance: 101 - 104: 60.141 distance: 102 - 103: 62.733 distance: 102 - 110: 28.496 distance: 104 - 105: 58.018 distance: 105 - 106: 55.671 distance: 106 - 108: 46.892 distance: 107 - 109: 40.429 distance: 108 - 109: 42.800