Starting phenix.real_space_refine on Sun Aug 24 19:22:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xez_22160/08_2025/6xez_22160.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xez_22160/08_2025/6xez_22160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xez_22160/08_2025/6xez_22160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xez_22160/08_2025/6xez_22160.map" model { file = "/net/cci-nas-00/data/ceres_data/6xez_22160/08_2025/6xez_22160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xez_22160/08_2025/6xez_22160.cif" } resolution = 3.5 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= 0.002 sd= 0.058 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 76 5.49 5 Mg 3 5.21 5 S 148 5.16 5 C 13519 2.51 5 N 3671 2.21 5 O 4309 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21742 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7459 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1383 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 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': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 88.721 102.304 119.424 1.00 68.21 S ATOM 2487 SG CYS A 306 88.421 100.924 122.609 1.00 63.53 S ATOM 2519 SG CYS A 310 86.803 104.423 121.909 1.00 60.93 S ATOM 3927 SG CYS A 487 86.518 86.967 105.077 1.00 80.68 S ATOM 5180 SG CYS A 645 87.725 84.546 108.337 1.00 88.48 S ATOM 5186 SG CYS A 646 88.285 87.912 107.513 1.00 83.87 S ATOM 10836 SG CYS E 5 35.198 82.097 55.078 1.00166.51 S ATOM 10857 SG CYS E 8 31.322 80.782 54.935 1.00172.10 S ATOM 10995 SG CYS E 26 34.582 78.680 55.069 1.00168.19 S ATOM 11016 SG CYS E 29 33.664 79.940 52.226 1.00172.63 S ATOM 11181 SG CYS E 50 56.471 65.217 50.133 1.00219.44 S ATOM 11211 SG CYS E 55 56.897 64.867 46.869 1.00232.67 S ATOM 11344 SG CYS E 72 55.192 62.162 47.361 1.00223.45 S ATOM 10918 SG CYS E 16 44.259 80.491 46.350 1.00182.34 S ATOM 10933 SG CYS E 19 42.754 82.711 44.924 1.00184.86 S ATOM 15454 SG CYS F 5 88.579 86.061 55.194 1.00180.72 S ATOM 15475 SG CYS F 8 85.587 84.904 54.927 1.00185.31 S ATOM 15613 SG CYS F 26 87.698 81.703 54.852 1.00198.76 S ATOM 15634 SG CYS F 29 89.784 82.795 52.868 1.00206.02 S ATOM 15799 SG CYS F 50 98.078 68.991 74.102 1.00227.89 S ATOM 15829 SG CYS F 55 101.194 68.363 74.238 1.00239.77 S ATOM 15962 SG CYS F 72 100.061 65.848 72.923 1.00235.51 S ATOM 15536 SG CYS F 16 98.784 82.792 61.307 1.00188.21 S ATOM 15551 SG CYS F 19 100.099 86.280 59.520 1.00196.10 S Time building chain proxies: 5.34, per 1000 atoms: 0.25 Number of scatterers: 21742 At special positions: 0 Unit cell: (152.9, 149.6, 185.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 148 16.00 P 76 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4309 8.00 N 3671 7.00 C 13519 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " 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 E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " Number of angles added : 28 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 31 sheets defined 41.7% alpha, 8.4% beta 32 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.970A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.655A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 198 removed outlier: 4.704A pdb=" N GLN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.698A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.587A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.533A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.524A pdb=" N THR A 259 " --> pdb=" O HIS A 256 " (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 306 through 318 removed outlier: 4.060A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.994A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.529A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 455 removed outlier: 3.881A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 467 through 480 removed outlier: 4.336A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.154A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 4.192A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.544A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.871A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.558A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 4.041A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 767 through 774 removed outlier: 3.794A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.687A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 854 through 867 removed outlier: 4.624A pdb=" N VAL A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.729A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.668A pdb=" N GLU A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) 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: 4.227A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 96 removed outlier: 4.130A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.553A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 173 through 177 removed outlier: 4.026A pdb=" N SER B 177 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.634A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'D' and resid 9 through 28 removed outlier: 4.389A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.909A pdb=" N GLN D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 4.094A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.622A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 4.067A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) 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 102 through 112 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.590A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 265 through 275 removed outlier: 3.835A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.551A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) 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 380 through 391 removed outlier: 4.109A pdb=" N LEU E 391 " --> pdb=" O VAL E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 430 Processing helix chain 'E' and resid 445 through 455 Processing helix chain 'E' and resid 489 through 497 removed outlier: 3.546A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL E 496 " --> pdb=" O GLN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 515 through 523 removed outlier: 3.850A pdb=" N ALA E 522 " --> pdb=" O GLN E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.698A pdb=" N LYS E 584 " --> pdb=" O ASP E 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.590A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.697A 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 102 through 112 removed outlier: 3.813A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.736A 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 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 275 removed outlier: 3.709A pdb=" N ALA F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 299 Processing helix chain 'F' and resid 310 through 319 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 391 removed outlier: 3.716A pdb=" N LEU F 384 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.922A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 580 through 585 removed outlier: 3.748A pdb=" N LYS F 584 " --> pdb=" O ASP F 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.814A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.533A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.513A pdb=" N VAL A 844 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.731A pdb=" N THR A 540 " --> pdb=" O MET A 666 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 543 through 544 Processing sheet with id=AB3, first strand: chain 'A' and resid 757 through 758 Processing sheet with id=AB4, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.629A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.061A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.917A pdb=" N LEU D 128 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.698A pdb=" N TRP D 154 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC1, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC2, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC3, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'E' and resid 208 through 209 removed outlier: 7.116A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 154 " --> pdb=" O ASP E 223 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP E 223 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.491A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 397 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE E 373 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 399 " --> pdb=" O PHE E 373 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS E 330 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR E 359 " --> pdb=" O CYS E 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 470 through 472 Processing sheet with id=AC7, first strand: chain 'E' and resid 510 through 512 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC9, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AD1, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AD2, first strand: chain 'F' and resid 152 through 156 removed outlier: 4.725A pdb=" N VAL F 154 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER F 166 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.568A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 511 through 512 753 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3784 1.32 - 1.44: 6140 1.44 - 1.57: 12017 1.57 - 1.69: 202 1.69 - 1.81: 212 Bond restraints: 22355 Sorted by residual: bond pdb=" F1 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.787 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" F1 AF3 F1004 " pdb="AL AF3 F1004 " ideal model delta sigma weight residual 1.637 1.787 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" F2 AF3 F1004 " pdb="AL AF3 F1004 " ideal model delta sigma weight residual 1.637 1.779 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" F2 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.779 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" F3 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 22350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 30166 2.92 - 5.83: 478 5.83 - 8.75: 76 8.75 - 11.66: 15 11.66 - 14.58: 7 Bond angle restraints: 30742 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 134.55 -12.85 1.80e+00 3.09e-01 5.10e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 132.81 -11.11 1.80e+00 3.09e-01 3.81e+01 angle pdb=" O1B ADP E 704 " pdb=" PB ADP E 704 " pdb=" O2B ADP E 704 " ideal model delta sigma weight residual 119.90 105.32 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O1B ADP F1003 " pdb=" PB ADP F1003 " pdb=" O2B ADP F1003 " ideal model delta sigma weight residual 119.90 105.35 14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C1' ADP F1003 " pdb=" C2' ADP F1003 " pdb=" C3' ADP F1003 " ideal model delta sigma weight residual 111.00 96.73 14.27 3.00e+00 1.11e-01 2.26e+01 ... (remaining 30737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 12946 34.01 - 68.01: 610 68.01 - 102.02: 55 102.02 - 136.03: 6 136.03 - 170.04: 8 Dihedral angle restraints: 13625 sinusoidal: 6039 harmonic: 7586 Sorted by residual: dihedral pdb=" C5' ADP A1004 " pdb=" O5' ADP A1004 " pdb=" PA ADP A1004 " pdb=" O2A ADP A1004 " ideal model delta sinusoidal sigma weight residual -60.00 110.04 -170.04 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP E 704 " pdb=" O3A ADP E 704 " pdb=" PB ADP E 704 " pdb=" PA ADP E 704 " ideal model delta sinusoidal sigma weight residual -60.00 87.69 -147.69 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2A ADP A1004 " pdb=" O3A ADP A1004 " pdb=" PA ADP A1004 " pdb=" PB ADP A1004 " ideal model delta sinusoidal sigma weight residual 300.00 157.79 142.21 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 13622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3488 0.123 - 0.247: 60 0.247 - 0.370: 19 0.370 - 0.493: 6 0.493 - 0.617: 1 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" C6 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" C5 1N7 A1006 " pdb=" C7 1N7 A1006 " both_signs ideal model delta sigma weight residual False -2.43 -2.86 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 1N7 A1005 " pdb=" C1 1N7 A1005 " pdb=" C15 1N7 A1005 " pdb=" C19 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.81 -2.40 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 3571 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 824 " 0.039 2.00e-02 2.50e+03 7.84e-02 6.14e+01 pdb=" CG ASP A 824 " -0.136 2.00e-02 2.50e+03 pdb=" OD1 ASP A 824 " 0.050 2.00e-02 2.50e+03 pdb=" OD2 ASP A 824 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 289 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C SER F 289 " 0.060 2.00e-02 2.50e+03 pdb=" O SER F 289 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS F 290 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 582 " 0.028 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYR F 582 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR F 582 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 582 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 582 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 582 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 582 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 582 " 0.006 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 5 1.90 - 2.65: 693 2.65 - 3.40: 31508 3.40 - 4.15: 51638 4.15 - 4.90: 88232 Nonbonded interactions: 172076 Sorted by model distance: nonbonded pdb=" O LEU E 65 " pdb=" OG SER E 80 " model vdw 1.146 3.040 nonbonded pdb=" O1B ADP E 704 " pdb=" F3 AF3 E 705 " model vdw 1.813 2.990 nonbonded pdb=" O2B ADP F1003 " pdb=" F3 AF3 F1004 " model vdw 1.813 2.990 nonbonded pdb=" O1B ADP F1003 " pdb=" F1 AF3 F1004 " model vdw 1.820 2.990 nonbonded pdb=" O2B ADP E 704 " pdb=" F1 AF3 E 705 " model vdw 1.820 2.990 ... (remaining 172071 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 41 or (resid 42 through 4 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 44 through 1 \ 91)) 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 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 50 or (resid 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 706)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 1005)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.310 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.014 0.830 22388 Z= 0.747 Angle : 1.167 57.152 30770 Z= 0.505 Chirality : 0.057 0.617 3574 Planarity : 0.005 0.078 3641 Dihedral : 19.277 170.035 8731 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.01 % Favored : 86.91 % Rotamer: Outliers : 10.77 % Allowed : 22.63 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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 aren not related in a simple way. whole: -4.50 (0.14), residues: 2551 helix: -2.11 (0.13), residues: 946 sheet: -3.54 (0.25), residues: 312 loop : -3.60 (0.14), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 533 TYR 0.051 0.002 TYR F 582 PHE 0.020 0.002 PHE A 471 TRP 0.021 0.002 TRP A 916 HIS 0.016 0.002 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.01063 (22355) covalent geometry : angle 0.96481 (30742) hydrogen bonds : bond 0.14162 ( 832) hydrogen bonds : angle 6.28838 ( 2227) metal coordination : bond 0.18994 ( 32) metal coordination : angle 21.75890 ( 28) Misc. bond : bond 0.82974 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 131 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 261 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 331 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (ttm-80) REVERT: A 431 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7432 (mm-30) REVERT: A 553 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7272 (ptt180) REVERT: A 668 MET cc_start: 0.8593 (ttp) cc_final: 0.8353 (ttt) REVERT: B 55 MET cc_start: 0.9535 (mmm) cc_final: 0.9279 (mmm) REVERT: B 165 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8340 (pttt) REVERT: B 174 MET cc_start: 0.9046 (tpt) cc_final: 0.8801 (tpp) REVERT: B 189 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8121 (mt) REVERT: C 38 ASP cc_start: 0.8737 (t0) cc_final: 0.8483 (t0) REVERT: E 274 MET cc_start: 0.8360 (mmm) cc_final: 0.8115 (mmp) REVERT: E 448 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8064 (pt) REVERT: F 62 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: F 502 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7649 (ptm160) REVERT: F 585 LEU cc_start: 0.3740 (OUTLIER) cc_final: 0.3531 (pt) outliers start: 237 outliers final: 178 residues processed: 356 average time/residue: 0.1544 time to fit residues: 87.5271 Evaluate side-chains 303 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 117 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 354 GLN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 81 GLN A 99 HIS A 117 GLN A 168 ASN A 184 GLN A 224 GLN A 360 ASN A 381 HIS A 404 ASN A 439 HIS A 489 ASN A 492 GLN A 524 GLN A 534 ASN A 568 ASN A 611 ASN A 810 HIS A 816 HIS A 911 ASN B 108 ASN B 157 GLN B 168 GLN C 34 GLN D 104 ASN E 46 ASN E 245 HIS E 275 GLN E 311 HIS E 354 GLN E 388 ASN E 395 HIS E 464 HIS E 470 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 51 ASN F 164 HIS F 177 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067842 restraints weight = 57099.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.068701 restraints weight = 30141.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069489 restraints weight = 17291.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069699 restraints weight = 14317.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.069831 restraints weight = 13004.757| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 22388 Z= 0.335 Angle : 0.848 25.767 30770 Z= 0.411 Chirality : 0.047 0.345 3574 Planarity : 0.005 0.055 3641 Dihedral : 16.174 156.990 4444 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 8.27 % Allowed : 25.35 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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 aren not related in a simple way. whole: -3.36 (0.15), residues: 2551 helix: -0.85 (0.16), residues: 953 sheet: -3.27 (0.24), residues: 329 loop : -3.09 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 750 TYR 0.025 0.002 TYR A 748 PHE 0.018 0.002 PHE A 471 TRP 0.017 0.002 TRP A 916 HIS 0.008 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00780 (22355) covalent geometry : angle 0.79394 (30742) hydrogen bonds : bond 0.06244 ( 832) hydrogen bonds : angle 5.37311 ( 2227) metal coordination : bond 0.02010 ( 32) metal coordination : angle 9.92919 ( 28) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 123 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 431 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7470 (mm-30) REVERT: A 668 MET cc_start: 0.8685 (ttp) cc_final: 0.8392 (ttt) REVERT: A 786 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 805 LEU cc_start: 0.8420 (tp) cc_final: 0.8206 (tp) REVERT: A 891 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8634 (tt) REVERT: B 55 MET cc_start: 0.9552 (mmm) cc_final: 0.9336 (mmm) REVERT: B 56 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: B 60 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8933 (mp0) REVERT: B 165 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8171 (pttt) REVERT: C 38 ASP cc_start: 0.8861 (t0) cc_final: 0.8390 (t0) REVERT: D 168 GLN cc_start: 0.9177 (mp10) cc_final: 0.8859 (mp10) REVERT: E 274 MET cc_start: 0.8461 (mmm) cc_final: 0.8154 (mmp) REVERT: F 41 LEU cc_start: 0.7252 (tt) cc_final: 0.6905 (pp) REVERT: F 333 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6339 (mt) REVERT: F 429 MET cc_start: 0.6095 (mmm) cc_final: 0.5863 (mmt) REVERT: F 502 ARG cc_start: 0.8017 (mmt180) cc_final: 0.7754 (ptm160) outliers start: 182 outliers final: 130 residues processed: 295 average time/residue: 0.1511 time to fit residues: 72.3082 Evaluate side-chains 255 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 120 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 575 ILE Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 250 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN E 518 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 503 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.120477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070143 restraints weight = 57256.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071624 restraints weight = 27835.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072418 restraints weight = 14885.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072387 restraints weight = 14187.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.072490 restraints weight = 12333.005| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22388 Z= 0.177 Angle : 0.706 20.562 30770 Z= 0.344 Chirality : 0.042 0.230 3574 Planarity : 0.004 0.046 3641 Dihedral : 14.844 154.155 4301 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 7.04 % Allowed : 25.62 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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 aren not related in a simple way. whole: -2.52 (0.16), residues: 2551 helix: -0.01 (0.17), residues: 954 sheet: -2.88 (0.25), residues: 335 loop : -2.71 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 750 TYR 0.018 0.001 TYR F 582 PHE 0.016 0.001 PHE F 422 TRP 0.020 0.001 TRP F 506 HIS 0.012 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00407 (22355) covalent geometry : angle 0.66499 (30742) hydrogen bonds : bond 0.05036 ( 832) hydrogen bonds : angle 4.79282 ( 2227) metal coordination : bond 0.01373 ( 32) metal coordination : angle 7.88361 ( 28) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 131 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8480 (m-80) cc_final: 0.7943 (m-80) REVERT: A 370 GLU cc_start: 0.8664 (tp30) cc_final: 0.8273 (tp30) REVERT: A 431 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7384 (mm-30) REVERT: A 548 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 633 MET cc_start: 0.8781 (tmm) cc_final: 0.8461 (tmm) REVERT: A 648 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8499 (tt) REVERT: A 668 MET cc_start: 0.8648 (ttp) cc_final: 0.8337 (ttt) REVERT: A 786 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8685 (mp) REVERT: A 891 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 902 MET cc_start: 0.8830 (ttp) cc_final: 0.8542 (ttm) REVERT: B 56 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: B 80 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8308 (ttt-90) REVERT: B 155 GLU cc_start: 0.8078 (pm20) cc_final: 0.7816 (pm20) REVERT: B 165 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8187 (pttt) REVERT: C 38 ASP cc_start: 0.8762 (t0) cc_final: 0.8262 (t0) REVERT: C 50 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8306 (mt-10) REVERT: D 94 MET cc_start: 0.8483 (mtp) cc_final: 0.8254 (mtp) REVERT: D 168 GLN cc_start: 0.9142 (mp10) cc_final: 0.8833 (mp10) REVERT: F 41 LEU cc_start: 0.7078 (tt) cc_final: 0.6815 (pp) REVERT: F 202 LYS cc_start: 0.1888 (OUTLIER) cc_final: 0.1642 (tptp) REVERT: F 383 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8545 (p0) REVERT: F 399 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (pt) REVERT: F 429 MET cc_start: 0.6068 (mmm) cc_final: 0.5856 (mmt) REVERT: F 474 MET cc_start: 0.5964 (mmm) cc_final: 0.5760 (mmm) REVERT: F 502 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7837 (ptm160) REVERT: F 506 TRP cc_start: 0.2174 (OUTLIER) cc_final: 0.1729 (m100) REVERT: F 576 MET cc_start: 0.4716 (tpp) cc_final: 0.4373 (tpp) outliers start: 155 outliers final: 108 residues processed: 275 average time/residue: 0.1406 time to fit residues: 60.7172 Evaluate side-chains 238 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 120 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 77 optimal weight: 0.0670 chunk 238 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 237 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 overall best weight: 1.1838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.121813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071910 restraints weight = 56671.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072683 restraints weight = 29074.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073474 restraints weight = 17155.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073628 restraints weight = 13943.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.073721 restraints weight = 12229.448| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22388 Z= 0.134 Angle : 0.649 16.588 30770 Z= 0.319 Chirality : 0.040 0.220 3574 Planarity : 0.004 0.042 3641 Dihedral : 14.238 147.330 4260 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 6.27 % Allowed : 26.67 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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 aren not related in a simple way. whole: -1.98 (0.17), residues: 2551 helix: 0.47 (0.17), residues: 952 sheet: -2.56 (0.27), residues: 320 loop : -2.45 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 750 TYR 0.017 0.001 TYR D 138 PHE 0.021 0.001 PHE F 422 TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00298 (22355) covalent geometry : angle 0.62236 (30742) hydrogen bonds : bond 0.04391 ( 832) hydrogen bonds : angle 4.47577 ( 2227) metal coordination : bond 0.01137 ( 32) metal coordination : angle 6.16318 ( 28) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 129 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8342 (m-80) cc_final: 0.7893 (m-80) REVERT: A 340 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: A 370 GLU cc_start: 0.8638 (tp30) cc_final: 0.8261 (tp30) REVERT: A 431 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7347 (mm-30) REVERT: A 477 ASP cc_start: 0.8927 (t70) cc_final: 0.8672 (t0) REVERT: A 548 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8913 (tt) REVERT: A 633 MET cc_start: 0.8927 (tmm) cc_final: 0.8690 (tmm) REVERT: A 668 MET cc_start: 0.8559 (ttp) cc_final: 0.8271 (ttt) REVERT: A 786 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 891 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 56 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: B 58 LYS cc_start: 0.9405 (mtpt) cc_final: 0.9070 (mtmm) REVERT: B 65 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: B 155 GLU cc_start: 0.7904 (pm20) cc_final: 0.7694 (pm20) REVERT: B 165 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8468 (mmmt) REVERT: C 38 ASP cc_start: 0.8637 (t0) cc_final: 0.8073 (t0) REVERT: D 94 MET cc_start: 0.8462 (mtp) cc_final: 0.8184 (mtp) REVERT: D 168 GLN cc_start: 0.9156 (mp10) cc_final: 0.8847 (mp10) REVERT: E 274 MET cc_start: 0.8369 (mmp) cc_final: 0.8107 (mmm) REVERT: E 290 HIS cc_start: 0.5479 (OUTLIER) cc_final: 0.5274 (t-170) REVERT: E 448 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7733 (pt) REVERT: F 41 LEU cc_start: 0.7046 (tt) cc_final: 0.6810 (pp) REVERT: F 274 MET cc_start: 0.7901 (mmm) cc_final: 0.7682 (mmm) REVERT: F 333 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6158 (mt) REVERT: F 378 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8297 (tpp) REVERT: F 399 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (pt) REVERT: F 502 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7772 (ptm160) REVERT: F 503 ASN cc_start: 0.3831 (OUTLIER) cc_final: 0.3254 (p0) outliers start: 138 outliers final: 95 residues processed: 253 average time/residue: 0.1400 time to fit residues: 57.0129 Evaluate side-chains 230 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 123 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 222 optimal weight: 0.0050 chunk 32 optimal weight: 0.7980 chunk 254 optimal weight: 10.0000 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 492 GLN B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.122687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069953 restraints weight = 56249.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072108 restraints weight = 24247.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.073496 restraints weight = 14642.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.074295 restraints weight = 10699.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.074699 restraints weight = 8898.854| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22388 Z= 0.112 Angle : 0.626 15.136 30770 Z= 0.306 Chirality : 0.040 0.214 3574 Planarity : 0.004 0.041 3641 Dihedral : 13.858 135.339 4236 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.27 % Allowed : 27.21 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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 aren not related in a simple way. whole: -1.60 (0.17), residues: 2551 helix: 0.76 (0.17), residues: 954 sheet: -2.39 (0.27), residues: 321 loop : -2.20 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 594 TYR 0.016 0.001 TYR F 582 PHE 0.013 0.001 PHE F 346 TRP 0.012 0.001 TRP A 916 HIS 0.015 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00240 (22355) covalent geometry : angle 0.60385 (30742) hydrogen bonds : bond 0.04089 ( 832) hydrogen bonds : angle 4.27266 ( 2227) metal coordination : bond 0.01092 ( 32) metal coordination : angle 5.47853 ( 28) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 127 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8278 (m-80) cc_final: 0.7839 (m-80) REVERT: A 340 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: A 370 GLU cc_start: 0.8528 (tp30) cc_final: 0.8155 (tp30) REVERT: A 431 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7269 (mm-30) REVERT: A 477 ASP cc_start: 0.8840 (t70) cc_final: 0.8629 (t0) REVERT: A 668 MET cc_start: 0.8547 (ttp) cc_final: 0.8279 (ttt) REVERT: A 786 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 891 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 902 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8467 (ttm) REVERT: B 56 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: B 58 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9019 (mtmm) REVERT: B 80 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8214 (ttt-90) REVERT: B 155 GLU cc_start: 0.7844 (pm20) cc_final: 0.7554 (pm20) REVERT: B 165 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8465 (mmmt) REVERT: D 94 MET cc_start: 0.8540 (mtp) cc_final: 0.8281 (mtp) REVERT: D 168 GLN cc_start: 0.9018 (mp10) cc_final: 0.8727 (mp10) REVERT: E 65 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7151 (tp) REVERT: E 235 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6769 (mm) REVERT: E 274 MET cc_start: 0.8332 (mmp) cc_final: 0.8042 (mmm) REVERT: F 41 LEU cc_start: 0.7186 (tt) cc_final: 0.6956 (pp) REVERT: F 274 MET cc_start: 0.7977 (mmm) cc_final: 0.7750 (mmm) REVERT: F 333 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6612 (mt) REVERT: F 339 ARG cc_start: 0.1871 (OUTLIER) cc_final: 0.0824 (ptp90) REVERT: F 397 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7837 (t) REVERT: F 399 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8380 (pt) REVERT: F 474 MET cc_start: 0.6209 (mmm) cc_final: 0.5996 (mmm) REVERT: F 503 ASN cc_start: 0.4313 (OUTLIER) cc_final: 0.3463 (p0) outliers start: 116 outliers final: 81 residues processed: 232 average time/residue: 0.1531 time to fit residues: 56.1531 Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 123 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2209 > 50: distance: 48 - 53: 3.172 distance: 53 - 54: 5.871 distance: 54 - 55: 6.654 distance: 55 - 56: 4.264 distance: 57 - 58: 6.799 distance: 58 - 59: 22.759 distance: 58 - 61: 11.563 distance: 59 - 60: 25.506 distance: 59 - 65: 21.481 distance: 61 - 62: 3.636 distance: 62 - 63: 4.447 distance: 62 - 64: 5.648 distance: 65 - 66: 8.092 distance: 65 - 71: 8.635 distance: 66 - 67: 8.779 distance: 66 - 69: 4.680 distance: 67 - 68: 10.718 distance: 67 - 72: 6.541 distance: 69 - 70: 9.765 distance: 70 - 71: 10.070 distance: 72 - 73: 9.412 distance: 73 - 74: 9.234 distance: 73 - 76: 5.443 distance: 74 - 75: 5.334 distance: 74 - 77: 3.853 distance: 77 - 78: 20.415 distance: 78 - 79: 46.027 distance: 78 - 81: 21.215 distance: 79 - 80: 26.602 distance: 79 - 86: 46.006 distance: 81 - 82: 7.978 distance: 82 - 83: 11.207 distance: 83 - 84: 11.804 distance: 83 - 85: 10.832 distance: 86 - 87: 52.221 distance: 87 - 88: 34.557 distance: 87 - 90: 23.192 distance: 88 - 89: 13.788 distance: 88 - 94: 17.700 distance: 90 - 91: 5.114 distance: 91 - 92: 7.194 distance: 91 - 93: 4.752 distance: 94 - 95: 8.472 distance: 94 - 100: 10.435 distance: 95 - 96: 5.933 distance: 95 - 98: 6.011 distance: 96 - 97: 4.528 distance: 98 - 99: 8.626 distance: 99 - 100: 6.341 distance: 102 - 103: 16.058 distance: 102 - 105: 12.945 distance: 103 - 104: 15.765 distance: 103 - 106: 7.657 distance: 106 - 107: 5.165 distance: 106 - 112: 9.041 distance: 107 - 108: 9.437 distance: 107 - 110: 15.061 distance: 108 - 109: 5.712 distance: 108 - 113: 3.450 distance: 110 - 111: 3.574 distance: 111 - 112: 14.038 distance: 113 - 114: 4.722 distance: 115 - 116: 3.542 distance: 115 - 124: 6.346 distance: 117 - 118: 4.314 distance: 118 - 119: 4.199 distance: 120 - 121: 3.752 distance: 121 - 122: 4.958 distance: 121 - 123: 6.709