Starting phenix.real_space_refine on Sun Sep 29 01:52:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhe_39288/09_2024/8yhe_39288_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhe_39288/09_2024/8yhe_39288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhe_39288/09_2024/8yhe_39288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhe_39288/09_2024/8yhe_39288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhe_39288/09_2024/8yhe_39288_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yhe_39288/09_2024/8yhe_39288_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 76 5.49 5 S 86 5.16 5 C 13105 2.51 5 N 3633 2.21 5 O 4274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21183 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 675 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 4 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1415 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1508 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1529 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1518 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1428 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1515 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain breaks: 6 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "H" Number of atoms: 4127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4127 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain breaks: 10 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "I" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1310 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1529 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 191} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1931 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 6 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1091 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "M" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 963 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 24, 'rna3p': 21} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 635 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 1, 'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 236 SG CYS A 71 62.915 76.038 31.454 1.00165.68 S ATOM 295 SG CYS A 81 60.779 78.474 33.457 1.00164.22 S ATOM 310 SG CYS A 84 60.492 78.423 29.790 1.00151.01 S ATOM 328 SG CYS A 87 59.172 75.373 31.670 1.00141.91 S ATOM 1209 SG CYS B 71 35.567 70.023 51.937 1.00144.22 S ATOM 1283 SG CYS B 81 33.564 69.778 53.607 1.00128.33 S ATOM 1298 SG CYS B 84 33.008 67.422 51.062 1.00133.83 S ATOM 1318 SG CYS B 87 35.204 66.408 53.430 1.00110.20 S ATOM 2619 SG CYS C 71 25.454 46.305 74.410 1.00 80.30 S ATOM 2693 SG CYS C 81 22.610 45.310 76.854 1.00 81.51 S ATOM 2714 SG CYS C 84 23.759 42.863 74.254 1.00 71.77 S ATOM 2734 SG CYS C 87 26.098 43.521 76.863 1.00 75.56 S ATOM 4140 SG CYS D 71 59.774 24.793 124.561 1.00 80.84 S ATOM 4214 SG CYS D 81 61.454 22.352 127.755 1.00 89.67 S ATOM 4235 SG CYS D 84 62.754 22.995 124.874 1.00 83.86 S ATOM 4255 SG CYS D 87 61.799 26.247 126.502 1.00 66.64 S ATOM 5673 SG CYS E 71 73.579 43.881 148.563 1.00 83.17 S ATOM 5747 SG CYS E 81 76.410 44.665 151.011 1.00 84.22 S ATOM 5768 SG CYS E 84 75.868 47.026 148.185 1.00 89.17 S ATOM 5788 SG CYS E 87 73.275 46.990 150.671 1.00 65.11 S ATOM 7184 SG CYS F 71 65.819 67.710 170.366 1.00111.39 S ATOM 7226 SG CYS F 81 67.083 70.367 172.865 1.00125.43 S ATOM 7241 SG CYS F 84 64.713 71.523 170.000 1.00107.50 S ATOM 7261 SG CYS F 87 63.473 69.505 172.626 1.00 96.63 S ATOM 15568 SG CYS J 71 36.990 26.297 99.281 1.00 84.02 S ATOM 15642 SG CYS J 81 36.025 23.068 101.330 1.00 83.40 S ATOM 15663 SG CYS J 84 38.983 22.933 98.900 1.00 63.77 S ATOM 15683 SG CYS J 87 39.125 25.025 101.917 1.00 74.06 S Time building chain proxies: 12.18, per 1000 atoms: 0.57 Number of scatterers: 21183 At special positions: 0 Unit cell: (91.2, 121.6, 211.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 86 16.00 P 76 15.00 O 4274 8.00 N 3633 7.00 C 13105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 81 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" ND1 HIS H 62 " pdb="ZN ZN H 702 " - pdb=" ND1 HIS H 148 " pdb="ZN ZN H 702 " - pdb=" ND1 HIS H 64 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " Number of angles added : 42 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4820 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 34 sheets defined 36.4% alpha, 19.4% beta 19 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 7.24 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.841A pdb=" N GLY B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.681A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 113' Processing helix chain 'B' and resid 155 through 172 removed outlier: 4.584A pdb=" N SER B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 156 through 172 Processing helix chain 'D' and resid 24 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 156 through 172 Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 172 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.554A pdb=" N GLY E 180 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 51 through 67 removed outlier: 3.799A pdb=" N LEU F 55 " --> pdb=" O PHE F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.701A pdb=" N ILE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 113' Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'F' and resid 176 through 180 removed outlier: 3.597A pdb=" N GLY F 180 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 removed outlier: 4.206A pdb=" N GLY G 21 " --> pdb=" O LEU G 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 22 " --> pdb=" O ASP G 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 18 through 22' Processing helix chain 'G' and resid 28 through 42 Processing helix chain 'G' and resid 47 through 53 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 127 through 142 Processing helix chain 'H' and resid 43 through 53 Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.694A pdb=" N LEU H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 107 Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 208 through 219 removed outlier: 3.964A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 245 removed outlier: 4.479A pdb=" N TYR H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 268 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 273 through 277 Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.610A pdb=" N SER H 299 " --> pdb=" O THR H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 331 removed outlier: 4.224A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 330 " --> pdb=" O HIS H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 384 Processing helix chain 'H' and resid 399 through 412 Processing helix chain 'H' and resid 470 through 479 removed outlier: 3.568A pdb=" N PHE H 474 " --> pdb=" O ASP H 470 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN H 479 " --> pdb=" O ASP H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 541 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 572 through 593 Processing helix chain 'H' and resid 596 through 603 Processing helix chain 'I' and resid 470 through 485 removed outlier: 3.947A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 540 Processing helix chain 'I' and resid 542 through 554 removed outlier: 3.701A pdb=" N ILE I 546 " --> pdb=" O GLN I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 592 removed outlier: 3.801A pdb=" N ILE I 591 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 606 removed outlier: 4.354A pdb=" N ASN I 604 " --> pdb=" O ASN I 600 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE I 605 " --> pdb=" O ILE I 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 51 through 66 Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.999A pdb=" N ILE J 113 " --> pdb=" O THR J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 109 through 113' Processing helix chain 'J' and resid 156 through 172 removed outlier: 3.631A pdb=" N LEU J 160 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 180 Processing helix chain 'K' and resid 379 through 385 Processing helix chain 'K' and resid 401 through 413 removed outlier: 3.721A pdb=" N ILE K 405 " --> pdb=" O GLU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 487 removed outlier: 3.686A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K 487 " --> pdb=" O ASN K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 527 through 540 Processing helix chain 'K' and resid 541 through 553 removed outlier: 3.558A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 590 Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 470 through 486 removed outlier: 3.638A pdb=" N PHE L 474 " --> pdb=" O ASP L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 523 Processing helix chain 'L' and resid 527 through 536 Processing helix chain 'L' and resid 546 through 554 Processing helix chain 'L' and resid 573 through 593 Processing helix chain 'L' and resid 596 through 604 removed outlier: 3.938A pdb=" N ASN L 604 " --> pdb=" O ASN L 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 119 Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 122 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 122 Processing sheet with id=AB2, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB3, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 122 Processing sheet with id=AB5, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'F' and resid 114 through 122 Processing sheet with id=AB8, first strand: chain 'G' and resid 115 through 117 removed outlier: 6.945A pdb=" N LYS G 5 " --> pdb=" O TYR G 161 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR G 161 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE G 7 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AC1, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC2, first strand: chain 'G' and resid 189 through 195 removed outlier: 3.551A pdb=" N ILE G 189 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE G 191 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS G 200 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 2 through 4 removed outlier: 7.011A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP H 56 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASP H 126 " --> pdb=" O ASN H 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE H 83 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.294A pdb=" N ASN H 163 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE H 193 " --> pdb=" O ASN H 163 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU H 165 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU H 192 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 225 through 228 removed outlier: 6.533A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER H 313 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE H 227 " --> pdb=" O SER H 313 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR H 252 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL H 251 " --> pdb=" O ILE H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'H' and resid 454 through 456 removed outlier: 6.129A pdb=" N VAL K 435 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE K 468 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU K 437 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 458 through 459 Processing sheet with id=AC9, first strand: chain 'I' and resid 467 through 469 Processing sheet with id=AD1, first strand: chain 'J' and resid 99 through 101 Processing sheet with id=AD2, first strand: chain 'J' and resid 99 through 101 Processing sheet with id=AD3, first strand: chain 'J' and resid 114 through 122 Processing sheet with id=AD4, first strand: chain 'K' and resid 141 through 142 removed outlier: 3.872A pdb=" N THR K 142 " --> pdb=" O PHE K 156 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE K 156 " --> pdb=" O THR K 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 164 through 166 removed outlier: 6.905A pdb=" N LEU K 165 " --> pdb=" O ILE K 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 392 through 394 Processing sheet with id=AD7, first strand: chain 'L' and resid 434 through 437 879 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 5.72 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: 3956 1.32 - 1.45: 5666 1.45 - 1.57: 11747 1.57 - 1.70: 157 1.70 - 1.82: 132 Bond restraints: 21658 Sorted by residual: bond pdb=" C SER J 76 " pdb=" N ARG J 77 " ideal model delta sigma weight residual 1.330 1.459 -0.129 1.30e-02 5.92e+03 9.84e+01 bond pdb=" C ASN H 98 " pdb=" N ASP H 99 " ideal model delta sigma weight residual 1.334 1.211 0.123 1.33e-02 5.65e+03 8.55e+01 bond pdb=" C LYS D 110 " pdb=" N GLU D 111 " ideal model delta sigma weight residual 1.332 1.452 -0.120 1.40e-02 5.10e+03 7.34e+01 bond pdb=" C THR J 11 " pdb=" N MET J 12 " ideal model delta sigma weight residual 1.330 1.453 -0.123 1.46e-02 4.69e+03 7.11e+01 bond pdb=" C GLU D 111 " pdb=" N GLN D 112 " ideal model delta sigma weight residual 1.332 1.216 0.116 1.40e-02 5.10e+03 6.86e+01 ... (remaining 21653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 28634 2.83 - 5.65: 810 5.65 - 8.48: 133 8.48 - 11.31: 17 11.31 - 14.13: 2 Bond angle restraints: 29596 Sorted by residual: angle pdb=" N GLY F 91 " pdb=" CA GLY F 91 " pdb=" C GLY F 91 " ideal model delta sigma weight residual 112.48 123.15 -10.67 1.21e+00 6.83e-01 7.77e+01 angle pdb=" CA VAL D 70 " pdb=" C VAL D 70 " pdb=" N CYS D 71 " ideal model delta sigma weight residual 116.40 108.24 8.16 1.12e+00 7.97e-01 5.30e+01 angle pdb=" O VAL D 70 " pdb=" C VAL D 70 " pdb=" N CYS D 71 " ideal model delta sigma weight residual 123.20 130.68 -7.48 1.08e+00 8.57e-01 4.79e+01 angle pdb=" N ILE L 525 " pdb=" CA ILE L 525 " pdb=" C ILE L 525 " ideal model delta sigma weight residual 112.96 106.27 6.69 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C SER J 16 " pdb=" N PRO J 17 " pdb=" CA PRO J 17 " ideal model delta sigma weight residual 119.92 112.77 7.15 1.07e+00 8.73e-01 4.46e+01 ... (remaining 29591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 12588 35.08 - 70.15: 562 70.15 - 105.23: 41 105.23 - 140.30: 0 140.30 - 175.38: 2 Dihedral angle restraints: 13193 sinusoidal: 5775 harmonic: 7418 Sorted by residual: dihedral pdb=" O4' U M -6 " pdb=" C1' U M -6 " pdb=" N1 U M -6 " pdb=" C2 U M -6 " ideal model delta sinusoidal sigma weight residual 200.00 42.16 157.84 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 47.38 -175.38 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA ARG H 562 " pdb=" C ARG H 562 " pdb=" N ASN H 563 " pdb=" CA ASN H 563 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 13190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3379 0.153 - 0.305: 73 0.305 - 0.458: 1 0.458 - 0.611: 1 0.611 - 0.763: 1 Chirality restraints: 3455 Sorted by residual: chirality pdb=" CB VAL L 552 " pdb=" CA VAL L 552 " pdb=" CG1 VAL L 552 " pdb=" CG2 VAL L 552 " both_signs ideal model delta sigma weight residual False -2.63 -1.87 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CB VAL G 96 " pdb=" CA VAL G 96 " pdb=" CG1 VAL G 96 " pdb=" CG2 VAL G 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.95e+00 chirality pdb=" CB VAL G 122 " pdb=" CA VAL G 122 " pdb=" CG1 VAL G 122 " pdb=" CG2 VAL G 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 3452 not shown) Planarity restraints: 3527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 255 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO H 256 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO H 256 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO H 256 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 64 " 0.038 2.00e-02 2.50e+03 3.86e-02 2.24e+01 pdb=" CG HIS H 64 " -0.079 2.00e-02 2.50e+03 pdb=" ND1 HIS H 64 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS H 64 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS H 64 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS H 64 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 138 " 0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ASP H 138 " -0.081 2.00e-02 2.50e+03 pdb=" O ASP H 138 " 0.028 2.00e-02 2.50e+03 pdb=" N THR H 139 " 0.028 2.00e-02 2.50e+03 ... (remaining 3524 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 805 2.69 - 3.24: 19208 3.24 - 3.79: 35228 3.79 - 4.35: 46943 4.35 - 4.90: 75844 Nonbonded interactions: 178028 Sorted by model distance: nonbonded pdb=" OD2 ASP H 169 " pdb="ZN ZN H 701 " model vdw 2.133 2.230 nonbonded pdb=" OG SER C 16 " pdb=" O GLY C 180 " model vdw 2.291 3.040 nonbonded pdb=" O LEU D 120 " pdb=" O2' U M 16 " model vdw 2.302 3.040 nonbonded pdb=" O GLY E 53 " pdb=" OG SER E 57 " model vdw 2.308 3.040 nonbonded pdb=" OG1 THR E 126 " pdb=" OG SER E 128 " model vdw 2.312 3.040 ... (remaining 178023 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 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 24 or (resid 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 31 or (resid 32 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 68 or (resid 69 and (n \ ame N or name CA or name C or name O or name CB )) or resid 70 through 74 or (re \ sid 78 through 79 and (name N or name CA or name C or name O or name CB )) or re \ sid 80 through 94 or (resid 95 through 96 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 through 109 or (resid 110 through 111 and (name N \ or name CA or name C or name O or name CB )) or resid 112 through 154 or (resid \ 155 through 156 and (name N or name CA or name C or name O or name CB )) or res \ id 157 through 194 or resid 301)) selection = (chain 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 40 or (resid 41 and (name N or name CA or name C or name O \ or name CB )) or resid 42 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 through 74 or (resid 78 throug \ h 79 and (name N or name CA or name C or name O or name CB )) or resid 80 throug \ h 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 through 114 or (resid 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 or (resid 120 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 133 o \ r (resid 134 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 35 through 154 or (resid 155 through 156 and (name N or name CA or name C or nam \ e O or name CB )) or resid 157 through 165 or (resid 166 and (name N or name CA \ or name C or name O or name CB )) or resid 167 through 186 or (resid 187 and (na \ me N or name CA or name C or name O or name CB )) or resid 188 through 194 or re \ sid 301)) selection = (chain 'D' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 24 or (resid 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 31 or (resid 32 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 40 or (resid 41 and (n \ ame N or name CA or name C or name O or name CB )) or resid 42 through 63 or (re \ sid 64 through 65 and (name N or name CA or name C or name O or name CB )) or re \ sid 66 through 68 or (resid 69 and (name N or name CA or name C or name O or nam \ e CB )) or resid 70 through 74 or (resid 78 through 79 and (name N or name CA or \ name C or name O or name CB )) or resid 80 through 82 or (resid 83 and (name N \ or name CA or name C or name O or name CB )) or resid 84 through 94 or (resid 95 \ through 96 and (name N or name CA or name C or name O or name CB )) or resid 97 \ through 109 or (resid 110 through 111 and (name N or name CA or name C or name \ O or name CB )) or resid 112 through 114 or (resid 115 and (name N or name CA or \ name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (name \ N or name CA or name C or name O or name CB )) or resid 119 or (resid 120 and ( \ name N or name CA or name C or name O or name CB )) or resid 131 through 133 or \ (resid 134 and (name N or name CA or name C or name O or name CB )) or resid 135 \ through 155 or (resid 156 and (name N or name CA or name C or name O or name CB \ )) or resid 157 through 165 or (resid 166 and (name N or name CA or name C or n \ ame O or name CB )) or resid 167 through 186 or (resid 187 and (name N or name C \ A or name C or name O or name CB )) or resid 188 through 194 or resid 301)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 24 or (resid 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 31 or (resid 32 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 40 or (resid 41 and (n \ ame N or name CA or name C or name O or name CB )) or resid 42 through 63 or (re \ sid 64 through 65 and (name N or name CA or name C or name O or name CB )) or re \ sid 66 through 68 or (resid 69 and (name N or name CA or name C or name O or nam \ e CB )) or resid 70 through 74 or (resid 78 through 79 and (name N or name CA or \ name C or name O or name CB )) or resid 80 through 82 or (resid 83 and (name N \ or name CA or name C or name O or name CB )) or resid 84 through 109 or (resid 1 \ 10 through 111 and (name N or name CA or name C or name O or name CB )) or resid \ 112 through 114 or (resid 115 and (name N or name CA or name C or name O or nam \ e CB )) or resid 116 through 117 or (resid 118 and (name N or name CA or name C \ or name O or name CB )) or resid 119 or (resid 120 and (name N or name CA or nam \ e C or name O or name CB )) or resid 131 through 133 or (resid 134 and (name N o \ r name CA or name C or name O or name CB )) or resid 135 through 165 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or r \ esid 188 through 194 or resid 301)) selection = (chain 'F' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 31 or (resid 32 through 34 and (nam \ e N or name CA or name C or name O or name CB )) or resid 35 through 40 or (resi \ d 41 and (name N or name CA or name C or name O or name CB )) or resid 42 throug \ h 63 or (resid 64 through 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 through 68 or (resid 69 and (name N or name CA or name C or na \ me O or name CB )) or resid 70 through 109 or (resid 110 through 111 and (name N \ or name CA or name C or name O or name CB )) or resid 112 through 114 or (resid \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throu \ gh 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 or (resid 120 and (name N or name CA or name C or name O or name CB ) \ ) or resid 131 through 133 or (resid 134 and (name N or name CA or name C or nam \ e O or name CB )) or resid 135 through 165 or (resid 166 and (name N or name CA \ or name C or name O or name CB )) or resid 167 through 186 or (resid 187 and (na \ me N or name CA or name C or name O or name CB )) or resid 188 through 194 or re \ sid 301)) selection = (chain 'J' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 24 or (resid 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 31 or (resid 32 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 40 or (resid 41 and (n \ ame N or name CA or name C or name O or name CB )) or resid 42 through 63 or (re \ sid 64 through 65 and (name N or name CA or name C or name O or name CB )) or re \ sid 66 through 68 or (resid 69 and (name N or name CA or name C or name O or nam \ e CB )) or resid 70 through 74 or (resid 78 through 79 and (name N or name CA or \ name C or name O or name CB )) or resid 80 through 82 or (resid 83 and (name N \ or name CA or name C or name O or name CB )) or resid 84 through 94 or (resid 95 \ through 96 and (name N or name CA or name C or name O or name CB )) or resid 97 \ through 109 or (resid 110 through 111 and (name N or name CA or name C or name \ O or name CB )) or resid 112 through 114 or (resid 115 and (name N or name CA or \ name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (name \ N or name CA or name C or name O or name CB )) or resid 119 or (resid 120 and ( \ name N or name CA or name C or name O or name CB )) or resid 131 through 133 or \ (resid 134 and (name N or name CA or name C or name O or name CB )) or resid 135 \ through 154 or (resid 155 through 156 and (name N or name CA or name C or name \ O or name CB )) or resid 157 through 165 or (resid 166 and (name N or name CA or \ name C or name O or name CB )) or resid 167 through 186 or (resid 187 and (name \ N or name CA or name C or name O or name CB )) or resid 188 through 194 or resi \ d 301)) } ncs_group { reference = (chain 'I' and (resid 434 through 438 or (resid 439 through 440 and (name N or n \ ame CA or name C or name O or name CB )) or resid 441 or (resid 442 through 443 \ and (name N or name CA or name C or name O or name CB )) or resid 444 through 48 \ 4 or (resid 485 through 486 and (name N or name CA or name C or name O or name C \ B )) or resid 487 through 488 or resid 510 or (resid 511 through 514 and (name N \ or name CA or name C or name O or name CB )) or resid 515 through 519 or (resid \ 520 and (name N or name CA or name C or name O or name CB )) or resid 521 throu \ gh 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) or \ resid 525 through 527 or (resid 528 and (name N or name CA or name C or name O \ or name CB )) or resid 529 through 531 or (resid 532 and (name N or name CA or n \ ame C or name O or name CB )) or resid 533 or (resid 534 through 535 and (name N \ or name CA or name C or name O or name CB )) or resid 536 or (resid 537 and (na \ me N or name CA or name C or name O or name CB )) or (resid 545 through 547 and \ (name N or name CA or name C or name O or name CB )) or resid 548 through 550 or \ (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 2 through 553 or (resid 554 and (name N or name CA or name C or name O or name C \ B )) or resid 555 through 560 or (resid 561 through 562 and (name N or name CA o \ r name C or name O or name CB )) or resid 563 through 567 or (resid 572 and (nam \ e N or name CA or name C or name O or name CB )) or resid 573 through 574 or (re \ sid 575 and (name N or name CA or name C or name O or name CB )) or resid 576 th \ rough 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 593 or (resid 594 and (name N or name CA or name C or name \ O or name CB )) or resid 595 through 596 or (resid 597 through 598 and (name N \ or name CA or name C or name O or name CB )) or resid 599 through 607 or (resid \ 608 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 434 through 461 or resid 465 through 487 or (resid 488 and \ (name N or name CA or name C or name O or name CB )) or resid 510 through 608)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.040 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 54.070 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.008 0.205 21658 Z= 0.511 Angle : 1.117 14.132 29596 Z= 0.658 Chirality : 0.062 0.763 3455 Planarity : 0.008 0.121 3527 Dihedral : 18.568 175.378 8373 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 2.27 % Allowed : 29.52 % Favored : 68.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.14), residues: 2471 helix: -1.52 (0.15), residues: 837 sheet: -1.07 (0.22), residues: 474 loop : -2.18 (0.15), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 473 HIS 0.041 0.004 HIS H 64 PHE 0.069 0.003 PHE G 191 TYR 0.033 0.002 TYR H 382 ARG 0.015 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 360 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7455 (tp30) REVERT: B 93 MET cc_start: 0.8343 (mmt) cc_final: 0.8068 (mmt) REVERT: D 178 ASN cc_start: 0.8549 (m-40) cc_final: 0.8331 (m-40) REVERT: D 196 ASP cc_start: 0.8391 (p0) cc_final: 0.7979 (p0) REVERT: E 166 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7982 (mtmt) REVERT: F 12 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: F 32 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7903 (mm-40) REVERT: F 93 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7663 (tpp) REVERT: G 109 GLU cc_start: 0.8389 (pt0) cc_final: 0.8090 (pt0) REVERT: G 207 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6657 (mmm160) REVERT: H 91 GLU cc_start: 0.7337 (mp0) cc_final: 0.6968 (mp0) REVERT: H 365 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: I 453 MET cc_start: 0.7933 (ttt) cc_final: 0.7421 (ttp) REVERT: I 561 ARG cc_start: 0.7118 (mtp-110) cc_final: 0.6892 (ttm-80) REVERT: J 156 LYS cc_start: 0.7543 (tppp) cc_final: 0.7084 (ptpp) REVERT: L 515 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6831 (pp20) REVERT: L 577 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7757 (tp30) outliers start: 46 outliers final: 23 residues processed: 391 average time/residue: 0.3432 time to fit residues: 208.6929 Evaluate side-chains 347 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 321 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain I residue 589 SER Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain K residue 455 PHE Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 199 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 HIS H 244 ASN H 469 ASN I 443 ASN ** I 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 ASN K 510 HIS L 472 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21658 Z= 0.185 Angle : 0.574 9.473 29596 Z= 0.307 Chirality : 0.042 0.288 3455 Planarity : 0.005 0.080 3527 Dihedral : 14.883 174.356 3930 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 3.50 % Allowed : 26.70 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2471 helix: 0.15 (0.17), residues: 850 sheet: -0.76 (0.23), residues: 463 loop : -1.77 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 473 HIS 0.005 0.001 HIS H 160 PHE 0.025 0.001 PHE D 133 TYR 0.012 0.001 TYR L 599 ARG 0.006 0.001 ARG H 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 356 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8202 (mmt) cc_final: 0.7968 (mmt) REVERT: D 111 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: D 196 ASP cc_start: 0.8297 (p0) cc_final: 0.7978 (p0) REVERT: E 115 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8417 (mmt-90) REVERT: E 120 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8686 (mp) REVERT: E 187 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7760 (mp0) REVERT: F 165 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8096 (mp) REVERT: G 53 ASP cc_start: 0.7886 (t0) cc_final: 0.7610 (t0) REVERT: G 207 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6999 (mmm-85) REVERT: G 235 GLU cc_start: 0.4820 (tp30) cc_final: 0.4598 (tp30) REVERT: H 91 GLU cc_start: 0.7398 (mp0) cc_final: 0.7062 (mp0) REVERT: H 183 ASP cc_start: 0.8332 (t0) cc_final: 0.8029 (t0) REVERT: H 377 ASP cc_start: 0.8270 (m-30) cc_final: 0.7872 (m-30) REVERT: H 381 ASP cc_start: 0.7798 (m-30) cc_final: 0.7503 (m-30) REVERT: I 529 ASN cc_start: 0.8121 (m110) cc_final: 0.7579 (m-40) REVERT: I 588 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8059 (mp) REVERT: K 515 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: K 540 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6979 (mtmt) REVERT: L 444 MET cc_start: 0.6980 (mmm) cc_final: 0.6695 (mmm) REVERT: L 515 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7018 (tt0) REVERT: L 587 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5672 (mm) outliers start: 71 outliers final: 34 residues processed: 400 average time/residue: 0.3391 time to fit residues: 205.9564 Evaluate side-chains 356 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 315 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 455 PHE Chi-restraints excluded: chain K residue 467 GLU Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 576 ILE Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN D 178 ASN E 152 ASN F 112 GLN F 178 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN J 69 ASN K 553 HIS L 472 ASN L 553 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21658 Z= 0.388 Angle : 0.630 9.409 29596 Z= 0.329 Chirality : 0.045 0.234 3455 Planarity : 0.004 0.065 3527 Dihedral : 14.584 171.303 3894 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 5.08 % Allowed : 24.68 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2471 helix: 0.78 (0.17), residues: 864 sheet: -0.70 (0.22), residues: 468 loop : -1.54 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 473 HIS 0.004 0.001 HIS F 119 PHE 0.019 0.002 PHE L 458 TYR 0.015 0.001 TYR H 268 ARG 0.006 0.001 ARG H 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 349 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8415 (mmt) cc_final: 0.8089 (mmt) REVERT: D 5 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8934 (ptp) REVERT: D 13 LYS cc_start: 0.8363 (pttt) cc_final: 0.7814 (ttmt) REVERT: D 111 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: D 196 ASP cc_start: 0.8461 (p0) cc_final: 0.8160 (p0) REVERT: E 187 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7878 (mp0) REVERT: F 93 MET cc_start: 0.8404 (tpp) cc_final: 0.8112 (tpt) REVERT: F 111 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: F 165 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (mp) REVERT: G 155 LYS cc_start: 0.8037 (tttt) cc_final: 0.7690 (tttp) REVERT: H 176 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6861 (mm-40) REVERT: H 178 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7786 (mmm) REVERT: H 267 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7337 (mp0) REVERT: H 305 SER cc_start: 0.8331 (t) cc_final: 0.7992 (p) REVERT: H 365 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5880 (mp0) REVERT: H 377 ASP cc_start: 0.8397 (m-30) cc_final: 0.7921 (m-30) REVERT: H 381 ASP cc_start: 0.7858 (m-30) cc_final: 0.7564 (m-30) REVERT: I 518 GLU cc_start: 0.7867 (tp30) cc_final: 0.7147 (tp30) REVERT: I 529 ASN cc_start: 0.8089 (m110) cc_final: 0.7448 (m-40) REVERT: I 547 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8081 (ttmt) REVERT: I 588 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7975 (mp) REVERT: K 401 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: K 515 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: K 540 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7080 (mtmt) REVERT: L 444 MET cc_start: 0.7425 (mmm) cc_final: 0.7051 (mmm) REVERT: L 480 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7353 (pp20) REVERT: L 515 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6959 (tt0) REVERT: L 587 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5809 (mm) outliers start: 103 outliers final: 52 residues processed: 419 average time/residue: 0.3451 time to fit residues: 218.0784 Evaluate side-chains 378 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 401 GLU Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 455 PHE Chi-restraints excluded: chain K residue 467 GLU Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 576 ILE Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 155 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN F 112 GLN H 148 HIS ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN J 69 ASN K 472 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21658 Z= 0.297 Angle : 0.565 10.116 29596 Z= 0.297 Chirality : 0.043 0.273 3455 Planarity : 0.004 0.060 3527 Dihedral : 14.502 170.734 3893 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 5.08 % Allowed : 24.33 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2471 helix: 1.18 (0.18), residues: 865 sheet: -0.62 (0.22), residues: 468 loop : -1.40 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 564 HIS 0.004 0.001 HIS L 553 PHE 0.019 0.001 PHE E 133 TYR 0.024 0.001 TYR H 268 ARG 0.007 0.001 ARG H 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 337 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7568 (mtt-85) REVERT: B 93 MET cc_start: 0.8420 (mmt) cc_final: 0.8121 (mmt) REVERT: B 197 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7915 (ptp90) REVERT: D 111 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: D 196 ASP cc_start: 0.8494 (p0) cc_final: 0.8190 (p0) REVERT: E 12 MET cc_start: 0.9314 (ttp) cc_final: 0.9069 (ttp) REVERT: E 187 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7875 (mp0) REVERT: F 93 MET cc_start: 0.8408 (tpp) cc_final: 0.8056 (tpt) REVERT: F 165 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8209 (mp) REVERT: G 128 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7707 (tm) REVERT: G 155 LYS cc_start: 0.8065 (tttt) cc_final: 0.7709 (tttp) REVERT: H 176 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6849 (mm-40) REVERT: H 178 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: H 305 SER cc_start: 0.8340 (t) cc_final: 0.8015 (p) REVERT: H 365 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5808 (mp0) REVERT: H 377 ASP cc_start: 0.8441 (m-30) cc_final: 0.7933 (m-30) REVERT: H 381 ASP cc_start: 0.7865 (m-30) cc_final: 0.7656 (m-30) REVERT: H 532 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8566 (ttmm) REVERT: H 542 GLN cc_start: 0.8099 (mt0) cc_final: 0.7854 (tt0) REVERT: H 547 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8200 (tttp) REVERT: I 529 ASN cc_start: 0.8049 (m110) cc_final: 0.7321 (m-40) REVERT: I 547 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8076 (ttmt) REVERT: I 588 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7945 (mp) REVERT: J 13 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8222 (ttmt) REVERT: J 105 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8409 (tp) REVERT: K 158 GLU cc_start: 0.6971 (mp0) cc_final: 0.6303 (mp0) REVERT: K 453 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6320 (ttp) REVERT: K 515 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: K 540 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7058 (mtmt) REVERT: L 444 MET cc_start: 0.7450 (mmm) cc_final: 0.7195 (mmm) REVERT: L 461 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6686 (tm-30) REVERT: L 480 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7323 (pp20) REVERT: L 487 SER cc_start: 0.7145 (p) cc_final: 0.6927 (m) REVERT: L 515 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7002 (tt0) REVERT: L 587 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5714 (mm) outliers start: 103 outliers final: 59 residues processed: 404 average time/residue: 0.3534 time to fit residues: 214.0352 Evaluate side-chains 380 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 306 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 547 LYS Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 456 SER Chi-restraints excluded: chain K residue 467 GLU Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 558 ASN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 576 ILE Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 3 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 125 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN H 101 GLN H 269 ASN ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN J 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 21658 Z= 0.372 Angle : 0.594 10.671 29596 Z= 0.310 Chirality : 0.044 0.246 3455 Planarity : 0.004 0.057 3527 Dihedral : 14.405 170.253 3884 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 6.07 % Allowed : 23.49 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2471 helix: 1.33 (0.18), residues: 866 sheet: -0.70 (0.22), residues: 476 loop : -1.33 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 176 HIS 0.010 0.002 HIS H 148 PHE 0.019 0.002 PHE E 133 TYR 0.026 0.001 TYR H 268 ARG 0.005 0.001 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 315 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.8442 (mmt) cc_final: 0.8107 (mmt) REVERT: B 107 ASN cc_start: 0.8702 (m110) cc_final: 0.8200 (m110) REVERT: B 197 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7909 (ptp90) REVERT: C 154 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: D 111 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: D 127 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8043 (mptp) REVERT: D 196 ASP cc_start: 0.8547 (p0) cc_final: 0.8242 (p0) REVERT: E 116 GLU cc_start: 0.8573 (tt0) cc_final: 0.8186 (pt0) REVERT: E 187 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7874 (mp0) REVERT: F 93 MET cc_start: 0.8430 (tpp) cc_final: 0.8132 (tpt) REVERT: F 165 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8199 (mp) REVERT: G 128 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7733 (tm) REVERT: G 155 LYS cc_start: 0.8109 (tttt) cc_final: 0.7736 (tttp) REVERT: H 178 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: H 184 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7699 (mmt) REVERT: H 305 SER cc_start: 0.8305 (t) cc_final: 0.8043 (p) REVERT: H 365 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: H 377 ASP cc_start: 0.8489 (m-30) cc_final: 0.7919 (m-30) REVERT: H 381 ASP cc_start: 0.7884 (m-30) cc_final: 0.7669 (m-30) REVERT: H 467 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6969 (tt0) REVERT: H 532 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8606 (ttmm) REVERT: H 542 GLN cc_start: 0.8128 (mt0) cc_final: 0.7868 (tt0) REVERT: I 529 ASN cc_start: 0.8130 (m110) cc_final: 0.7866 (m-40) REVERT: I 547 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8106 (ttmt) REVERT: I 588 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7917 (mp) REVERT: J 13 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8238 (ttmt) REVERT: J 105 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8599 (tp) REVERT: K 158 GLU cc_start: 0.6930 (mp0) cc_final: 0.6294 (mp0) REVERT: K 453 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6574 (ttt) REVERT: K 515 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: K 540 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7072 (mtmt) REVERT: L 444 MET cc_start: 0.7604 (mmm) cc_final: 0.7293 (mmm) REVERT: L 515 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6828 (tp30) REVERT: L 587 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5648 (mm) outliers start: 123 outliers final: 76 residues processed: 399 average time/residue: 0.3545 time to fit residues: 211.6262 Evaluate side-chains 391 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 299 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 469 ASN Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 559 THR Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 456 SER Chi-restraints excluded: chain K residue 467 GLU Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 542 GLN Chi-restraints excluded: chain K residue 558 ASN Chi-restraints excluded: chain K residue 559 THR Chi-restraints excluded: chain K residue 568 GLU Chi-restraints excluded: chain K residue 582 THR Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 462 LYS Chi-restraints excluded: chain L residue 576 ILE Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.9990 chunk 221 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 114 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 129 optimal weight: 0.0870 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN H 373 HIS ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN J 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21658 Z= 0.171 Angle : 0.527 11.701 29596 Z= 0.279 Chirality : 0.041 0.317 3455 Planarity : 0.003 0.052 3527 Dihedral : 14.459 171.681 3884 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 3.75 % Allowed : 25.96 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2471 helix: 1.66 (0.18), residues: 854 sheet: -0.56 (0.22), residues: 469 loop : -1.23 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 473 HIS 0.010 0.001 HIS H 148 PHE 0.023 0.001 PHE D 133 TYR 0.027 0.001 TYR H 268 ARG 0.004 0.000 ARG G 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 326 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.7181 (t) cc_final: 0.6661 (p) REVERT: B 68 GLU cc_start: 0.7986 (mp0) cc_final: 0.7695 (mp0) REVERT: B 93 MET cc_start: 0.8340 (mmt) cc_final: 0.8082 (mmt) REVERT: B 107 ASN cc_start: 0.8736 (m110) cc_final: 0.8263 (m110) REVERT: B 197 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7844 (ptp90) REVERT: C 154 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: D 111 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: D 196 ASP cc_start: 0.8467 (p0) cc_final: 0.8190 (p0) REVERT: E 12 MET cc_start: 0.9288 (ttp) cc_final: 0.9049 (ttp) REVERT: E 75 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: E 120 LEU cc_start: 0.9059 (mp) cc_final: 0.8849 (mt) REVERT: E 187 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7844 (mp0) REVERT: F 93 MET cc_start: 0.8344 (tpp) cc_final: 0.8070 (tpt) REVERT: F 140 GLU cc_start: 0.8482 (mp0) cc_final: 0.8261 (mp0) REVERT: G 128 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7832 (tm) REVERT: G 131 MET cc_start: 0.8037 (mmp) cc_final: 0.7599 (tpp) REVERT: G 155 LYS cc_start: 0.8115 (tttt) cc_final: 0.7736 (tttp) REVERT: H 184 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7422 (mmt) REVERT: H 340 PHE cc_start: 0.6474 (t80) cc_final: 0.6267 (t80) REVERT: H 365 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: H 377 ASP cc_start: 0.8466 (m-30) cc_final: 0.7889 (m-30) REVERT: H 381 ASP cc_start: 0.7755 (m-30) cc_final: 0.7548 (m-30) REVERT: H 467 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7000 (tt0) REVERT: H 542 GLN cc_start: 0.8097 (mt0) cc_final: 0.7896 (tt0) REVERT: I 547 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8079 (tppt) REVERT: I 588 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7943 (mp) REVERT: J 13 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8142 (ttmt) REVERT: K 158 GLU cc_start: 0.6543 (mp0) cc_final: 0.6172 (mp0) REVERT: K 515 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: K 540 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7035 (mtmt) REVERT: L 444 MET cc_start: 0.7469 (mmm) cc_final: 0.7173 (mmm) REVERT: L 480 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7448 (pp20) REVERT: L 515 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6919 (tp30) REVERT: L 587 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5608 (mm) outliers start: 76 outliers final: 42 residues processed: 381 average time/residue: 0.3632 time to fit residues: 209.5541 Evaluate side-chains 359 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 305 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 462 LYS Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 559 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 542 GLN Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 558 ASN Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 HIS ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN J 69 ASN J 178 ASN K 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21658 Z= 0.194 Angle : 0.524 11.431 29596 Z= 0.276 Chirality : 0.041 0.298 3455 Planarity : 0.003 0.050 3527 Dihedral : 14.387 172.757 3882 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 4.24 % Allowed : 25.72 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2471 helix: 1.78 (0.18), residues: 860 sheet: -0.51 (0.22), residues: 471 loop : -1.16 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 473 HIS 0.006 0.001 HIS H 148 PHE 0.016 0.001 PHE D 133 TYR 0.017 0.001 TYR H 268 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 316 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.7055 (t) cc_final: 0.6542 (p) REVERT: B 68 GLU cc_start: 0.7995 (mp0) cc_final: 0.7690 (mp0) REVERT: B 162 GLN cc_start: 0.8319 (mm110) cc_final: 0.7991 (mm-40) REVERT: B 197 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7836 (ptp90) REVERT: C 154 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: D 111 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: D 127 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7955 (mptp) REVERT: D 196 ASP cc_start: 0.8383 (p0) cc_final: 0.8146 (p0) REVERT: E 12 MET cc_start: 0.9279 (ttp) cc_final: 0.9071 (ttp) REVERT: E 75 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: E 120 LEU cc_start: 0.9045 (mp) cc_final: 0.8820 (mt) REVERT: E 187 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7849 (mp0) REVERT: F 93 MET cc_start: 0.8282 (tpp) cc_final: 0.8034 (tpt) REVERT: F 140 GLU cc_start: 0.8553 (mp0) cc_final: 0.8208 (mp0) REVERT: F 157 ASP cc_start: 0.7671 (t0) cc_final: 0.7125 (t0) REVERT: G 128 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7843 (tm) REVERT: G 131 MET cc_start: 0.7953 (mmp) cc_final: 0.7520 (tpp) REVERT: G 155 LYS cc_start: 0.8134 (tttt) cc_final: 0.7769 (tttp) REVERT: H 176 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6896 (mm-40) REVERT: H 184 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7483 (mpp) REVERT: H 188 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8661 (t0) REVERT: H 305 SER cc_start: 0.8376 (t) cc_final: 0.8072 (p) REVERT: H 365 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: H 377 ASP cc_start: 0.8464 (m-30) cc_final: 0.7849 (m-30) REVERT: H 467 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7063 (tt0) REVERT: H 542 GLN cc_start: 0.8091 (mt0) cc_final: 0.7876 (tt0) REVERT: I 547 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8091 (tppt) REVERT: I 588 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7983 (mp) REVERT: J 13 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8146 (ttmt) REVERT: J 87 CYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8038 (m) REVERT: K 453 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6270 (ttp) REVERT: K 515 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: K 540 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7035 (mtmt) REVERT: L 444 MET cc_start: 0.7530 (mmm) cc_final: 0.7190 (mmm) REVERT: L 480 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7432 (pp20) REVERT: L 515 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6858 (tp30) REVERT: L 587 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5640 (mm) outliers start: 86 outliers final: 53 residues processed: 378 average time/residue: 0.3588 time to fit residues: 202.3758 Evaluate side-chains 370 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 300 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 462 LYS Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 559 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 542 GLN Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 568 GLU Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN K 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21658 Z= 0.293 Angle : 0.562 11.219 29596 Z= 0.293 Chirality : 0.042 0.257 3455 Planarity : 0.004 0.049 3527 Dihedral : 14.350 171.348 3882 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 4.44 % Allowed : 25.17 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2471 helix: 1.76 (0.18), residues: 867 sheet: -0.61 (0.22), residues: 481 loop : -1.14 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 125 HIS 0.007 0.001 HIS H 148 PHE 0.018 0.001 PHE E 133 TYR 0.015 0.001 TYR K 191 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 310 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.7099 (t) cc_final: 0.6598 (p) REVERT: B 68 GLU cc_start: 0.7968 (mp0) cc_final: 0.7619 (mp0) REVERT: B 107 ASN cc_start: 0.8711 (m110) cc_final: 0.8168 (m110) REVERT: B 162 GLN cc_start: 0.8325 (mm110) cc_final: 0.8018 (mm-40) REVERT: B 197 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7817 (ptp90) REVERT: C 154 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: D 62 MET cc_start: 0.8469 (mtt) cc_final: 0.8091 (mtt) REVERT: D 111 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: D 127 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7976 (mptp) REVERT: D 196 ASP cc_start: 0.8510 (p0) cc_final: 0.8256 (p0) REVERT: E 75 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: E 120 LEU cc_start: 0.9118 (mp) cc_final: 0.8882 (mt) REVERT: E 187 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7878 (mp0) REVERT: F 93 MET cc_start: 0.8322 (tpp) cc_final: 0.8062 (tpt) REVERT: F 140 GLU cc_start: 0.8570 (mp0) cc_final: 0.8266 (mp0) REVERT: G 128 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7852 (tm) REVERT: G 131 MET cc_start: 0.7929 (mmp) cc_final: 0.7460 (tpp) REVERT: G 155 LYS cc_start: 0.8156 (tttt) cc_final: 0.7785 (tttp) REVERT: H 184 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: H 188 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8639 (t0) REVERT: H 298 GLN cc_start: 0.7968 (mt0) cc_final: 0.7229 (mp10) REVERT: H 305 SER cc_start: 0.8361 (t) cc_final: 0.8072 (p) REVERT: H 365 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5846 (mp0) REVERT: H 409 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: H 467 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7028 (tt0) REVERT: H 532 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8611 (ttmm) REVERT: H 542 GLN cc_start: 0.8110 (mt0) cc_final: 0.7889 (tt0) REVERT: I 547 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8125 (tppt) REVERT: I 588 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7886 (mp) REVERT: J 13 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8169 (ttmt) REVERT: J 87 CYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8100 (m) REVERT: K 453 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6378 (ttp) REVERT: K 515 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: K 540 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7082 (mtmt) REVERT: L 444 MET cc_start: 0.7629 (mmm) cc_final: 0.7188 (mmm) REVERT: L 480 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7464 (pp20) REVERT: L 515 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6805 (tp30) REVERT: L 587 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5606 (mm) outliers start: 90 outliers final: 59 residues processed: 376 average time/residue: 0.3530 time to fit residues: 199.5408 Evaluate side-chains 375 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 300 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 559 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 542 GLN Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 568 GLU Chi-restraints excluded: chain K residue 582 THR Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21658 Z= 0.271 Angle : 0.559 11.774 29596 Z= 0.291 Chirality : 0.042 0.278 3455 Planarity : 0.004 0.048 3527 Dihedral : 14.348 170.988 3882 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 4.49 % Allowed : 25.47 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2471 helix: 1.78 (0.18), residues: 867 sheet: -0.58 (0.22), residues: 476 loop : -1.15 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 473 HIS 0.007 0.001 HIS H 148 PHE 0.016 0.001 PHE E 133 TYR 0.015 0.001 TYR K 191 ARG 0.003 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 304 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.7246 (t) cc_final: 0.6743 (p) REVERT: B 68 GLU cc_start: 0.7975 (mp0) cc_final: 0.7612 (mp0) REVERT: B 107 ASN cc_start: 0.8697 (m110) cc_final: 0.8145 (m110) REVERT: B 162 GLN cc_start: 0.8327 (mm110) cc_final: 0.8024 (mm-40) REVERT: B 197 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7829 (ptp90) REVERT: C 152 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8531 (t0) REVERT: C 154 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: D 27 ASP cc_start: 0.8326 (m-30) cc_final: 0.8089 (m-30) REVERT: D 111 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: D 127 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7942 (mptp) REVERT: D 196 ASP cc_start: 0.8524 (p0) cc_final: 0.8265 (p0) REVERT: E 12 MET cc_start: 0.9303 (ttp) cc_final: 0.9081 (ttp) REVERT: E 75 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: E 120 LEU cc_start: 0.9111 (mp) cc_final: 0.8887 (mt) REVERT: E 187 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7878 (mp0) REVERT: F 93 MET cc_start: 0.8270 (tpp) cc_final: 0.8012 (tpt) REVERT: F 140 GLU cc_start: 0.8577 (mp0) cc_final: 0.8326 (mp0) REVERT: G 54 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: G 128 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7828 (tm) REVERT: G 131 MET cc_start: 0.7903 (mmp) cc_final: 0.7392 (tpp) REVERT: G 155 LYS cc_start: 0.8153 (tttt) cc_final: 0.7775 (tttp) REVERT: G 207 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.7214 (mmm-85) REVERT: H 176 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6894 (mm-40) REVERT: H 188 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8619 (t0) REVERT: H 365 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5840 (mp0) REVERT: H 409 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7643 (ttm-80) REVERT: H 467 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7039 (tt0) REVERT: H 473 TRP cc_start: 0.6517 (t60) cc_final: 0.6233 (t60) REVERT: H 532 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8605 (ttmm) REVERT: H 542 GLN cc_start: 0.8121 (mt0) cc_final: 0.7900 (tt0) REVERT: I 450 TYR cc_start: 0.6879 (m-80) cc_final: 0.6665 (m-80) REVERT: I 547 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8126 (tppt) REVERT: I 588 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7912 (mp) REVERT: J 13 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8137 (ttmt) REVERT: J 87 CYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8095 (m) REVERT: K 453 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6319 (ttp) REVERT: K 515 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: K 540 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7066 (mtmt) REVERT: L 480 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7456 (pp20) REVERT: L 515 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6812 (tp30) REVERT: L 587 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5611 (mm) outliers start: 91 outliers final: 63 residues processed: 371 average time/residue: 0.3581 time to fit residues: 200.1891 Evaluate side-chains 375 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 294 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 559 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 542 GLN Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 568 GLU Chi-restraints excluded: chain K residue 582 THR Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 0.4980 chunk 254 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 ASN E 152 ASN ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN L 565 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21658 Z= 0.180 Angle : 0.550 13.239 29596 Z= 0.285 Chirality : 0.041 0.291 3455 Planarity : 0.003 0.047 3527 Dihedral : 14.393 170.998 3882 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 3.85 % Allowed : 26.31 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2471 helix: 1.83 (0.18), residues: 861 sheet: -0.57 (0.22), residues: 476 loop : -1.13 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 473 HIS 0.007 0.001 HIS H 148 PHE 0.017 0.001 PHE D 133 TYR 0.018 0.001 TYR K 191 ARG 0.003 0.000 ARG C 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 303 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.7250 (t) cc_final: 0.6744 (p) REVERT: B 68 GLU cc_start: 0.7985 (mp0) cc_final: 0.7620 (mp0) REVERT: B 107 ASN cc_start: 0.8697 (m110) cc_final: 0.8165 (m110) REVERT: B 162 GLN cc_start: 0.8321 (mm110) cc_final: 0.8008 (mm-40) REVERT: B 197 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7817 (ptp90) REVERT: C 152 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8516 (t0) REVERT: C 154 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: D 111 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: D 127 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7908 (mptp) REVERT: D 196 ASP cc_start: 0.8511 (p0) cc_final: 0.8248 (p0) REVERT: E 75 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: E 120 LEU cc_start: 0.9054 (mp) cc_final: 0.8832 (mt) REVERT: E 187 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7852 (mp0) REVERT: F 93 MET cc_start: 0.8272 (tpp) cc_final: 0.8040 (tpt) REVERT: F 140 GLU cc_start: 0.8522 (mp0) cc_final: 0.8296 (mp0) REVERT: G 54 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.6217 (m-80) REVERT: G 128 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7744 (tm) REVERT: G 131 MET cc_start: 0.7867 (mmp) cc_final: 0.7350 (tpp) REVERT: G 155 LYS cc_start: 0.8151 (tttt) cc_final: 0.7784 (tttp) REVERT: G 207 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7226 (mmm-85) REVERT: H 176 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.6880 (mm-40) REVERT: H 188 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8602 (t0) REVERT: H 365 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: H 409 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: H 467 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7031 (tt0) REVERT: H 473 TRP cc_start: 0.6557 (t60) cc_final: 0.6297 (t60) REVERT: H 542 GLN cc_start: 0.8103 (mt0) cc_final: 0.7887 (tt0) REVERT: I 450 TYR cc_start: 0.6912 (m-80) cc_final: 0.6666 (m-80) REVERT: I 547 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8056 (tppt) REVERT: I 588 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8007 (mp) REVERT: J 13 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8113 (ttmt) REVERT: J 87 CYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8074 (m) REVERT: K 453 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6249 (ttp) REVERT: K 467 GLU cc_start: 0.7233 (pt0) cc_final: 0.6631 (pt0) REVERT: K 515 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: K 540 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7050 (mtmt) REVERT: L 444 MET cc_start: 0.7464 (mmt) cc_final: 0.6804 (mmm) REVERT: L 461 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7054 (tm-30) REVERT: L 480 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7484 (pp20) REVERT: L 515 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6813 (tp30) REVERT: L 587 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5617 (mm) outliers start: 78 outliers final: 56 residues processed: 361 average time/residue: 0.3556 time to fit residues: 191.9050 Evaluate side-chains 371 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 297 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 365 GLU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 577 GLU Chi-restraints excluded: chain H residue 588 LEU Chi-restraints excluded: chain I residue 514 ILE Chi-restraints excluded: chain I residue 559 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 453 MET Chi-restraints excluded: chain K residue 477 ILE Chi-restraints excluded: chain K residue 514 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 540 LYS Chi-restraints excluded: chain K residue 542 GLN Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 568 GLU Chi-restraints excluded: chain L residue 441 THR Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 0.0020 chunk 215 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 ASN E 152 ASN ** H 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114303 restraints weight = 26216.342| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.04 r_work: 0.3188 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21658 Z= 0.196 Angle : 0.708 59.199 29596 Z= 0.393 Chirality : 0.042 0.382 3455 Planarity : 0.003 0.046 3527 Dihedral : 14.398 171.009 3882 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 4.29 % Allowed : 26.06 % Favored : 69.64 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2471 helix: 1.83 (0.18), residues: 861 sheet: -0.56 (0.22), residues: 476 loop : -1.12 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 473 HIS 0.007 0.001 HIS H 148 PHE 0.021 0.001 PHE E 144 TYR 0.016 0.001 TYR K 191 ARG 0.003 0.000 ARG E 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5322.41 seconds wall clock time: 95 minutes 26.44 seconds (5726.44 seconds total)