Starting phenix.real_space_refine on Sun Dec 10 05:54:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5r_10703/12_2023/6y5r_10703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5r_10703/12_2023/6y5r_10703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5r_10703/12_2023/6y5r_10703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5r_10703/12_2023/6y5r_10703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5r_10703/12_2023/6y5r_10703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5r_10703/12_2023/6y5r_10703.pdb" } resolution = 3.76 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= 0.001 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 93 5.16 5 C 8825 2.51 5 N 2257 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 677": "OD1" <-> "OD2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A ASP 929": "OD1" <-> "OD2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 677": "OD1" <-> "OD2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13592 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6723 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 879, 6636 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 100 Conformer: "B" Number of residues, atoms: 879, 6636 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 100 bond proxies already assigned to first conformer: 6699 Chain: "B" Number of atoms: 6763 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 879, 6666 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 879, 6666 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 6720 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N AMET A 905 " occ=0.50 ... (8 atoms not shown) pdb=" CB BMET A 905 " occ=0.50 residue: pdb=" N ALYS A 906 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS A 906 " occ=0.50 residue: pdb=" N ALYS A 907 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS A 907 " occ=0.50 residue: pdb=" N AASP A 908 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 908 " occ=0.50 residue: pdb=" N ALEU A 909 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU A 909 " occ=0.50 residue: pdb=" N AALA A 910 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 910 " occ=0.50 residue: pdb=" N ATHR A 911 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR A 911 " occ=0.50 residue: pdb=" N APHE A 912 " occ=0.50 ... (8 atoms not shown) pdb=" CB BPHE A 912 " occ=0.50 residue: pdb=" N ALEU A 913 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU A 913 " occ=0.50 residue: pdb=" N ATYR A 914 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTYR A 914 " occ=0.50 residue: pdb=" N AHIS A 915 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS A 915 " occ=0.50 residue: pdb=" N ALEU A 916 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU A 916 " occ=0.50 ... (remaining 16 not shown) Time building chain proxies: 12.51, per 1000 atoms: 0.92 Number of scatterers: 13592 At special positions: 0 Unit cell: (107.415, 106.764, 147.126, 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 93 16.00 O 2417 8.00 N 2257 7.00 C 8825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1104 " - " ASN A 377 " " NAG B1104 " - " ASN B 377 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN B 328 " Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 5.2 seconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 62.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.777A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.462A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.646A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.594A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.922A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.530A pdb=" N VAL A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 376' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.775A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.635A pdb=" N SER A 452 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.762A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.322A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Proline residue: A 541 - end of helix removed outlier: 3.504A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.959A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.526A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.807A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 675 removed outlier: 3.605A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.792A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.192A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.882A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.507A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 906 through 919 Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 932 through 946 removed outlier: 4.046A pdb=" N GLU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.840A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.733A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.319A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.611A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.563A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.811A pdb=" N VAL B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 376' Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.753A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 489 Proline residue: B 466 - end of helix removed outlier: 3.668A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.256A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix removed outlier: 3.571A pdb=" N ASP B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 4.043A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.856A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 675 removed outlier: 3.790A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.688A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.057A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.826A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.932A pdb=" N LYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.182A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 884 through 888 removed outlier: 4.452A pdb=" N LYS B 887 " --> pdb=" O VAL B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 919 removed outlier: 3.761A pdb=" N AALA B 910 " --> pdb=" O ALYS B 906 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N BTHR B 911 " --> pdb=" O BLYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 931 No H-bonds generated for 'chain 'B' and resid 929 through 931' Processing helix chain 'B' and resid 932 through 946 removed outlier: 3.945A pdb=" N GLU B 938 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 4.078A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.491A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN A 859 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A1054 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP A 861 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN A1056 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TRP A 863 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 921 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.523A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B1056 " --> pdb=" O TRP B 863 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 921 " --> pdb=" O ILE B 890 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2367 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: 4.77 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4284 1.35 - 1.48: 3541 1.48 - 1.60: 5922 1.60 - 1.73: 0 1.73 - 1.86: 148 Bond restraints: 13895 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 13890 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.12: 304 106.12 - 113.08: 7775 113.08 - 120.05: 4645 120.05 - 127.02: 6013 127.02 - 133.99: 171 Bond angle restraints: 18908 Sorted by residual: angle pdb=" N BGLU A 919 " pdb=" CA BGLU A 919 " pdb=" C BGLU A 919 " ideal model delta sigma weight residual 110.91 115.72 -4.81 1.17e+00 7.31e-01 1.69e+01 angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 115.92 6.46 1.81e+00 3.05e-01 1.27e+01 angle pdb=" N VAL B 494 " pdb=" CA VAL B 494 " pdb=" C VAL B 494 " ideal model delta sigma weight residual 111.90 109.28 2.62 8.10e-01 1.52e+00 1.04e+01 angle pdb=" CA CYS B 640 " pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 1.00e+01 angle pdb=" N ARG A 454 " pdb=" CA ARG A 454 " pdb=" C ARG A 454 " ideal model delta sigma weight residual 110.44 106.95 3.49 1.20e+00 6.94e-01 8.48e+00 ... (remaining 18903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 7572 16.49 - 32.98: 514 32.98 - 49.46: 86 49.46 - 65.95: 15 65.95 - 82.44: 4 Dihedral angle restraints: 8191 sinusoidal: 3071 harmonic: 5120 Sorted by residual: dihedral pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " pdb=" SG CYS B 640 " pdb=" CB CYS B 640 " ideal model delta sinusoidal sigma weight residual 93.00 48.74 44.26 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 154.20 25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLN B 707 " pdb=" C GLN B 707 " pdb=" N LEU B 708 " pdb=" CA LEU B 708 " ideal model delta harmonic sigma weight residual -180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 8188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1860 0.054 - 0.107: 342 0.107 - 0.161: 46 0.161 - 0.214: 1 0.214 - 0.268: 3 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA CYS B 640 " pdb=" N CYS B 640 " pdb=" C CYS B 640 " pdb=" CB CYS B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2249 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 640 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C CYS B 640 " -0.046 2.00e-02 2.50e+03 pdb=" O CYS B 640 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 641 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 142 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 143 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 442 " -0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 443 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " -0.023 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2124 2.76 - 3.29: 14024 3.29 - 3.83: 22822 3.83 - 4.36: 26503 4.36 - 4.90: 45833 Nonbonded interactions: 111306 Sorted by model distance: nonbonded pdb=" OD1 ASN A 859 " pdb=" OG SER A 889 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR B 308 " pdb=" OG SER B 482 " model vdw 2.240 2.440 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.248 2.520 nonbonded pdb=" O PRO B1058 " pdb=" OH TYR B1070 " model vdw 2.260 2.440 nonbonded pdb=" O ILE A1043 " pdb=" OG SER A1047 " model vdw 2.288 2.440 ... (remaining 111301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 341 or (resid 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 393 or (resid \ 394 and (name N or name CA or name C or name O or name CB )) or resid 395 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 428 or (resid 429 and (name N or name CA or name C or name O o \ r name CB )) or resid 430 through 491 or (resid 492 and (name N or name CA or na \ me C or name O or name CB )) or resid 493 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 through 715 or (resid \ 716 and (name N or name CA or name C or name O or name CB )) or resid 717 throug \ h 856 or (resid 857 and (name N or name CA or name C or name O or name CB )) or \ resid 858 through 882 or (resid 883 and (name N or name CA or name C or name O o \ r name CB )) or resid 884 through 896 or resid 920 through 928 or (resid 929 and \ (name N or name CA or name C or name O or name CB )) or resid 930 or (resid 931 \ and (name N or name CA or name C or name O or name CB )) or resid 932 through 9 \ 37 or (resid 938 through 939 and (name N or name CA or name C or name O or name \ CB )) or resid 940 or (resid 941 and (name N or name CA or name C or name O or n \ ame CB )) or resid 942 through 1045 or (resid 1046 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1047 through 1078 or (resid 1079 and (name \ N or name CA or name C or name O or name CB )) or resid 1080 through 1081 or (re \ sid 1082 and (name N or name CA or name C or name O or name CB )) or resid 1083 \ through 1093 or resid 1104)) selection = (chain 'B' and (resid 102 through 112 or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 118 or (resid 119 \ through 121 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 3 through 211 or (resid 212 and (name N or name CA or name C or name O or name C \ B )) or resid 213 through 286 or (resid 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 through 352 or (resid 353 and \ (name N or name CA or name C or name O or name CB )) or resid 354 through 364 or \ (resid 365 through 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 through 417 or (resid 418 and (name N or name CA or name C or name \ O or name CB )) or resid 419 through 420 or (resid 421 and (name N or name CA o \ r name C or name O or name CB )) or resid 422 through 462 or (resid 463 and (nam \ e N or name CA or name C or name O or name CB )) or resid 464 through 616 or (re \ sid 617 and (name N or name CA or name C or name O or name CB )) or resid 618 th \ rough 634 or (resid 635 and (name N or name CA or name C or name O or name CB )) \ or resid 636 through 814 or (resid 815 and (name N or name CA or name C or name \ O or name CB )) or resid 816 or (resid 817 and (name N or name CA or name C or \ name O or name CB )) or resid 818 through 872 or (resid 873 and (name N or name \ CA or name C or name O or name CB )) or resid 874 through 896 or resid 920 throu \ gh 942 or (resid 943 through 946 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1028 through 1030 or (resid 1031 and (name N or name CA or na \ me C or name O or name CB )) or resid 1032 through 1071 or (resid 1072 and (name \ N or name CA or name C or name O or name CB )) or resid 1073 through 1093 or re \ sid 1104)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 4.320 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: 0.000 Extract box with map and model: 18.670 Check model and map are aligned: 0.280 Set scattering table: 0.120 Process input model: 47.090 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.004 0.054 13895 Z= 0.233 Angle : 0.640 8.623 18908 Z= 0.379 Chirality : 0.042 0.268 2252 Planarity : 0.004 0.042 2348 Dihedral : 11.394 82.440 4881 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % 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: -2.26 (0.18), residues: 1768 helix: -0.81 (0.15), residues: 960 sheet: -1.87 (0.45), residues: 92 loop : -2.34 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.002 0.001 HIS B 790 PHE 0.014 0.001 PHE B1073 TYR 0.009 0.001 TYR B 628 ARG 0.003 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2534 time to fit residues: 68.0099 Evaluate side-chains 114 residues out of total 1438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9554 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 51.481 > 50: distance: 84 - 87: 15.190 distance: 87 - 88: 12.888 distance: 88 - 89: 16.771 distance: 88 - 91: 29.909 distance: 89 - 90: 17.973 distance: 89 - 95: 9.038 distance: 91 - 92: 23.937 distance: 95 - 96: 6.620 distance: 96 - 97: 12.455 distance: 97 - 98: 12.140 distance: 97 - 99: 7.553 distance: 99 - 100: 25.122 distance: 100 - 101: 19.476 distance: 100 - 103: 3.345 distance: 101 - 102: 15.556 distance: 101 - 108: 10.227 distance: 103 - 104: 26.095 distance: 104 - 105: 10.904 distance: 105 - 106: 7.206 distance: 105 - 107: 6.078 distance: 108 - 109: 10.510 distance: 108 - 114: 5.143 distance: 109 - 110: 22.133 distance: 109 - 112: 19.726 distance: 110 - 111: 4.376 distance: 110 - 115: 19.924 distance: 112 - 113: 5.298 distance: 113 - 114: 9.418 distance: 115 - 116: 6.180 distance: 116 - 117: 17.997 distance: 116 - 119: 12.988 distance: 117 - 118: 11.009 distance: 117 - 122: 19.665 distance: 118 - 149: 15.262 distance: 119 - 120: 12.164 distance: 122 - 123: 11.157 distance: 123 - 124: 16.150 distance: 123 - 126: 12.356 distance: 124 - 125: 9.163 distance: 124 - 136: 14.886 distance: 125 - 157: 20.085 distance: 126 - 127: 14.776 distance: 127 - 128: 5.574 distance: 127 - 129: 3.150 distance: 128 - 130: 18.238 distance: 129 - 131: 17.626 distance: 129 - 132: 10.251 distance: 130 - 131: 7.262 distance: 131 - 133: 8.670 distance: 132 - 134: 13.452 distance: 133 - 135: 8.521 distance: 134 - 135: 17.625 distance: 136 - 137: 17.596 distance: 137 - 138: 12.266 distance: 137 - 140: 14.813 distance: 138 - 139: 4.260 distance: 138 - 141: 12.973 distance: 139 - 165: 15.965 distance: 141 - 142: 7.873 distance: 142 - 143: 6.576 distance: 142 - 145: 9.497 distance: 143 - 144: 7.664 distance: 143 - 149: 13.613 distance: 144 - 172: 16.289 distance: 145 - 146: 15.025 distance: 146 - 147: 14.512 distance: 146 - 148: 11.521 distance: 149 - 150: 23.825 distance: 150 - 151: 13.226 distance: 150 - 153: 5.153 distance: 151 - 152: 22.915 distance: 151 - 157: 11.585 distance: 152 - 177: 21.560 distance: 153 - 154: 3.108 distance: 154 - 155: 6.060 distance: 154 - 156: 16.494 distance: 157 - 158: 21.908 distance: 158 - 159: 12.143 distance: 158 - 161: 15.639 distance: 159 - 160: 26.386 distance: 159 - 165: 8.269 distance: 160 - 182: 14.704 distance: 161 - 162: 8.238 distance: 162 - 163: 17.162 distance: 162 - 164: 20.278