Starting phenix.real_space_refine on Sat Jul 4 21:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imm_60693/07_2026/9imm_60693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imm_60693/07_2026/9imm_60693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9imm_60693/07_2026/9imm_60693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imm_60693/07_2026/9imm_60693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9imm_60693/07_2026/9imm_60693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imm_60693/07_2026/9imm_60693.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 108 5.49 5 S 155 5.16 5 C 14158 2.51 5 N 3862 2.21 5 O 4647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22938 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7473 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PTRANS': 30, 'TRANS': 895} Conformer: "B" Number of residues, atoms: 925, 7447 Classifications: {'peptide': 925} Link IDs: {'PTRANS': 30, 'TRANS': 894} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7622 Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1408 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4500 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4488 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 584, 4488 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 553} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "O" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 223 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 6, None: 1} Not linked: pdbres="ATP O 1 " pdbres=" U O 2 " Chain: "P" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 853 Unusual residues: {'ATP': 1} Classifications: {'RNA': 39, 'undetermined': 1} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 2, 'rna3p': 36, None: 1} Not linked: pdbres="ATP P 1 " pdbres=" U P 2 " Chain: "Q" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "R" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 955 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 21} Link IDs: {'rna2p': 3, 'rna3p': 41} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 130.229 69.259 45.544 1.00 51.96 S ATOM 2487 SG CYS A 306 129.594 66.323 43.190 1.00 53.73 S ATOM 2519 SG CYS A 310 132.337 66.147 45.849 1.00 47.80 S ATOM 3927 SG CYS A 487 112.533 80.564 48.407 1.00 49.22 S ATOM 5180 SG CYS A 645 111.746 78.432 45.412 1.00 39.76 S ATOM 5186 SG CYS A 646 115.363 79.482 46.149 1.00 49.92 S ATOM 10956 SG CYS E 16 93.753 113.517 96.231 1.00140.33 S ATOM 10971 SG CYS E 19 95.916 114.252 99.453 1.00124.37 S ATOM 10874 SG CYS E 5 87.559 107.022 103.995 1.00108.40 S ATOM 10895 SG CYS E 8 84.152 107.422 105.690 1.00118.32 S ATOM 11033 SG CYS E 26 84.266 106.957 101.888 1.00 59.38 S ATOM 11050 SG CYS E 29 85.273 110.098 103.273 1.00 89.96 S ATOM 11215 SG CYS E 50 91.349 107.549 77.220 1.00 99.30 S ATOM 11245 SG CYS E 55 93.040 110.990 76.786 1.00104.48 S ATOM 11378 SG CYS E 72 89.251 110.453 75.878 1.00 87.89 S ATOM 15456 SG CYS F 16 104.467 123.490 52.735 1.00 46.64 S ATOM 15471 SG CYS F 19 107.313 126.023 52.424 1.00114.01 S ATOM 15374 SG CYS F 5 102.052 126.058 64.464 1.00118.76 S ATOM 15395 SG CYS F 8 99.394 128.298 66.109 1.00 87.18 S ATOM 15533 SG CYS F 26 98.304 125.358 63.978 1.00 82.75 S ATOM 15550 SG CYS F 29 99.687 128.398 62.381 1.00 59.80 S ATOM 15715 SG CYS F 50 95.086 108.148 44.884 1.00123.65 S ATOM 15745 SG CYS F 55 95.588 109.242 41.235 1.00153.53 S ATOM 15878 SG CYS F 72 92.088 109.434 42.777 1.00119.30 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 726 " occ=0.70 ... (20 atoms not shown) pdb=" NH2BARG A 726 " occ=0.30 residue: pdb=" N AMET E 474 " occ=0.90 ... (6 atoms not shown) pdb=" CE AMET E 474 " occ=0.90 residue: pdb=" N AMET F 474 " occ=0.52 ... (6 atoms not shown) pdb=" CE AMET F 474 " occ=0.52 Time building chain proxies: 6.50, per 1000 atoms: 0.28 Number of scatterers: 22938 At special positions: 0 Unit cell: (169.74, 175.48, 159.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 155 16.00 P 108 15.00 O 4647 8.00 N 3862 7.00 C 14158 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 28 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5062 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 29 sheets defined 43.0% alpha, 15.3% beta 39 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.652A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.504A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.640A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.686A pdb=" N ASN A 138 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS A 139 " --> pdb=" O GLU A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 179 through 199 removed outlier: 3.836A pdb=" N ARG A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 3.939A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.531A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.706A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.593A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.753A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.558A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.987A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 481 removed outlier: 3.838A pdb=" N ASP A 481 " --> pdb=" O LYS A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.704A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.635A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.565A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 3.987A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 899 " --> pdb=" O LEU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.683A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.212A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 55 removed outlier: 5.245A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 96 removed outlier: 4.218A pdb=" N MET B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.745A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.525A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.670A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.604A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 3.720A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.503A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.650A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 44 removed outlier: 4.307A pdb=" N LEU D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 removed outlier: 3.838A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.661A pdb=" N TYR D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.541A pdb=" N ALA D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.802A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.663A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.717A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 265 through 273 removed outlier: 3.651A pdb=" N GLY E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.819A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.752A pdb=" N VAL E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'E' and resid 380 through 390 removed outlier: 3.583A pdb=" N ASN E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 457 Processing helix chain 'E' and resid 489 through 503 Processing helix chain 'E' and resid 504 through 509 removed outlier: 3.764A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 527 removed outlier: 3.585A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.631A pdb=" N GLN E 537 " --> pdb=" O VAL E 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 537' Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 578 through 585 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.685A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.834A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 273 Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.840A pdb=" N GLY F 294 " --> pdb=" O HIS F 290 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.581A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 430 removed outlier: 3.694A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET F 429 " --> pdb=" O VAL F 425 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.627A pdb=" N ALA F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 Processing helix chain 'F' and resid 504 through 509 removed outlier: 3.751A pdb=" N LYS F 508 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 527 Processing helix chain 'F' and resid 552 through 557 Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 578 through 585 Processing helix chain 'G' and resid 19 through 23 removed outlier: 4.421A pdb=" N CYS G 23 " --> pdb=" O GLN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.391A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 106 removed outlier: 3.536A pdb=" N ASP A 109 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.233A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 5.899A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.818A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.543A pdb=" N VAL A 844 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.573A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.766A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AB4, first strand: chain 'E' and resid 69 through 72 removed outlier: 3.894A pdb=" N PHE E 81 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB6, first strand: chain 'E' and resid 162 through 167 removed outlier: 7.762A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 224 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 347 through 348 removed outlier: 3.960A pdb=" N LYS E 347 " --> pdb=" O CYS E 330 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N THR E 367 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N HIS E 395 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP E 369 " --> pdb=" O HIS E 395 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL E 397 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 440 through 441 Processing sheet with id=AB9, first strand: chain 'E' and resid 530 through 532 removed outlier: 6.355A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP E 542 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N AMET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AC4, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'F' and resid 192 through 198 removed outlier: 6.303A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL F 157 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU F 162 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 347 through 348 removed outlier: 4.060A pdb=" N LYS F 347 " --> pdb=" O CYS F 330 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F 308 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR F 279 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 440 through 441 Processing sheet with id=AC9, first strand: chain 'F' and resid 530 through 532 removed outlier: 6.324A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR F 541 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY F 571 " --> pdb=" O TYR F 541 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR F 543 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU F 573 " --> pdb=" O TYR F 543 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE F 545 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 575 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR F 547 " --> pdb=" O ILE F 575 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET F 576 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N AMET F 474 " --> pdb=" O MET F 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 481 through 482 Processing sheet with id=AD2, first strand: chain 'G' and resid 64 through 68 removed outlier: 4.083A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N SER G 13 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU G 29 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU G 44 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR G 35 " --> pdb=" O GLY G 38 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3559 1.31 - 1.44: 6979 1.44 - 1.57: 12653 1.57 - 1.69: 213 1.69 - 1.82: 219 Bond restraints: 23623 Sorted by residual: bond pdb=" CA ALA D 74 " pdb=" C ALA D 74 " ideal model delta sigma weight residual 1.522 1.428 0.094 1.40e-02 5.10e+03 4.53e+01 bond pdb=" C3' ATP O 1 " pdb=" O3' ATP O 1 " ideal model delta sigma weight residual 1.423 1.484 -0.061 1.10e-02 8.26e+03 3.10e+01 bond pdb=" CA MET D 67 " pdb=" C MET D 67 " ideal model delta sigma weight residual 1.523 1.455 0.067 1.41e-02 5.03e+03 2.27e+01 bond pdb=" C ARG F 173 " pdb=" N PRO F 174 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.18e-02 7.18e+03 2.15e+01 bond pdb=" CA ASN E 46 " pdb=" C ASN E 46 " ideal model delta sigma weight residual 1.517 1.473 0.044 1.02e-02 9.61e+03 1.86e+01 ... (remaining 23618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 32435 4.35 - 8.70: 122 8.70 - 13.05: 23 13.05 - 17.40: 6 17.40 - 21.75: 1 Bond angle restraints: 32587 Sorted by residual: angle pdb=" C PHE A 504 " pdb=" N PRO A 505 " pdb=" CA PRO A 505 " ideal model delta sigma weight residual 120.31 108.46 11.85 9.80e-01 1.04e+00 1.46e+02 angle pdb=" N ALA D 74 " pdb=" CA ALA D 74 " pdb=" C ALA D 74 " ideal model delta sigma weight residual 112.54 97.89 14.65 1.22e+00 6.72e-01 1.44e+02 angle pdb=" N ASN D 176 " pdb=" CA ASN D 176 " pdb=" C ASN D 176 " ideal model delta sigma weight residual 112.57 101.50 11.07 1.13e+00 7.83e-01 9.60e+01 angle pdb=" N PRO A 505 " pdb=" CA PRO A 505 " pdb=" C PRO A 505 " ideal model delta sigma weight residual 111.57 97.17 14.40 1.52e+00 4.33e-01 8.98e+01 angle pdb=" N MET D 67 " pdb=" CA MET D 67 " pdb=" C MET D 67 " ideal model delta sigma weight residual 113.20 102.38 10.82 1.21e+00 6.83e-01 8.00e+01 ... (remaining 32582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 13581 34.98 - 69.96: 631 69.96 - 104.94: 59 104.94 - 139.92: 2 139.92 - 174.90: 8 Dihedral angle restraints: 14281 sinusoidal: 6437 harmonic: 7844 Sorted by residual: dihedral pdb=" C4' A R 17 " pdb=" C3' A R 17 " pdb=" C2' A R 17 " pdb=" C1' A R 17 " ideal model delta sinusoidal sigma weight residual -35.00 29.03 -64.03 1 8.00e+00 1.56e-02 8.43e+01 dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual 200.00 44.05 155.95 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" C5' A R 17 " pdb=" C4' A R 17 " pdb=" C3' A R 17 " pdb=" O3' A R 17 " ideal model delta sinusoidal sigma weight residual 147.00 86.88 60.12 1 8.00e+00 1.56e-02 7.53e+01 ... (remaining 14278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 3795 0.205 - 0.411: 17 0.411 - 0.616: 1 0.616 - 0.821: 2 0.821 - 1.027: 1 Chirality restraints: 3816 Sorted by residual: chirality pdb=" CA TRP D 182 " pdb=" N TRP D 182 " pdb=" C TRP D 182 " pdb=" CB TRP D 182 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA PHE A 504 " pdb=" N PHE A 504 " pdb=" C PHE A 504 " pdb=" CB PHE A 504 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C3' ATP O 1 " pdb=" C2' ATP O 1 " pdb=" C4' ATP O 1 " pdb=" O3' ATP O 1 " both_signs ideal model delta sigma weight residual False -2.63 -3.31 0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3813 not shown) Planarity restraints: 3778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 69 " -0.048 2.00e-02 2.50e+03 9.58e-02 9.19e+01 pdb=" C GLN D 69 " 0.166 2.00e-02 2.50e+03 pdb=" O GLN D 69 " -0.064 2.00e-02 2.50e+03 pdb=" N MET D 70 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 65 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C LEU E 65 " 0.085 2.00e-02 2.50e+03 pdb=" O LEU E 65 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY E 66 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 61 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C LYS D 61 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS D 61 " 0.028 2.00e-02 2.50e+03 pdb=" N MET D 62 " 0.026 2.00e-02 2.50e+03 ... (remaining 3775 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 15 2.27 - 2.93: 9923 2.93 - 3.59: 33498 3.59 - 4.24: 55343 4.24 - 4.90: 89780 Nonbonded interactions: 188559 Sorted by model distance: nonbonded pdb=" O ASN A 138 " pdb=" OD1 ASN A 138 " model vdw 1.616 3.040 nonbonded pdb=" OG1 THR F 61 " pdb=" OE1 GLN F 62 " model vdw 2.173 3.040 nonbonded pdb=" O THR E 250 " pdb=" NE2 HIS E 395 " model vdw 2.195 3.120 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.214 3.040 nonbonded pdb=" O GLN G 49 " pdb=" OH TYR G 89 " model vdw 2.219 3.040 ... (remaining 188554 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 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 276 or resid 278 through 703)) selection = chain 'F' } 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=0.30 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: 8.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.440 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 0.094 23657 Z= 0.270 Angle : 0.829 21.748 32615 Z= 0.506 Chirality : 0.053 1.027 3816 Planarity : 0.006 0.096 3778 Dihedral : 18.528 174.897 9219 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.03 % Favored : 95.82 % Rotamer: Outliers : 1.37 % Allowed : 18.05 % Favored : 80.58 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2632 helix: -0.00 (0.17), residues: 992 sheet: -0.97 (0.26), residues: 352 loop : -1.31 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 365 TYR 0.026 0.001 TYR F 253 PHE 0.049 0.002 PHE D 49 TRP 0.015 0.001 TRP D 182 HIS 0.025 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.27 (23623) covalent geometry : angle 0.82259 / 0.51 (32587) hydrogen bonds : bond 0.20004 / 13.38 ( 970) hydrogen bonds : angle 6.93769 / 4.88 ( 2609) metal coordination : bond 0.01339 / 0.89 ( 32) metal coordination : angle 3.52888 / 2.50 ( 28) Misc. bond : bond 0.01886 / 0.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 174 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6940 (tpt) REVERT: D 175 ASP cc_start: 0.4171 (OUTLIER) cc_final: 0.3968 (t0) outliers start: 31 outliers final: 11 residues processed: 226 average time/residue: 0.1714 time to fit residues: 60.8021 Evaluate side-chains 208 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 69 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN E 404 GLN ** E 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN F 268 ASN F 404 GLN G 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.193653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.146779 restraints weight = 68256.498| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.43 r_work: 0.3466 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23657 Z= 0.144 Angle : 0.620 9.467 32615 Z= 0.333 Chirality : 0.043 0.326 3816 Planarity : 0.005 0.066 3778 Dihedral : 17.223 171.498 4513 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 1.94 % Allowed : 17.08 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2632 helix: 0.10 (0.16), residues: 1028 sheet: -0.97 (0.26), residues: 362 loop : -1.24 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 155 TYR 0.016 0.001 TYR F 253 PHE 0.032 0.002 PHE A 340 TRP 0.017 0.001 TRP D 182 HIS 0.010 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (23623) covalent geometry : angle 0.61411 / 0.33 (32587) hydrogen bonds : bond 0.05962 / 4.13 ( 970) hydrogen bonds : angle 5.18396 / 3.66 ( 2609) metal coordination : bond 0.01158 / 0.73 ( 32) metal coordination : angle 2.99586 / 2.15 ( 28) Misc. bond : bond 0.00268 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8596 (tp) cc_final: 0.8368 (tt) REVERT: B 77 GLU cc_start: 0.8608 (tt0) cc_final: 0.8401 (mt-10) REVERT: B 171 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 174 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7017 (tpt) REVERT: D 175 ASP cc_start: 0.4565 (OUTLIER) cc_final: 0.4223 (t0) REVERT: D 179 ASN cc_start: 0.5964 (m110) cc_final: 0.5469 (t0) REVERT: E 199 THR cc_start: 0.4036 (p) cc_final: 0.3557 (t) REVERT: E 383 ASP cc_start: 0.6768 (m-30) cc_final: 0.6186 (p0) REVERT: E 572 ILE cc_start: 0.4376 (tp) cc_final: 0.4122 (tt) REVERT: F 71 TYR cc_start: 0.6253 (m-80) cc_final: 0.5905 (m-80) outliers start: 44 outliers final: 25 residues processed: 237 average time/residue: 0.1651 time to fit residues: 62.1833 Evaluate side-chains 219 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 40 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3429 > 50: distance: 25 - 40: 3.582 distance: 29 - 47: 11.036 distance: 33 - 54: 13.870 distance: 36 - 40: 3.669 distance: 37 - 62: 17.209 distance: 41 - 42: 3.772 distance: 41 - 44: 6.094 distance: 42 - 43: 3.050 distance: 42 - 47: 9.347 distance: 43 - 70: 14.024 distance: 44 - 45: 3.171 distance: 44 - 46: 14.604 distance: 47 - 48: 6.190 distance: 48 - 49: 5.126 distance: 48 - 51: 7.518 distance: 49 - 50: 14.728 distance: 49 - 54: 6.700 distance: 50 - 76: 16.140 distance: 51 - 52: 8.650 distance: 51 - 53: 11.363 distance: 54 - 55: 4.721 distance: 55 - 56: 5.928 distance: 56 - 57: 17.572 distance: 57 - 83: 36.101 distance: 58 - 59: 5.881 distance: 59 - 60: 28.059 distance: 59 - 61: 10.545 distance: 62 - 63: 10.666 distance: 63 - 64: 12.636 distance: 63 - 66: 7.081 distance: 64 - 65: 12.483 distance: 64 - 70: 4.151 distance: 65 - 91: 29.162 distance: 66 - 67: 6.152 distance: 67 - 68: 11.453 distance: 67 - 69: 24.359 distance: 70 - 71: 13.958 distance: 71 - 72: 14.802 distance: 71 - 74: 29.781 distance: 72 - 73: 13.472 distance: 72 - 76: 10.371 distance: 73 - 100: 29.424 distance: 74 - 75: 27.626 distance: 76 - 77: 16.697 distance: 77 - 78: 16.902 distance: 77 - 80: 12.137 distance: 78 - 79: 15.808 distance: 78 - 83: 40.367 distance: 79 - 109: 17.718 distance: 80 - 81: 16.808 distance: 80 - 82: 18.808 distance: 83 - 84: 46.606 distance: 84 - 85: 7.501 distance: 84 - 87: 10.616 distance: 85 - 86: 11.633 distance: 85 - 91: 9.905 distance: 87 - 88: 18.182 distance: 88 - 89: 18.985 distance: 88 - 90: 19.533 distance: 91 - 92: 4.353 distance: 92 - 93: 11.108 distance: 92 - 95: 9.249 distance: 93 - 94: 9.960 distance: 93 - 100: 13.922 distance: 95 - 96: 18.777 distance: 96 - 97: 3.752 distance: 97 - 99: 6.642 distance: 100 - 101: 8.518 distance: 101 - 102: 5.582 distance: 101 - 104: 8.715 distance: 102 - 103: 7.360 distance: 102 - 109: 5.261 distance: 104 - 105: 13.665 distance: 105 - 106: 6.606 distance: 106 - 107: 7.196 distance: 106 - 108: 8.825 distance: 110 - 111: 4.198 distance: 110 - 113: 4.554 distance: 111 - 112: 12.368 distance: 111 - 117: 3.923 distance: 113 - 114: 8.103 distance: 114 - 115: 5.633 distance: 114 - 116: 7.728