Starting phenix.real_space_refine on Sun Jul 5 10:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fyh_29578/07_2026/8fyh_29578.cif" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1862 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 14 6.06 5 P 16 5.49 5 S 118 5.16 5 C 16116 2.51 5 N 4722 2.21 5 O 4652 1.98 5 H 195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s 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: 25833 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2931 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 10 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 852 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 12, 'GLU:plan': 24, 'ARG:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 362 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2654 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 12, 'TRANS': 354} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2722 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 6, 'ASN:plan1': 10, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 199 Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3425 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 25, 'TRANS': 488} Chain breaks: 6 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 27, 'TYR:plan': 8, 'ARG:plan': 17, 'GLN:plan1': 13, 'PHE:plan': 6, 'ASN:plan1': 17, 'ASP:plan': 16, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 460 Chain: "E" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 696 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2931 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 10 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 852 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 12, 'GLU:plan': 24, 'ARG:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 362 Chain: "I" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2654 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 12, 'TRANS': 354} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "J" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2722 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 6, 'ASN:plan1': 10, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 199 Chain: "G" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3425 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 25, 'TRANS': 488} Chain breaks: 6 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 27, 'TYR:plan': 8, 'ARG:plan': 17, 'GLN:plan1': 13, 'PHE:plan': 6, 'ASN:plan1': 17, 'ASP:plan': 16, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 460 Chain: "K" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 696 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Inner-chain residues flagged as termini: ['pdbres=" G M 13 "'] Classifications: {'RNA': 18} Modifications used: {'5*END': 2, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10238 SG CYS A 528 90.339 116.747 101.330 1.00 60.88 S ATOM 10283 SG CYS A 535 90.228 113.510 103.412 1.00 64.47 S ATOM 10306 SG CYS A 539 87.780 116.324 104.167 1.00 62.99 S ATOM 10238 SG CYS A 528 90.339 116.747 101.330 1.00 60.88 S ATOM 10319 SG CYS A 541 86.635 117.692 101.125 1.00 58.37 S ATOM 10371 SG CYS A 548 87.792 114.126 100.436 1.00 52.02 S ATOM 10406 SG CYS A 552 88.656 116.974 97.981 1.00 54.69 S ATOM 10283 SG CYS A 535 90.228 113.510 103.412 1.00 64.47 S ATOM 10371 SG CYS A 548 87.792 114.126 100.436 1.00 52.02 S ATOM 10417 SG CYS A 554 91.461 113.258 99.843 1.00 63.09 S ATOM 10440 SG CYS A 558 89.164 110.638 101.245 1.00 60.11 S ATOM 10483 SG CYS A 565 80.615 107.180 84.657 1.00 41.18 S ATOM 10500 SG CYS A 567 77.901 104.647 83.793 1.00 42.37 S ATOM 10529 SG CYS A 571 78.377 107.825 81.753 1.00 43.37 S ATOM 10568 SG CYS A 576 76.870 107.831 85.365 1.00 41.61 S ATOM 10529 SG CYS A 571 78.377 107.825 81.753 1.00 43.37 S ATOM 10635 SG CYS A 585 79.879 110.752 83.790 1.00 40.34 S ATOM 10687 SG CYS A 593 81.762 109.337 80.816 1.00 45.19 S ATOM 10752 SG CYS A 606 78.593 111.403 80.386 1.00 45.47 S ATOM 10483 SG CYS A 565 80.615 107.180 84.657 1.00 41.18 S ATOM 10581 SG CYS A 578 80.133 109.766 87.445 1.00 39.24 S ATOM 10635 SG CYS A 585 79.879 110.752 83.790 1.00 40.34 S ATOM 10666 SG CYS A 590 83.240 109.917 85.431 1.00 40.89 S ATOM 9400 SG CYS A 286 90.777 127.789 90.691 1.00 47.70 S ATOM 9422 SG CYS A 289 89.985 128.993 87.154 1.00 48.85 S ATOM 9464 SG CYS A 294 88.805 131.009 90.118 1.00 52.79 S ATOM 22853 SG CYS G 528 59.702 94.795 98.482 1.00 66.92 S ATOM 22898 SG CYS G 535 59.018 98.554 98.482 1.00 75.43 S ATOM 22921 SG CYS G 539 60.623 96.897 101.551 1.00 72.84 S ATOM 22853 SG CYS G 528 59.702 94.795 98.482 1.00 66.92 S ATOM 22934 SG CYS G 541 62.975 94.420 100.451 1.00 66.08 S ATOM 22986 SG CYS G 548 62.570 97.127 97.799 1.00 59.26 S ATOM 23021 SG CYS G 552 62.658 93.378 96.783 1.00 62.91 S ATOM 22898 SG CYS G 535 59.018 98.554 98.482 1.00 75.43 S ATOM 22986 SG CYS G 548 62.570 97.127 97.799 1.00 59.26 S ATOM 23032 SG CYS G 554 59.866 97.024 95.106 1.00 68.11 S ATOM 23055 SG CYS G 558 61.321 100.342 96.145 1.00 60.99 S ATOM 23098 SG CYS G 565 77.208 97.039 86.046 1.00 51.59 S ATOM 23115 SG CYS G 567 80.326 99.205 85.523 1.00 52.76 S ATOM 23144 SG CYS G 571 80.441 95.423 85.244 1.00 50.12 S ATOM 23183 SG CYS G 576 79.995 97.323 88.679 1.00 48.33 S ATOM 23144 SG CYS G 571 80.441 95.423 85.244 1.00 50.12 S ATOM 23250 SG CYS G 585 77.790 93.647 87.384 1.00 47.91 S ATOM 23302 SG CYS G 593 77.778 93.291 83.553 1.00 52.35 S ATOM 23367 SG CYS G 606 80.365 91.604 85.781 1.00 52.79 S ATOM 23098 SG CYS G 565 77.208 97.039 86.046 1.00 51.59 S ATOM 23196 SG CYS G 578 75.887 96.170 89.555 1.00 47.84 S ATOM 23250 SG CYS G 585 77.790 93.647 87.384 1.00 47.91 S ATOM 23281 SG CYS G 590 74.200 94.646 86.600 1.00 49.28 S ATOM 22015 SG CYS G 286 63.244 80.196 95.522 1.00 53.44 S ATOM 22037 SG CYS G 289 65.666 77.827 93.732 1.00 52.91 S ATOM 22079 SG CYS G 294 64.902 77.319 97.365 1.00 57.60 S Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="ZN ZN A 801 " occ=0.47 residue: pdb="ZN ZN A 802 " occ=0.40 residue: pdb="ZN ZN A 803 " occ=0.67 residue: pdb="ZN ZN A 804 " occ=0.49 residue: pdb="ZN ZN A 805 " occ=0.62 residue: pdb="ZN ZN A 806 " occ=0.00 residue: pdb="ZN ZN A 807 " occ=0.51 residue: pdb="ZN ZN G 801 " occ=0.47 residue: pdb="ZN ZN G 802 " occ=0.29 residue: pdb="ZN ZN G 803 " occ=0.68 residue: pdb="ZN ZN G 804 " occ=0.37 residue: pdb="ZN ZN G 805 " occ=0.57 ... (remaining 2 not shown) Time building chain proxies: 6.34, per 1000 atoms: 0.25 Number of scatterers: 25833 At special positions: 0 Unit cell: (171.214, 203.117, 146.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 14 29.99 S 118 16.00 P 16 15.00 O 4652 8.00 N 4722 7.00 C 16116 6.00 H 195 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 457 " distance=1.79 Simple disulfide: pdb=" SG CYS G 325 " - pdb=" SG CYS G 457 " distance=1.82 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 530 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 528 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 528 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 541 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 548 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 554 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 558 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 548 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 571 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 565 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 576 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 606 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 593 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 571 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 578 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 590 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 565 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 294 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 286 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 289 " pdb=" ZN G 801 " pdb="ZN ZN G 801 " - pdb=" NE2 HIS G 530 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 528 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 539 " pdb="ZN ZN G 801 " - pdb=" SG CYS G 535 " pdb=" ZN G 802 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 528 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 552 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 541 " pdb="ZN ZN G 802 " - pdb=" SG CYS G 548 " pdb=" ZN G 803 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 558 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 554 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 535 " pdb="ZN ZN G 803 " - pdb=" SG CYS G 548 " pdb=" ZN G 804 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 567 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 565 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 571 " pdb="ZN ZN G 804 " - pdb=" SG CYS G 576 " pdb=" ZN G 805 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 585 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 606 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 593 " pdb="ZN ZN G 805 " - pdb=" SG CYS G 571 " pdb=" ZN G 806 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 585 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 578 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 590 " pdb="ZN ZN G 806 " - pdb=" SG CYS G 565 " pdb=" ZN G 807 " pdb="ZN ZN G 807 " - pdb=" ND1 HIS G 297 " pdb="ZN ZN G 807 " - pdb=" SG CYS G 294 " pdb="ZN ZN G 807 " - pdb=" SG CYS G 289 " pdb="ZN ZN G 807 " - pdb=" SG CYS G 286 " Number of angles added : 72 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7092 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 46 sheets defined 24.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 80 through 105 removed outlier: 3.546A pdb=" N GLU B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Proline residue: B 93 - end of helix removed outlier: 3.535A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 5.599A pdb=" N THR B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR B 117 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 459 through 470 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.587A pdb=" N GLU B 542 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 544 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 589 through 602 Processing helix chain 'B' and resid 607 through 625 Processing helix chain 'B' and resid 628 through 643 removed outlier: 3.679A pdb=" N ASN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 652 through 666 Processing helix chain 'B' and resid 670 through 689 Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.587A pdb=" N GLY C 130 " --> pdb=" O HIS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'D' and resid 4 through 27 Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.210A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 61 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 335 through 345 Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'A' and resid 467 through 479 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 653 through 664 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 730 through 734 removed outlier: 4.258A pdb=" N TYR A 733 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.806A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 149 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.555A pdb=" N ARG E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 210 Processing helix chain 'F' and resid 255 through 262 Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'H' and resid 81 through 105 Proline residue: H 93 - end of helix removed outlier: 3.614A pdb=" N LEU H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 5.878A pdb=" N THR H 116 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR H 117 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 459 through 470 Processing helix chain 'H' and resid 502 through 508 removed outlier: 3.555A pdb=" N ARG H 508 " --> pdb=" O ASP H 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 544 removed outlier: 3.538A pdb=" N GLU H 542 " --> pdb=" O SER H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 589 through 602 Processing helix chain 'H' and resid 607 through 625 Processing helix chain 'H' and resid 628 through 643 removed outlier: 3.813A pdb=" N ASN H 633 " --> pdb=" O ASP H 629 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET H 637 " --> pdb=" O ASN H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 643 through 651 Processing helix chain 'H' and resid 652 through 666 Processing helix chain 'H' and resid 670 through 689 Processing helix chain 'I' and resid 127 through 131 removed outlier: 3.611A pdb=" N GLY I 130 " --> pdb=" O HIS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 279 Processing helix chain 'J' and resid 4 through 27 Processing helix chain 'J' and resid 348 through 350 No H-bonds generated for 'chain 'J' and resid 348 through 350' Processing helix chain 'J' and resid 355 through 362 Processing helix chain 'J' and resid 406 through 409 Processing helix chain 'G' and resid 23 through 61 Processing helix chain 'G' and resid 168 through 178 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 239 through 250 Processing helix chain 'G' and resid 273 through 278 Processing helix chain 'G' and resid 278 through 284 Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 438 through 453 Processing helix chain 'G' and resid 455 through 463 Processing helix chain 'G' and resid 467 through 479 Processing helix chain 'G' and resid 539 through 544 Processing helix chain 'G' and resid 576 through 581 Processing helix chain 'G' and resid 609 through 614 Processing helix chain 'G' and resid 652 through 664 Processing helix chain 'G' and resid 688 through 691 Processing helix chain 'G' and resid 730 through 734 removed outlier: 4.120A pdb=" N TYR G 733 " --> pdb=" O ASP G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 742 removed outlier: 4.006A pdb=" N TYR G 741 " --> pdb=" O ASP G 737 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 151 Processing helix chain 'K' and resid 159 through 164 Processing helix chain 'L' and resid 192 through 209 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 270 through 272 No H-bonds generated for 'chain 'L' and resid 270 through 272' Processing helix chain 'L' and resid 276 through 281 Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 164 removed outlier: 3.502A pdb=" N GLU B 316 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 229 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE F 227 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL F 226 " --> pdb=" O HIS F 242 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS F 242 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.647A pdb=" N THR B 358 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 316 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 229 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE F 227 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 203 through 206 removed outlier: 3.545A pdb=" N SER B 247 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 441 removed outlier: 6.302A pdb=" N PHE B 429 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 489 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN B 431 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE B 491 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N LEU B 433 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 557 through 560 removed outlier: 3.832A pdb=" N TYR B 557 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 35 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.953A pdb=" N ARG C 436 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 87 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE C 434 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 415 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 96 through 101 removed outlier: 4.129A pdb=" N LEU C 111 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 121 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER C 137 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 123 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N LYS A 99 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 137 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.537A pdb=" N ALA C 166 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 176 " --> pdb=" O CYS C 182 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N CYS C 182 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.412A pdb=" N LEU C 215 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE C 228 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 217 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 241 through 244 Processing sheet with id=AB2, first strand: chain 'C' and resid 309 through 315 removed outlier: 3.976A pdb=" N CYS C 311 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 323 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS C 332 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE C 352 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB4, first strand: chain 'D' and resid 47 through 54 removed outlier: 3.618A pdb=" N GLN D 48 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG D 65 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE D 63 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 77 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 121 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER D 83 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE D 117 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 139 through 143 Processing sheet with id=AB6, first strand: chain 'D' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'D' and resid 230 through 235 Processing sheet with id=AB8, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AB9, first strand: chain 'D' and resid 320 through 325 removed outlier: 5.779A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AC2, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.545A pdb=" N SER A 114 " --> pdb=" O GLY A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.252A pdb=" N PHE A 120 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N SER A 652 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 619 through 623 Processing sheet with id=AC5, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.901A pdb=" N ILE A 715 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU A 645 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 713 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.742A pdb=" N GLU H 316 " --> pdb=" O LYS L 229 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS L 229 " --> pdb=" O GLU H 316 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE L 227 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU L 240 " --> pdb=" O ILE L 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 232 through 233 removed outlier: 3.742A pdb=" N GLU H 316 " --> pdb=" O LYS L 229 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS L 229 " --> pdb=" O GLU H 316 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE L 227 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 203 through 206 removed outlier: 3.625A pdb=" N SER H 247 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 438 through 443 removed outlier: 6.266A pdb=" N PHE H 429 " --> pdb=" O ILE H 487 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL H 489 " --> pdb=" O PHE H 429 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLN H 431 " --> pdb=" O VAL H 489 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE H 491 " --> pdb=" O GLN H 431 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N LEU H 433 " --> pdb=" O ILE H 491 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 557 through 560 removed outlier: 3.723A pdb=" N TYR H 557 " --> pdb=" O ILE H 528 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL J 35 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU J 34 " --> pdb=" O GLN J 403 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE J 398 " --> pdb=" O SER J 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 82 through 87 removed outlier: 7.015A pdb=" N ARG I 436 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER I 87 " --> pdb=" O ILE I 434 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE I 434 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN I 415 " --> pdb=" O VAL I 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 96 through 101 removed outlier: 6.727A pdb=" N VAL I 116 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL I 99 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA I 114 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE I 101 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL I 112 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU I 111 " --> pdb=" O CYS I 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN I 136 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU I 125 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU I 134 " --> pdb=" O GLU I 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 149 through 154 removed outlier: 3.507A pdb=" N LYS I 184 " --> pdb=" O ILE I 174 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN I 176 " --> pdb=" O CYS I 182 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N CYS I 182 " --> pdb=" O ASN I 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 193 through 198 removed outlier: 6.420A pdb=" N LEU I 215 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE I 228 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU I 217 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 241 through 244 Processing sheet with id=AD7, first strand: chain 'I' and resid 309 through 315 removed outlier: 3.894A pdb=" N CYS I 311 " --> pdb=" O LYS I 322 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER I 323 " --> pdb=" O ALA I 327 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA I 327 " --> pdb=" O SER I 323 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS I 332 " --> pdb=" O ILE I 352 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE I 352 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 369 through 370 Processing sheet with id=AD9, first strand: chain 'J' and resid 49 through 54 removed outlier: 4.763A pdb=" N ARG J 65 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP J 52 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE J 63 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN J 77 " --> pdb=" O ASN J 122 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN J 122 " --> pdb=" O ASN J 77 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU J 79 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS J 120 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE J 81 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 139 through 143 Processing sheet with id=AE2, first strand: chain 'J' and resid 184 through 185 Processing sheet with id=AE3, first strand: chain 'J' and resid 232 through 235 Processing sheet with id=AE4, first strand: chain 'J' and resid 280 through 281 Processing sheet with id=AE5, first strand: chain 'J' and resid 322 through 325 removed outlier: 5.625A pdb=" N ASP J 346 " --> pdb=" O LEU J 366 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU J 366 " --> pdb=" O ASP J 346 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 82 through 85 Processing sheet with id=AE7, first strand: chain 'G' and resid 114 through 115 removed outlier: 5.617A pdb=" N SER G 114 " --> pdb=" O GLY G 686 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 114 through 115 removed outlier: 5.617A pdb=" N SER G 114 " --> pdb=" O GLY G 686 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 619 through 623 Processing sheet with id=AF1, first strand: chain 'G' and resid 642 through 645 removed outlier: 6.803A pdb=" N ILE G 715 " --> pdb=" O ILE G 643 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU G 645 " --> pdb=" O ILE G 713 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE G 713 " --> pdb=" O GLU G 645 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2841 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: 6.14 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 195 1.13 - 1.30: 4197 1.30 - 1.47: 11351 1.47 - 1.64: 10590 1.64 - 1.81: 152 Bond restraints: 26485 Sorted by residual: bond pdb=" C8 G M 14 " pdb=" H8 G M 14 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C6 U M 22 " pdb=" H6 U M 22 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" C6 U M 16 " pdb=" H6 U M 16 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C6 U M 4 " pdb=" H6 U M 4 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C8 G M 15 " pdb=" H8 G M 15 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.37e+01 ... (remaining 26480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 36259 2.57 - 5.14: 271 5.14 - 7.71: 7 7.71 - 10.28: 1 10.28 - 12.84: 1 Bond angle restraints: 36539 Sorted by residual: angle pdb=" C THR A 310 " pdb=" CA THR A 310 " pdb=" CB THR A 310 " ideal model delta sigma weight residual 116.54 110.18 6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C5' G M 1 " pdb=" O5' G M 1 " pdb="HO5' G M 1 " ideal model delta sigma weight residual 120.00 107.16 12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N ILE I 265 " pdb=" CA ILE I 265 " pdb=" C ILE I 265 " ideal model delta sigma weight residual 112.29 108.34 3.95 9.40e-01 1.13e+00 1.77e+01 angle pdb=" O4' G M 21 " pdb=" C4' G M 21 " pdb=" C3' G M 21 " ideal model delta sigma weight residual 104.00 107.99 -3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" CA ASN A 434 " pdb=" CB ASN A 434 " pdb=" CG ASN A 434 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 ... (remaining 36534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.99: 14815 29.99 - 59.98: 510 59.98 - 89.97: 24 89.97 - 119.96: 1 119.96 - 149.95: 2 Dihedral angle restraints: 15352 sinusoidal: 4526 harmonic: 10826 Sorted by residual: dihedral pdb=" C5' G M 7 " pdb=" C4' G M 7 " pdb=" C3' G M 7 " pdb=" O3' G M 7 " ideal model delta sinusoidal sigma weight residual 147.00 100.36 46.64 1 8.00e+00 1.56e-02 4.70e+01 dihedral pdb=" O4' G M 7 " pdb=" C4' G M 7 " pdb=" C3' G M 7 " pdb=" C2' G M 7 " ideal model delta sinusoidal sigma weight residual 24.00 -19.31 43.31 1 8.00e+00 1.56e-02 4.08e+01 dihedral pdb=" C3' G M 7 " pdb=" C4' G M 7 " pdb=" O4' G M 7 " pdb=" C1' G M 7 " ideal model delta sinusoidal sigma weight residual -2.00 35.87 -37.87 1 8.00e+00 1.56e-02 3.16e+01 ... (remaining 15349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3476 0.057 - 0.114: 578 0.114 - 0.170: 43 0.170 - 0.227: 5 0.227 - 0.284: 12 Chirality restraints: 4114 Sorted by residual: chirality pdb=" C3' G M 3 " pdb=" C4' G M 3 " pdb=" O3' G M 3 " pdb=" C2' G M 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' G M 15 " pdb=" C4' G M 15 " pdb=" O3' G M 15 " pdb=" C2' G M 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN A 434 " pdb=" N ASN A 434 " pdb=" C ASN A 434 " pdb=" CB ASN A 434 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 4111 not shown) Planarity restraints: 4720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A M 18 " 0.076 2.00e-02 2.50e+03 3.77e-02 4.62e+01 pdb=" N9 A M 18 " 0.002 2.00e-02 2.50e+03 pdb=" C8 A M 18 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A M 18 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A M 18 " 0.016 2.00e-02 2.50e+03 pdb=" C6 A M 18 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A M 18 " 0.026 2.00e-02 2.50e+03 pdb=" N1 A M 18 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A M 18 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A M 18 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A M 18 " 0.008 2.00e-02 2.50e+03 pdb=" H8 A M 18 " -0.085 2.00e-02 2.50e+03 pdb=" H2 A M 18 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G M 1 " 0.081 2.00e-02 2.50e+03 2.98e-02 3.10e+01 pdb=" N9 G M 1 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G M 1 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G M 1 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G M 1 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G M 1 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G M 1 " 0.037 2.00e-02 2.50e+03 pdb=" N1 G M 1 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G M 1 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G M 1 " -0.029 2.00e-02 2.50e+03 pdb=" N3 G M 1 " -0.014 2.00e-02 2.50e+03 pdb=" C4 G M 1 " -0.009 2.00e-02 2.50e+03 pdb=" H8 G M 1 " -0.052 2.00e-02 2.50e+03 pdb=" H1 G M 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A M 6 " 0.059 2.00e-02 2.50e+03 2.98e-02 2.90e+01 pdb=" N9 A M 6 " 0.002 2.00e-02 2.50e+03 pdb=" C8 A M 6 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A M 6 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A M 6 " 0.013 2.00e-02 2.50e+03 pdb=" C6 A M 6 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A M 6 " 0.020 2.00e-02 2.50e+03 pdb=" N1 A M 6 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A M 6 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A M 6 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A M 6 " 0.008 2.00e-02 2.50e+03 pdb=" H8 A M 6 " -0.067 2.00e-02 2.50e+03 pdb=" H2 A M 6 " -0.052 2.00e-02 2.50e+03 ... (remaining 4717 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 76 2.08 - 2.71: 1485 2.71 - 3.34: 31650 3.34 - 3.97: 50973 3.97 - 4.60: 72674 Nonbonded interactions: 156858 Sorted by model distance: nonbonded pdb="HO2' G M 20 " pdb=" O5' G M 21 " model vdw 1.454 2.450 nonbonded pdb="HO2' G M 8 " pdb=" O5' G M 9 " model vdw 1.486 2.450 nonbonded pdb=" O ASP C 303 " pdb=" OD1 ASP C 303 " model vdw 1.508 2.800 nonbonded pdb="HO2' G M 14 " pdb=" O4' G M 15 " model vdw 1.537 2.450 nonbonded pdb=" SD MET I 366 " pdb=" O ILE I 413 " model vdw 1.582 3.200 ... (remaining 156853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } 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=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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.290 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.490 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 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 : 0.003 0.246 26348 Z= 0.183 Angle : 0.583 33.161 36168 Z= 0.321 Chirality : 0.044 0.284 4114 Planarity : 0.003 0.036 4706 Dihedral : 14.526 149.954 8222 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.62 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 24.56 % Favored : 75.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3596 helix: 1.92 (0.19), residues: 802 sheet: -0.63 (0.18), residues: 866 loop : -0.84 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.011 0.001 TYR I 308 PHE 0.014 0.001 PHE B 86 TRP 0.035 0.001 TRP I 331 HIS 0.005 0.001 HIS D 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (26290) covalent geometry : angle 0.51474 / 0.30 (36092) SS BOND : bond 0.22944 / 11.60 ( 2) SS BOND : angle 24.01724 / 11.04 ( 4) hydrogen bonds : bond 0.18019 / 12.69 ( 1032) hydrogen bonds : angle 7.72543 / 5.47 ( 2841) metal coordination : bond 0.00523 / 0.37 ( 56) metal coordination : angle 2.45207 / 2.02 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1311 time to fit residues: 24.7213 Evaluate side-chains 101 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN D 311 HIS D 329 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS H 504 GLN H 507 HIS H 667 ASN J 176 HIS J 311 HIS J 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.045213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.034442 restraints weight = 258986.342| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.56 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26348 Z= 0.188 Angle : 0.538 11.871 36168 Z= 0.273 Chirality : 0.041 0.137 4114 Planarity : 0.004 0.038 4706 Dihedral : 6.827 157.506 4059 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.51 % Favored : 92.27 % Rotamer: Outliers : 2.66 % Allowed : 22.88 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3596 helix: 2.19 (0.19), residues: 808 sheet: -0.56 (0.18), residues: 850 loop : -1.03 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 414 TYR 0.015 0.001 TYR H 495 PHE 0.017 0.001 PHE I 289 TRP 0.015 0.001 TRP L 243 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (26290) covalent geometry : angle 0.50852 / 0.27 (36092) SS BOND : bond 0.00814 / 0.40 ( 2) SS BOND : angle 0.93805 / 0.55 ( 4) hydrogen bonds : bond 0.03623 / 2.55 ( 1032) hydrogen bonds : angle 5.52074 / 3.87 ( 2841) metal coordination : bond 0.01618 / 1.11 ( 56) metal coordination : angle 3.97348 / 3.19 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 SER cc_start: 0.8842 (t) cc_final: 0.8522 (p) REVERT: D 279 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7376 (pt) REVERT: A 444 MET cc_start: 0.8100 (tmm) cc_final: 0.7623 (tmm) REVERT: G 576 CYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7720 (t) REVERT: K 150 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7554 (mmm160) REVERT: L 190 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6477 (m-80) outliers start: 51 outliers final: 28 residues processed: 143 average time/residue: 0.1352 time to fit residues: 34.0145 Evaluate side-chains 131 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain H residue 661 VAL Chi-restraints excluded: chain H residue 663 MET Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 355 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 297 HIS Chi-restraints excluded: chain G residue 576 CYS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain K residue 150 ARG Chi-restraints excluded: chain L residue 190 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: 61.6077 > 50: distance: 92 - 247: 17.422 distance: 146 - 255: 3.686 distance: 149 - 252: 5.536 distance: 163 - 243: 11.948 distance: 166 - 240: 8.819 distance: 177 - 224: 20.047 distance: 180 - 221: 8.721 distance: 189 - 209: 17.794 distance: 191 - 194: 10.868 distance: 192 - 206: 28.170 distance: 194 - 195: 11.292 distance: 195 - 196: 8.656 distance: 195 - 198: 11.870 distance: 196 - 197: 42.332 distance: 196 - 202: 19.642 distance: 198 - 199: 9.168 distance: 199 - 200: 9.104 distance: 199 - 201: 10.751 distance: 203 - 204: 26.860 distance: 204 - 205: 21.135 distance: 204 - 206: 23.849 distance: 206 - 207: 20.016 distance: 207 - 208: 13.605 distance: 207 - 210: 11.467 distance: 208 - 209: 10.613 distance: 208 - 211: 9.487 distance: 211 - 212: 3.996 distance: 212 - 213: 4.804 distance: 213 - 214: 3.131 distance: 213 - 221: 9.141 distance: 215 - 216: 12.539 distance: 216 - 217: 15.459 distance: 216 - 218: 7.946 distance: 217 - 219: 9.611 distance: 218 - 220: 9.605 distance: 219 - 220: 14.542 distance: 221 - 222: 3.310 distance: 222 - 223: 3.344 distance: 222 - 225: 6.094 distance: 223 - 224: 14.655 distance: 225 - 226: 6.543 distance: 226 - 227: 12.340 distance: 227 - 228: 4.909 distance: 228 - 229: 5.228 distance: 229 - 230: 6.169 distance: 229 - 231: 5.292 distance: 232 - 233: 8.060 distance: 233 - 234: 3.343 distance: 233 - 236: 3.054 distance: 234 - 235: 12.570 distance: 234 - 240: 4.661 distance: 236 - 237: 4.221 distance: 236 - 238: 3.365 distance: 237 - 239: 12.065 distance: 240 - 241: 8.689 distance: 241 - 242: 7.961 distance: 242 - 243: 11.670 distance: 242 - 244: 5.169 distance: 244 - 245: 4.206 distance: 245 - 246: 9.194 distance: 245 - 248: 7.628 distance: 246 - 247: 8.086 distance: 246 - 252: 3.225 distance: 248 - 249: 7.128 distance: 248 - 250: 11.281 distance: 249 - 251: 7.536 distance: 252 - 253: 3.765 distance: 253 - 254: 3.221 distance: 253 - 256: 6.207 distance: 254 - 255: 4.644 distance: 254 - 263: 8.839 distance: 256 - 257: 4.755 distance: 257 - 258: 8.381 distance: 258 - 260: 7.276 distance: 259 - 261: 5.256 distance: 260 - 262: 6.833 distance: 263 - 264: 5.008 distance: 264 - 265: 13.234 distance: 264 - 267: 7.262 distance: 265 - 266: 6.233 distance: 265 - 268: 10.018