Starting phenix.real_space_refine on Fri Jan 16 02:32:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qlp_18487/01_2026/8qlp_18487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qlp_18487/01_2026/8qlp_18487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qlp_18487/01_2026/8qlp_18487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qlp_18487/01_2026/8qlp_18487.map" model { file = "/net/cci-nas-00/data/ceres_data/8qlp_18487/01_2026/8qlp_18487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qlp_18487/01_2026/8qlp_18487.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 P 160 5.49 5 Mg 4 5.21 5 S 87 5.16 5 C 20000 2.51 5 N 5281 2.21 5 O 6199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31731 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3432 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3639 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 2 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "D" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 391 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3481 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "F" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3639 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "H" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 391 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3448 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "J" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3639 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 2 Chain: "K" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "L" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 391 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3474 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "N" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3639 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 2 Chain: "O" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "P" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 391 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.23, per 1000 atoms: 0.23 Number of scatterers: 31731 At special positions: 0 Unit cell: (113.75, 170.3, 217.75, 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) S 87 16.00 P 160 15.00 Mg 4 11.99 O 6199 8.00 N 5281 7.00 C 20000 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6562 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 41 sheets defined 39.4% alpha, 17.0% beta 48 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.546A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.549A pdb=" N ARG A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.666A pdb=" N LEU A 203 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 281 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 368 removed outlier: 4.024A pdb=" N LYS A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 removed outlier: 3.901A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 removed outlier: 4.044A pdb=" N ALA B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.623A pdb=" N LYS B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.680A pdb=" N PHE B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.555A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.616A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 231 through 234 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 71 through 88 removed outlier: 3.513A pdb=" N LYS E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 removed outlier: 3.727A pdb=" N ARG E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 159 Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.981A pdb=" N LYS E 192 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.694A pdb=" N GLU E 202 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 203 " --> pdb=" O VAL E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'E' and resid 219 through 223 removed outlier: 4.610A pdb=" N PHE E 223 " --> pdb=" O GLU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 257 through 281 removed outlier: 3.545A pdb=" N CYS E 261 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG E 263 " --> pdb=" O PHE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 384 Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 31 removed outlier: 3.548A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 106 removed outlier: 3.712A pdb=" N ILE F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 removed outlier: 3.674A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 removed outlier: 3.833A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 231 through 234 removed outlier: 3.574A pdb=" N PHE F 234 " --> pdb=" O TRP F 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 234' Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 351 Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.663A pdb=" N TRP F 370 " --> pdb=" O ASN F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.517A pdb=" N LEU F 456 " --> pdb=" O ILE F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.626A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 491 " --> pdb=" O GLY F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'I' and resid 14 through 28 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 45 through 55 Processing helix chain 'I' and resid 71 through 89 Processing helix chain 'I' and resid 109 through 114 removed outlier: 3.866A pdb=" N ARG I 114 " --> pdb=" O PRO I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 138 Processing helix chain 'I' and resid 148 through 158 Processing helix chain 'I' and resid 243 through 248 Processing helix chain 'I' and resid 257 through 280 Processing helix chain 'I' and resid 300 through 302 No H-bonds generated for 'chain 'I' and resid 300 through 302' Processing helix chain 'I' and resid 353 through 368 removed outlier: 3.528A pdb=" N LYS I 366 " --> pdb=" O ARG I 362 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN I 367 " --> pdb=" O ARG I 363 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP I 368 " --> pdb=" O GLN I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 385 removed outlier: 3.901A pdb=" N LEU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER I 385 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 22 through 30 removed outlier: 4.044A pdb=" N ALA J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 62 removed outlier: 3.622A pdb=" N LYS J 62 " --> pdb=" O ASN J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 83 Processing helix chain 'J' and resid 97 through 106 Processing helix chain 'J' and resid 109 through 132 removed outlier: 3.680A pdb=" N PHE J 121 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 151 removed outlier: 3.555A pdb=" N TYR J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 214 removed outlier: 3.615A pdb=" N LEU J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 230 Processing helix chain 'J' and resid 231 through 234 Processing helix chain 'J' and resid 245 through 247 No H-bonds generated for 'chain 'J' and resid 245 through 247' Processing helix chain 'J' and resid 248 through 264 Processing helix chain 'J' and resid 331 through 351 Processing helix chain 'J' and resid 366 through 377 Processing helix chain 'J' and resid 451 through 463 Processing helix chain 'J' and resid 477 through 491 Processing helix chain 'J' and resid 502 through 506 Processing helix chain 'M' and resid 14 through 29 Processing helix chain 'M' and resid 44 through 56 Processing helix chain 'M' and resid 71 through 88 removed outlier: 3.816A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 114 removed outlier: 4.646A pdb=" N ARG M 114 " --> pdb=" O PRO M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 138 Processing helix chain 'M' and resid 146 through 159 Processing helix chain 'M' and resid 189 through 194 removed outlier: 3.893A pdb=" N LYS M 192 " --> pdb=" O ASP M 189 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET M 194 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 203 Processing helix chain 'M' and resid 234 through 238 Processing helix chain 'M' and resid 243 through 248 Processing helix chain 'M' and resid 257 through 281 Processing helix chain 'M' and resid 300 through 304 Processing helix chain 'M' and resid 353 through 368 removed outlier: 4.029A pdb=" N ASN M 367 " --> pdb=" O ARG M 363 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP M 368 " --> pdb=" O GLN M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 384 Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 22 through 31 removed outlier: 3.547A pdb=" N ALA N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 60 Processing helix chain 'N' and resid 77 through 83 Processing helix chain 'N' and resid 97 through 106 removed outlier: 3.713A pdb=" N ILE N 104 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 129 removed outlier: 3.674A pdb=" N LYS N 124 " --> pdb=" O LEU N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.832A pdb=" N TYR N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN N 149 " --> pdb=" O ASP N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 214 Processing helix chain 'N' and resid 226 through 230 Processing helix chain 'N' and resid 231 through 234 removed outlier: 3.574A pdb=" N PHE N 234 " --> pdb=" O TRP N 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 231 through 234' Processing helix chain 'N' and resid 245 through 247 No H-bonds generated for 'chain 'N' and resid 245 through 247' Processing helix chain 'N' and resid 248 through 264 Processing helix chain 'N' and resid 331 through 351 Processing helix chain 'N' and resid 366 through 377 Processing helix chain 'N' and resid 451 through 462 removed outlier: 3.517A pdb=" N LEU N 456 " --> pdb=" O ILE N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 465 No H-bonds generated for 'chain 'N' and resid 463 through 465' Processing helix chain 'N' and resid 477 through 491 removed outlier: 3.625A pdb=" N ASP N 484 " --> pdb=" O LEU N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.530A pdb=" N TYR N 505 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.222A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS A 4 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 8 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR A 64 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AA3, first strand: chain 'B' and resid 311 through 315 removed outlier: 6.118A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU B 3 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 286 removed outlier: 5.948A pdb=" N MET A 291 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 325 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.743A pdb=" N ARG A 186 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.677A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 139 through 143 removed outlier: 6.295A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.462A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS E 4 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE E 60 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE E 6 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 62 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER E 8 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR E 64 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL E 118 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 314 through 315 removed outlier: 6.330A pdb=" N CYS F 279 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS F 360 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU F 281 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 357 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL F 386 " --> pdb=" O ILE F 357 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE F 359 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE F 388 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA F 361 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR F 387 " --> pdb=" O ILE F 445 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE F 445 " --> pdb=" O THR F 387 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR F 389 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE F 443 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER F 417 " --> pdb=" O VAL F 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 413 " --> pdb=" O SER F 417 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE F 412 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU F 3 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS F 2 " --> pdb=" O GLN E 409 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AB4, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AB5, first strand: chain 'E' and resid 283 through 286 Processing sheet with id=AB6, first strand: chain 'E' and resid 318 through 322 Processing sheet with id=AB7, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB8, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.588A pdb=" N CYS F 20 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS F 270 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'F' and resid 94 through 95 removed outlier: 8.216A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL F 44 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU F 141 " --> pdb=" O LEU F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 8 removed outlier: 7.014A pdb=" N LYS I 4 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE I 60 " --> pdb=" O LYS I 4 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE I 6 " --> pdb=" O PHE I 60 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU I 62 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER I 8 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR I 64 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU I 97 " --> pdb=" O PHE I 60 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU I 62 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 311 through 315 removed outlier: 3.895A pdb=" N ASN J 296 " --> pdb=" O ASN J 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 311 through 315 removed outlier: 6.350A pdb=" N CYS J 279 " --> pdb=" O PHE J 358 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N HIS J 360 " --> pdb=" O CYS J 279 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU J 281 " --> pdb=" O HIS J 360 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY J 385 " --> pdb=" O ASN J 446 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER J 417 " --> pdb=" O VAL J 413 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE J 412 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU J 3 " --> pdb=" O ILE J 412 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 178 through 180 removed outlier: 6.490A pdb=" N TYR I 402 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 207 through 210 removed outlier: 3.836A pdb=" N ARG I 186 " --> pdb=" O THR I 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 285 through 286 Processing sheet with id=AC8, first strand: chain 'I' and resid 304 through 305 removed outlier: 3.658A pdb=" N PHE I 305 " --> pdb=" O VAL I 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 318 through 328 Processing sheet with id=AD1, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'J' and resid 42 through 45 removed outlier: 6.677A pdb=" N VAL J 43 " --> pdb=" O LYS J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 139 through 143 removed outlier: 6.296A pdb=" N TRP J 139 " --> pdb=" O GLN J 222 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU J 224 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU J 141 " --> pdb=" O LEU J 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.463A pdb=" N ILE M 5 " --> pdb=" O TRP M 33 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS M 4 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE M 60 " --> pdb=" O LYS M 4 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE M 6 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU M 62 " --> pdb=" O PHE M 6 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER M 8 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR M 64 " --> pdb=" O SER M 8 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL M 118 " --> pdb=" O PRO M 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 311 through 315 Processing sheet with id=AD6, first strand: chain 'N' and resid 311 through 315 removed outlier: 4.657A pdb=" N LEU N 305 " --> pdb=" O VAL N 278 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL N 278 " --> pdb=" O LEU N 305 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL N 386 " --> pdb=" O ILE N 357 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR N 387 " --> pdb=" O ILE N 445 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE N 445 " --> pdb=" O THR N 387 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR N 389 " --> pdb=" O ILE N 443 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE N 443 " --> pdb=" O THR N 389 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER N 417 " --> pdb=" O VAL N 413 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL N 413 " --> pdb=" O SER N 417 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE N 412 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU N 3 " --> pdb=" O ILE N 412 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS N 2 " --> pdb=" O GLN M 409 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 175 through 177 Processing sheet with id=AD8, first strand: chain 'M' and resid 207 through 210 Processing sheet with id=AD9, first strand: chain 'M' and resid 283 through 286 Processing sheet with id=AE1, first strand: chain 'M' and resid 311 through 313 Processing sheet with id=AE2, first strand: chain 'M' and resid 390 through 391 Processing sheet with id=AE3, first strand: chain 'N' and resid 19 through 20 removed outlier: 3.587A pdb=" N CYS N 20 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS N 270 " --> pdb=" O LEU N 13 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 38 through 39 Processing sheet with id=AE5, first strand: chain 'N' and resid 94 through 95 removed outlier: 8.217A pdb=" N LYS N 94 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL N 43 " --> pdb=" O LYS N 94 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY N 42 " --> pdb=" O PHE N 140 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL N 142 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL N 44 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP N 139 " --> pdb=" O GLN N 222 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU N 224 " --> pdb=" O TRP N 139 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU N 141 " --> pdb=" O LEU N 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 1165 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4897 1.31 - 1.44: 9728 1.44 - 1.56: 17759 1.56 - 1.69: 320 1.69 - 1.81: 134 Bond restraints: 32838 Sorted by residual: bond pdb=" CA PRO B 499 " pdb=" C PRO B 499 " ideal model delta sigma weight residual 1.514 1.550 -0.036 5.50e-03 3.31e+04 4.22e+01 bond pdb=" P U O 1 " pdb=" OP3 U O 1 " ideal model delta sigma weight residual 1.480 1.605 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" P U C 1 " pdb=" OP3 U C 1 " ideal model delta sigma weight residual 1.480 1.605 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" P U G 1 " pdb=" OP3 U G 1 " ideal model delta sigma weight residual 1.480 1.605 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" P U K 1 " pdb=" OP3 U K 1 " ideal model delta sigma weight residual 1.480 1.604 -0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 32833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 44470 3.03 - 6.06: 562 6.06 - 9.10: 42 9.10 - 12.13: 9 12.13 - 15.16: 2 Bond angle restraints: 45085 Sorted by residual: angle pdb=" N HIS I 160 " pdb=" CA HIS I 160 " pdb=" C HIS I 160 " ideal model delta sigma weight residual 113.97 98.81 15.16 1.28e+00 6.10e-01 1.40e+02 angle pdb=" N HIS A 160 " pdb=" CA HIS A 160 " pdb=" C HIS A 160 " ideal model delta sigma weight residual 114.04 99.41 14.63 1.24e+00 6.50e-01 1.39e+02 angle pdb=" C GLU I 82 " pdb=" N LYS I 83 " pdb=" CA LYS I 83 " ideal model delta sigma weight residual 120.44 109.63 10.81 1.30e+00 5.92e-01 6.92e+01 angle pdb=" N VAL J 317 " pdb=" CA VAL J 317 " pdb=" C VAL J 317 " ideal model delta sigma weight residual 107.77 117.67 -9.90 1.48e+00 4.57e-01 4.47e+01 angle pdb=" N LEU I 310 " pdb=" CA LEU I 310 " pdb=" C LEU I 310 " ideal model delta sigma weight residual 113.89 103.56 10.33 1.58e+00 4.01e-01 4.27e+01 ... (remaining 45080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 18635 31.70 - 63.41: 802 63.41 - 95.11: 72 95.11 - 126.81: 2 126.81 - 158.51: 14 Dihedral angle restraints: 19525 sinusoidal: 9358 harmonic: 10167 Sorted by residual: dihedral pdb=" CA GLU F 316 " pdb=" C GLU F 316 " pdb=" N VAL F 317 " pdb=" CA VAL F 317 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA SER A 104 " pdb=" C SER A 104 " pdb=" N TYR A 105 " pdb=" CA TYR A 105 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA TYR I 330 " pdb=" C TYR I 330 " pdb=" N PRO I 331 " pdb=" CA PRO I 331 " ideal model delta harmonic sigma weight residual 0.00 -20.71 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 19522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4053 0.072 - 0.145: 700 0.145 - 0.217: 131 0.217 - 0.290: 12 0.290 - 0.362: 4 Chirality restraints: 4900 Sorted by residual: chirality pdb=" CA ASP B 306 " pdb=" N ASP B 306 " pdb=" C ASP B 306 " pdb=" CB ASP B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ILE I 95 " pdb=" N ILE I 95 " pdb=" C ILE I 95 " pdb=" CB ILE I 95 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ASP N 306 " pdb=" N ASP N 306 " pdb=" C ASP N 306 " pdb=" CB ASP N 306 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4897 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR I 105 " -0.021 2.00e-02 2.50e+03 4.38e-02 1.91e+01 pdb=" C TYR I 105 " 0.076 2.00e-02 2.50e+03 pdb=" O TYR I 105 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP I 106 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 189 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASP E 189 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP E 189 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR E 190 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 275 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU I 275 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU I 275 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG I 276 " 0.022 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 293 2.56 - 3.15: 25964 3.15 - 3.73: 53367 3.73 - 4.32: 77067 4.32 - 4.90: 118701 Nonbonded interactions: 275392 Sorted by model distance: nonbonded pdb=" O ILE B 507 " pdb="MG MG B1000 " model vdw 1.980 2.170 nonbonded pdb=" O ILE J 507 " pdb="MG MG J1000 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASN F 468 " pdb="MG MG F1000 " model vdw 1.987 2.170 nonbonded pdb=" OD1 ASN N 468 " pdb="MG MG N1000 " model vdw 1.987 2.170 nonbonded pdb=" OP1 A C 3 " pdb="MG MG B1000 " model vdw 1.996 2.170 ... (remaining 275387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 417) selection = (chain 'E' and (resid 1 through 38 or resid 45 through 417)) selection = (chain 'I' and (resid 1 through 38 or resid 45 through 417)) selection = (chain 'M' and (resid 1 through 38 or resid 45 through 417)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } 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: 19.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.980 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.006 0.125 32838 Z= 0.436 Angle : 0.887 15.161 45085 Z= 0.602 Chirality : 0.057 0.362 4900 Planarity : 0.006 0.121 5160 Dihedral : 16.847 158.514 12963 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.35 % Rotamer: Outliers : 1.83 % Allowed : 2.65 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3435 helix: 0.32 (0.15), residues: 1181 sheet: -1.13 (0.20), residues: 644 loop : -1.26 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 114 TYR 0.017 0.001 TYR I 105 PHE 0.018 0.002 PHE E 45 TRP 0.030 0.002 TRP J 86 HIS 0.008 0.001 HIS N 329 Details of bonding type rmsd covalent geometry : bond 0.00643 (32838) covalent geometry : angle 0.88662 (45085) hydrogen bonds : bond 0.22573 ( 1261) hydrogen bonds : angle 8.75649 ( 3466) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 743 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8443 (pttm) cc_final: 0.8116 (pttm) REVERT: A 187 PHE cc_start: 0.8710 (m-80) cc_final: 0.8018 (m-80) REVERT: A 212 ASN cc_start: 0.8410 (p0) cc_final: 0.8140 (p0) REVERT: A 234 ASN cc_start: 0.8652 (t0) cc_final: 0.8369 (t0) REVERT: A 328 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7511 (mmtm) REVERT: A 336 MET cc_start: 0.6699 (mtt) cc_final: 0.6437 (mtt) REVERT: A 383 TYR cc_start: 0.6892 (t80) cc_final: 0.6509 (t80) REVERT: B 18 GLN cc_start: 0.7802 (mt0) cc_final: 0.7157 (mm-40) REVERT: B 56 TYR cc_start: 0.8380 (t80) cc_final: 0.8162 (t80) REVERT: B 87 ASP cc_start: 0.7537 (t0) cc_final: 0.7298 (t0) REVERT: B 428 LYS cc_start: 0.6127 (tptt) cc_final: 0.5677 (tppt) REVERT: E 188 HIS cc_start: 0.7021 (m-70) cc_final: 0.6613 (m-70) REVERT: E 190 TYR cc_start: 0.6711 (m-10) cc_final: 0.6196 (m-10) REVERT: E 262 GLN cc_start: 0.8657 (mp10) cc_final: 0.8270 (mp10) REVERT: E 319 TRP cc_start: 0.7771 (p-90) cc_final: 0.7524 (p-90) REVERT: I 39 LEU cc_start: 0.7233 (tp) cc_final: 0.7029 (tp) REVERT: I 64 THR cc_start: 0.9058 (m) cc_final: 0.8822 (p) REVERT: I 133 LYS cc_start: 0.8156 (tptm) cc_final: 0.7729 (tppt) REVERT: I 147 PRO cc_start: 0.7346 (Cg_endo) cc_final: 0.7115 (Cg_exo) REVERT: I 200 VAL cc_start: 0.6434 (m) cc_final: 0.6067 (p) REVERT: I 314 GLN cc_start: 0.5303 (OUTLIER) cc_final: 0.4940 (tp40) REVERT: I 318 HIS cc_start: 0.6830 (m90) cc_final: 0.6589 (m90) REVERT: I 335 LEU cc_start: 0.8065 (tp) cc_final: 0.7862 (tt) REVERT: I 406 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7293 (mm-30) REVERT: J 437 VAL cc_start: 0.8271 (t) cc_final: 0.7985 (t) REVERT: J 458 ASP cc_start: 0.7201 (m-30) cc_final: 0.6969 (m-30) REVERT: J 496 LEU cc_start: 0.7439 (mt) cc_final: 0.6727 (mp) REVERT: M 204 THR cc_start: 0.7380 (m) cc_final: 0.6612 (m) REVERT: M 223 PHE cc_start: 0.8105 (m-80) cc_final: 0.7508 (m-80) REVERT: M 229 LYS cc_start: 0.7991 (ptpp) cc_final: 0.7748 (mtmm) REVERT: M 318 HIS cc_start: 0.7765 (m90) cc_final: 0.7148 (m90) REVERT: M 413 LYS cc_start: 0.7681 (mttt) cc_final: 0.7479 (pttm) outliers start: 56 outliers final: 11 residues processed: 776 average time/residue: 0.2146 time to fit residues: 260.0200 Evaluate side-chains 416 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 404 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 314 GLN Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain M residue 208 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 302 GLN B 323 GLN E 87 GLN E 225 HIS E 267 GLN E 340 HIS ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN F 414 ASN F 446 ASN I 267 GLN I 314 GLN I 409 GLN J 326 HIS M 267 GLN N 90 ASN N 331 ASN N 374 GLN N 446 ASN N 454 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.120866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089236 restraints weight = 78809.431| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.59 r_work: 0.3477 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32838 Z= 0.169 Angle : 0.650 9.653 45085 Z= 0.345 Chirality : 0.044 0.204 4900 Planarity : 0.005 0.054 5160 Dihedral : 16.017 155.630 5870 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.16 % Allowed : 10.46 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3435 helix: 0.82 (0.14), residues: 1221 sheet: -1.07 (0.21), residues: 624 loop : -1.04 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 225 TYR 0.030 0.002 TYR E 402 PHE 0.032 0.002 PHE I 187 TRP 0.037 0.002 TRP I 294 HIS 0.019 0.002 HIS J 326 Details of bonding type rmsd covalent geometry : bond 0.00381 (32838) covalent geometry : angle 0.65034 (45085) hydrogen bonds : bond 0.05155 ( 1261) hydrogen bonds : angle 5.87928 ( 3466) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 476 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8785 (pttm) cc_final: 0.8548 (pttm) REVERT: A 187 PHE cc_start: 0.8453 (m-80) cc_final: 0.8191 (m-80) REVERT: A 203 LEU cc_start: 0.8082 (mp) cc_final: 0.7673 (tp) REVERT: A 260 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8213 (pt0) REVERT: A 277 MET cc_start: 0.8810 (mmm) cc_final: 0.8500 (mmm) REVERT: A 328 LYS cc_start: 0.8504 (mmmt) cc_final: 0.7769 (mmtm) REVERT: A 336 MET cc_start: 0.7404 (mtt) cc_final: 0.7002 (mtt) REVERT: B 18 GLN cc_start: 0.8114 (mt0) cc_final: 0.7406 (mm-40) REVERT: B 56 TYR cc_start: 0.8308 (t80) cc_final: 0.8097 (t80) REVERT: B 148 TYR cc_start: 0.7241 (t80) cc_final: 0.7006 (t80) REVERT: B 474 ASP cc_start: 0.5997 (t0) cc_final: 0.5780 (t70) REVERT: E 66 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7548 (tm-30) REVERT: E 291 MET cc_start: 0.7725 (pmm) cc_final: 0.7348 (pmm) REVERT: E 319 TRP cc_start: 0.7850 (p-90) cc_final: 0.7507 (p-90) REVERT: E 387 ASP cc_start: 0.8110 (t0) cc_final: 0.7746 (t70) REVERT: E 392 TYR cc_start: 0.8534 (p90) cc_final: 0.8145 (p90) REVERT: E 402 TYR cc_start: 0.8603 (m-80) cc_final: 0.8085 (m-80) REVERT: F 1 MET cc_start: 0.8306 (mmt) cc_final: 0.7979 (mmp) REVERT: I 133 LYS cc_start: 0.8135 (tptm) cc_final: 0.7808 (tppt) REVERT: I 200 VAL cc_start: 0.6515 (m) cc_final: 0.6105 (p) REVERT: I 231 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: I 277 MET cc_start: 0.8916 (tpp) cc_final: 0.8661 (tmm) REVERT: I 282 VAL cc_start: 0.5560 (OUTLIER) cc_final: 0.5353 (p) REVERT: I 295 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.5788 (m-10) REVERT: I 318 HIS cc_start: 0.7218 (m90) cc_final: 0.6893 (m90) REVERT: I 328 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8111 (mmmt) REVERT: I 335 LEU cc_start: 0.8260 (tp) cc_final: 0.8020 (tt) REVERT: J 18 GLN cc_start: 0.7831 (mt0) cc_final: 0.7631 (mt0) REVERT: J 29 LEU cc_start: 0.9247 (tp) cc_final: 0.8771 (mt) REVERT: J 496 LEU cc_start: 0.7684 (mt) cc_final: 0.7055 (mp) REVERT: M 156 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6116 (mt0) REVERT: M 190 TYR cc_start: 0.5966 (m-80) cc_final: 0.5504 (m-10) REVERT: M 204 THR cc_start: 0.7312 (m) cc_final: 0.6970 (m) REVERT: M 223 PHE cc_start: 0.8288 (m-80) cc_final: 0.7639 (m-80) REVERT: M 305 PHE cc_start: 0.7654 (t80) cc_final: 0.7419 (t80) REVERT: M 310 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7404 (tt) REVERT: M 315 LYS cc_start: 0.6652 (mmtt) cc_final: 0.6017 (pptt) REVERT: M 330 TYR cc_start: 0.7774 (t80) cc_final: 0.7480 (t80) REVERT: M 413 LYS cc_start: 0.7967 (mttt) cc_final: 0.7363 (pttm) outliers start: 66 outliers final: 28 residues processed: 521 average time/residue: 0.2019 time to fit residues: 170.2076 Evaluate side-chains 399 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 367 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 453 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 176 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 325 optimal weight: 0.0170 chunk 162 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 234 optimal weight: 0.9980 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN E 225 HIS E 267 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN J 47 GLN J 409 ASN N 236 ASN N 446 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.121293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.089612 restraints weight = 77820.569| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.58 r_work: 0.3478 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32838 Z= 0.133 Angle : 0.592 10.094 45085 Z= 0.312 Chirality : 0.043 0.301 4900 Planarity : 0.004 0.065 5160 Dihedral : 15.883 154.613 5852 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.73 % Allowed : 13.44 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3435 helix: 0.94 (0.15), residues: 1225 sheet: -1.02 (0.21), residues: 629 loop : -0.93 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 263 TYR 0.021 0.001 TYR N 150 PHE 0.036 0.002 PHE A 17 TRP 0.040 0.001 TRP I 294 HIS 0.009 0.001 HIS M 318 Details of bonding type rmsd covalent geometry : bond 0.00295 (32838) covalent geometry : angle 0.59201 (45085) hydrogen bonds : bond 0.04543 ( 1261) hydrogen bonds : angle 5.48996 ( 3466) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 410 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.6719 (t) cc_final: 0.6300 (p) REVERT: A 122 LYS cc_start: 0.8740 (pttm) cc_final: 0.8524 (pttm) REVERT: A 164 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7340 (tp) REVERT: A 203 LEU cc_start: 0.8102 (mp) cc_final: 0.7634 (tp) REVERT: A 217 PHE cc_start: 0.8346 (m-80) cc_final: 0.7676 (t80) REVERT: A 246 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8646 (pt) REVERT: A 277 MET cc_start: 0.8833 (mmm) cc_final: 0.8503 (mmm) REVERT: A 328 LYS cc_start: 0.8560 (mmmt) cc_final: 0.7849 (mppt) REVERT: A 336 MET cc_start: 0.7487 (mtt) cc_final: 0.6993 (mtt) REVERT: B 18 GLN cc_start: 0.8246 (mt0) cc_final: 0.7474 (mm-40) REVERT: B 56 TYR cc_start: 0.8320 (t80) cc_final: 0.8117 (t80) REVERT: B 148 TYR cc_start: 0.7089 (t80) cc_final: 0.6833 (t80) REVERT: B 348 GLU cc_start: 0.8799 (pt0) cc_final: 0.8241 (mm-30) REVERT: E 66 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 291 MET cc_start: 0.7655 (pmm) cc_final: 0.7393 (pmm) REVERT: E 319 TRP cc_start: 0.7987 (p-90) cc_final: 0.7538 (p-90) REVERT: E 402 TYR cc_start: 0.8523 (m-80) cc_final: 0.8108 (m-80) REVERT: E 411 VAL cc_start: 0.8739 (p) cc_final: 0.8452 (m) REVERT: I 37 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7649 (mp) REVERT: I 133 LYS cc_start: 0.8125 (tptm) cc_final: 0.7798 (tppt) REVERT: I 153 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6911 (mm) REVERT: I 200 VAL cc_start: 0.6490 (m) cc_final: 0.5995 (p) REVERT: I 219 TRP cc_start: 0.8615 (t60) cc_final: 0.8387 (t60) REVERT: I 277 MET cc_start: 0.8850 (tpp) cc_final: 0.8416 (tpp) REVERT: I 282 VAL cc_start: 0.5606 (OUTLIER) cc_final: 0.5313 (p) REVERT: I 295 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: I 318 HIS cc_start: 0.7232 (m90) cc_final: 0.6883 (m90) REVERT: I 328 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8314 (mmmt) REVERT: I 340 HIS cc_start: 0.6112 (m90) cc_final: 0.5908 (m90) REVERT: I 393 LEU cc_start: 0.8607 (tp) cc_final: 0.8402 (tp) REVERT: J 29 LEU cc_start: 0.9187 (tp) cc_final: 0.8792 (mt) REVERT: J 232 ARG cc_start: 0.8760 (mmm-85) cc_final: 0.8418 (mpt-90) REVERT: J 430 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8120 (tm-30) REVERT: J 496 LEU cc_start: 0.7803 (mt) cc_final: 0.7471 (mp) REVERT: M 156 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6188 (tt0) REVERT: M 190 TYR cc_start: 0.6087 (m-80) cc_final: 0.5561 (m-10) REVERT: M 193 LEU cc_start: 0.8339 (mt) cc_final: 0.8045 (tt) REVERT: M 223 PHE cc_start: 0.8445 (m-80) cc_final: 0.7610 (m-80) REVERT: M 271 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9008 (mmtt) REVERT: M 413 LYS cc_start: 0.7981 (mttt) cc_final: 0.7381 (pttm) REVERT: N 1 MET cc_start: 0.7584 (mmp) cc_final: 0.7245 (mmp) outliers start: 53 outliers final: 25 residues processed: 445 average time/residue: 0.1952 time to fit residues: 143.3170 Evaluate side-chains 389 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 358 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 150 TYR Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 446 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 134 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 190 optimal weight: 0.0970 chunk 291 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN E 156 GLN E 225 HIS E 267 GLN E 370 ASN F 402 ASN I 267 GLN ** I 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 446 ASN ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.117019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085064 restraints weight = 77753.824| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.51 r_work: 0.3392 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32838 Z= 0.220 Angle : 0.630 12.395 45085 Z= 0.331 Chirality : 0.044 0.280 4900 Planarity : 0.004 0.056 5160 Dihedral : 16.011 155.787 5852 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.58 % Allowed : 14.45 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3435 helix: 0.77 (0.15), residues: 1224 sheet: -1.31 (0.20), residues: 667 loop : -0.83 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 263 TYR 0.027 0.002 TYR E 190 PHE 0.030 0.002 PHE B 206 TRP 0.022 0.002 TRP F 231 HIS 0.009 0.002 HIS I 340 Details of bonding type rmsd covalent geometry : bond 0.00500 (32838) covalent geometry : angle 0.62990 (45085) hydrogen bonds : bond 0.04585 ( 1261) hydrogen bonds : angle 5.45045 ( 3466) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 361 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.6865 (t) cc_final: 0.6391 (p) REVERT: A 203 LEU cc_start: 0.8180 (mp) cc_final: 0.7714 (tp) REVERT: A 240 ARG cc_start: 0.8747 (mmt180) cc_final: 0.8246 (mmt90) REVERT: A 277 MET cc_start: 0.8938 (mmm) cc_final: 0.8570 (mmm) REVERT: A 328 LYS cc_start: 0.8618 (mmmt) cc_final: 0.7949 (mppt) REVERT: A 336 MET cc_start: 0.7459 (mtt) cc_final: 0.7051 (mtt) REVERT: B 18 GLN cc_start: 0.8366 (mt0) cc_final: 0.7473 (mm-40) REVERT: B 348 GLU cc_start: 0.8846 (pt0) cc_final: 0.8322 (mm-30) REVERT: E 66 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7606 (tm-30) REVERT: E 224 MET cc_start: 0.8147 (mmm) cc_final: 0.7904 (mmm) REVERT: E 319 TRP cc_start: 0.7977 (p-90) cc_final: 0.7461 (p-90) REVERT: I 37 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7529 (mp) REVERT: I 133 LYS cc_start: 0.8171 (tptm) cc_final: 0.7830 (tppt) REVERT: I 153 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6809 (mm) REVERT: I 160 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.6754 (p-80) REVERT: I 200 VAL cc_start: 0.6774 (m) cc_final: 0.6293 (p) REVERT: I 219 TRP cc_start: 0.8679 (t60) cc_final: 0.8441 (t60) REVERT: I 277 MET cc_start: 0.8924 (tpp) cc_final: 0.8720 (tpp) REVERT: I 282 VAL cc_start: 0.5563 (OUTLIER) cc_final: 0.5341 (p) REVERT: I 295 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: I 328 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8499 (mmmt) REVERT: J 496 LEU cc_start: 0.8249 (mt) cc_final: 0.7913 (mp) REVERT: M 156 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6440 (mt0) REVERT: M 190 TYR cc_start: 0.6252 (m-10) cc_final: 0.5664 (m-80) REVERT: M 223 PHE cc_start: 0.8549 (m-80) cc_final: 0.7728 (m-80) REVERT: M 271 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9073 (mmtt) REVERT: M 305 PHE cc_start: 0.7643 (t80) cc_final: 0.7287 (t80) REVERT: M 315 LYS cc_start: 0.6783 (mmtt) cc_final: 0.6162 (pptt) REVERT: M 394 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6822 (pp20) REVERT: M 413 LYS cc_start: 0.7992 (mttt) cc_final: 0.7472 (pttm) outliers start: 79 outliers final: 52 residues processed: 409 average time/residue: 0.1931 time to fit residues: 130.2242 Evaluate side-chains 391 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 334 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 486 ILE Chi-restraints excluded: chain J residue 501 LEU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 389 ASN Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 150 TYR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 16 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN E 225 HIS E 364 GLN F 446 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 HIS M 314 GLN M 364 GLN ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.114411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.082547 restraints weight = 78499.525| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.50 r_work: 0.3343 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32838 Z= 0.271 Angle : 0.657 12.819 45085 Z= 0.346 Chirality : 0.045 0.292 4900 Planarity : 0.005 0.052 5160 Dihedral : 16.137 155.653 5849 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.07 % Allowed : 15.23 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3435 helix: 0.64 (0.15), residues: 1216 sheet: -1.50 (0.20), residues: 660 loop : -0.92 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 263 TYR 0.020 0.002 TYR E 402 PHE 0.026 0.002 PHE N 358 TRP 0.026 0.002 TRP F 231 HIS 0.012 0.002 HIS I 340 Details of bonding type rmsd covalent geometry : bond 0.00618 (32838) covalent geometry : angle 0.65694 (45085) hydrogen bonds : bond 0.04734 ( 1261) hydrogen bonds : angle 5.53444 ( 3466) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 352 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7809 (m-40) REVERT: A 277 MET cc_start: 0.8986 (mmm) cc_final: 0.8659 (mmm) REVERT: A 291 MET cc_start: 0.8616 (tpt) cc_final: 0.8325 (tpt) REVERT: A 328 LYS cc_start: 0.8658 (mmmt) cc_final: 0.7990 (mppt) REVERT: A 336 MET cc_start: 0.7427 (mtt) cc_final: 0.7034 (mtt) REVERT: B 348 GLU cc_start: 0.8856 (pt0) cc_final: 0.8342 (mm-30) REVERT: E 66 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7662 (tm-30) REVERT: E 103 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7686 (tp) REVERT: F 247 LYS cc_start: 0.8962 (mttt) cc_final: 0.8717 (ttmm) REVERT: F 358 PHE cc_start: 0.7769 (t80) cc_final: 0.7485 (t80) REVERT: I 133 LYS cc_start: 0.8231 (tptm) cc_final: 0.7893 (tppt) REVERT: I 221 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: I 282 VAL cc_start: 0.5454 (OUTLIER) cc_final: 0.5086 (p) REVERT: I 295 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: I 301 GLU cc_start: 0.7610 (pm20) cc_final: 0.7241 (tm-30) REVERT: I 318 HIS cc_start: 0.7044 (m90) cc_final: 0.6642 (m90) REVERT: I 328 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8659 (mmmt) REVERT: J 327 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6372 (tt0) REVERT: M 156 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6639 (mt0) REVERT: M 181 PHE cc_start: 0.7948 (p90) cc_final: 0.7740 (p90) REVERT: M 190 TYR cc_start: 0.6423 (m-10) cc_final: 0.5966 (m-10) REVERT: M 223 PHE cc_start: 0.8643 (m-80) cc_final: 0.7864 (m-80) REVERT: M 271 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9101 (mmtt) REVERT: M 278 LYS cc_start: 0.9179 (mttm) cc_final: 0.8944 (tptp) REVERT: M 305 PHE cc_start: 0.7734 (t80) cc_final: 0.7398 (t80) REVERT: M 315 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6119 (pttm) REVERT: M 380 PHE cc_start: 0.8455 (t80) cc_final: 0.8123 (t80) REVERT: M 394 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6715 (pp20) REVERT: M 413 LYS cc_start: 0.8002 (mttt) cc_final: 0.7544 (pttm) REVERT: N 348 GLU cc_start: 0.8408 (pp20) cc_final: 0.8122 (tm-30) outliers start: 94 outliers final: 66 residues processed: 406 average time/residue: 0.2006 time to fit residues: 133.2011 Evaluate side-chains 392 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 320 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 221 TYR Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain I residue 414 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 327 GLU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 486 ILE Chi-restraints excluded: chain J residue 501 LEU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 SER Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 277 MET Chi-restraints excluded: chain M residue 388 GLU Chi-restraints excluded: chain M residue 389 ASN Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 390 LYS Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 324 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 334 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 222 optimal weight: 0.5980 chunk 275 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** I 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.085386 restraints weight = 77586.270| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.51 r_work: 0.3394 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32838 Z= 0.143 Angle : 0.575 12.882 45085 Z= 0.302 Chirality : 0.042 0.314 4900 Planarity : 0.004 0.052 5160 Dihedral : 15.952 154.615 5849 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.06 % Allowed : 16.44 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3435 helix: 0.92 (0.15), residues: 1220 sheet: -1.34 (0.20), residues: 676 loop : -0.86 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 232 TYR 0.036 0.001 TYR E 190 PHE 0.022 0.002 PHE M 273 TRP 0.027 0.001 TRP F 231 HIS 0.005 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00323 (32838) covalent geometry : angle 0.57521 (45085) hydrogen bonds : bond 0.04205 ( 1261) hydrogen bonds : angle 5.26204 ( 3466) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 368 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7944 (m-40) REVERT: A 203 LEU cc_start: 0.8232 (mp) cc_final: 0.7798 (tp) REVERT: A 277 MET cc_start: 0.8985 (mmm) cc_final: 0.8661 (mmm) REVERT: A 291 MET cc_start: 0.8594 (tpt) cc_final: 0.8331 (tpt) REVERT: A 328 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8003 (mppt) REVERT: A 336 MET cc_start: 0.7449 (mtt) cc_final: 0.7085 (mtt) REVERT: B 150 TYR cc_start: 0.8229 (t80) cc_final: 0.8009 (t80) REVERT: E 66 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7562 (tm-30) REVERT: E 224 MET cc_start: 0.8038 (mmm) cc_final: 0.7802 (mmm) REVERT: E 402 TYR cc_start: 0.8282 (m-80) cc_final: 0.7708 (m-80) REVERT: E 411 VAL cc_start: 0.8692 (p) cc_final: 0.8398 (m) REVERT: F 247 LYS cc_start: 0.8961 (mttt) cc_final: 0.8694 (ttmm) REVERT: I 122 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8791 (mmmt) REVERT: I 133 LYS cc_start: 0.8276 (tptm) cc_final: 0.7877 (tppt) REVERT: I 160 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.6768 (p-80) REVERT: I 221 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: I 295 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: I 301 GLU cc_start: 0.7581 (pm20) cc_final: 0.7283 (tm-30) REVERT: I 328 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8536 (mmmt) REVERT: J 232 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8251 (mpt-90) REVERT: J 497 LYS cc_start: 0.8505 (tppt) cc_final: 0.8299 (ttpp) REVERT: M 156 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6638 (mt0) REVERT: M 190 TYR cc_start: 0.6412 (m-10) cc_final: 0.5986 (m-10) REVERT: M 223 PHE cc_start: 0.8664 (m-80) cc_final: 0.7863 (m-80) REVERT: M 267 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8653 (tt0) REVERT: M 271 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9133 (mmtt) REVERT: M 278 LYS cc_start: 0.9181 (mttm) cc_final: 0.8942 (tptp) REVERT: M 287 MET cc_start: 0.8343 (mmm) cc_final: 0.7960 (mmm) REVERT: M 305 PHE cc_start: 0.7686 (t80) cc_final: 0.7445 (t80) REVERT: M 315 LYS cc_start: 0.7000 (mmtt) cc_final: 0.6128 (pttm) REVERT: M 380 PHE cc_start: 0.8415 (t80) cc_final: 0.8132 (t80) REVERT: M 394 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6645 (pp20) REVERT: M 413 LYS cc_start: 0.8036 (mttt) cc_final: 0.7527 (pttm) REVERT: N 348 GLU cc_start: 0.8343 (pp20) cc_final: 0.8038 (tm-30) REVERT: N 391 THR cc_start: 0.8755 (p) cc_final: 0.8496 (m) outliers start: 63 outliers final: 42 residues processed: 410 average time/residue: 0.1979 time to fit residues: 132.8209 Evaluate side-chains 380 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 333 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 221 TYR Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 270 optimal weight: 5.9990 chunk 358 optimal weight: 8.9990 chunk 350 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 313 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 267 GLN F 302 GLN ** I 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 ASN ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.116031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.083987 restraints weight = 77703.695| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.54 r_work: 0.3388 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32838 Z= 0.144 Angle : 0.576 13.475 45085 Z= 0.302 Chirality : 0.043 0.394 4900 Planarity : 0.004 0.054 5160 Dihedral : 15.899 154.872 5849 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.09 % Allowed : 16.90 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3435 helix: 0.96 (0.15), residues: 1227 sheet: -1.29 (0.20), residues: 676 loop : -0.79 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 232 TYR 0.023 0.001 TYR E 190 PHE 0.044 0.002 PHE A 17 TRP 0.030 0.001 TRP F 231 HIS 0.006 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (32838) covalent geometry : angle 0.57618 (45085) hydrogen bonds : bond 0.04139 ( 1261) hydrogen bonds : angle 5.18702 ( 3466) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 356 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8229 (t0) cc_final: 0.7923 (t0) REVERT: A 203 LEU cc_start: 0.8250 (mp) cc_final: 0.7796 (tp) REVERT: A 277 MET cc_start: 0.9007 (mmm) cc_final: 0.8684 (mmm) REVERT: A 328 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8013 (mppt) REVERT: A 336 MET cc_start: 0.7500 (mtt) cc_final: 0.7106 (mtt) REVERT: B 150 TYR cc_start: 0.8330 (t80) cc_final: 0.8128 (t80) REVERT: E 66 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7586 (tm-30) REVERT: E 224 MET cc_start: 0.8043 (mmm) cc_final: 0.7804 (mmm) REVERT: E 402 TYR cc_start: 0.8266 (m-80) cc_final: 0.7738 (m-80) REVERT: E 411 VAL cc_start: 0.8721 (p) cc_final: 0.8435 (m) REVERT: F 247 LYS cc_start: 0.8963 (mttt) cc_final: 0.8696 (ttmm) REVERT: F 303 MET cc_start: 0.8674 (tmm) cc_final: 0.8120 (ttm) REVERT: I 122 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8787 (mmmt) REVERT: I 133 LYS cc_start: 0.8259 (tptm) cc_final: 0.7895 (tppt) REVERT: I 160 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.6843 (p-80) REVERT: I 219 TRP cc_start: 0.8843 (t60) cc_final: 0.8310 (t60) REVERT: I 221 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: I 268 LEU cc_start: 0.9562 (mm) cc_final: 0.9257 (mm) REVERT: I 277 MET cc_start: 0.8893 (tpp) cc_final: 0.8543 (tpp) REVERT: I 295 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: I 318 HIS cc_start: 0.7526 (m90) cc_final: 0.7194 (m90) REVERT: I 328 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8713 (mmmt) REVERT: J 232 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8244 (mpt-90) REVERT: J 497 LYS cc_start: 0.8508 (tppt) cc_final: 0.8292 (ttpp) REVERT: M 156 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6645 (mt0) REVERT: M 190 TYR cc_start: 0.6592 (m-10) cc_final: 0.6114 (m-10) REVERT: M 193 LEU cc_start: 0.8357 (mt) cc_final: 0.7955 (tt) REVERT: M 223 PHE cc_start: 0.8652 (m-80) cc_final: 0.7857 (m-80) REVERT: M 224 MET cc_start: 0.8821 (mmm) cc_final: 0.8572 (mmm) REVERT: M 245 GLU cc_start: 0.9134 (tt0) cc_final: 0.8756 (tp30) REVERT: M 267 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: M 271 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9132 (mmtt) REVERT: M 278 LYS cc_start: 0.9189 (mttm) cc_final: 0.8932 (tptp) REVERT: M 287 MET cc_start: 0.8412 (mmm) cc_final: 0.8047 (mmm) REVERT: M 305 PHE cc_start: 0.7672 (t80) cc_final: 0.7418 (t80) REVERT: M 315 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6233 (pttm) REVERT: M 380 PHE cc_start: 0.8408 (t80) cc_final: 0.8126 (t80) REVERT: M 394 GLU cc_start: 0.7674 (mt-10) cc_final: 0.6602 (pp20) REVERT: M 413 LYS cc_start: 0.8029 (mttt) cc_final: 0.7507 (pttm) REVERT: N 348 GLU cc_start: 0.8345 (pp20) cc_final: 0.8041 (tm-30) REVERT: N 391 THR cc_start: 0.8742 (p) cc_final: 0.8508 (m) outliers start: 64 outliers final: 49 residues processed: 398 average time/residue: 0.1925 time to fit residues: 126.9015 Evaluate side-chains 388 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 221 TYR Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 389 ASN Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Chi-restraints excluded: chain N residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 245 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 250 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 322 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN E 225 HIS E 267 GLN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 HIS ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.116628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084863 restraints weight = 77767.091| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.48 r_work: 0.3389 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32838 Z= 0.153 Angle : 0.582 11.989 45085 Z= 0.305 Chirality : 0.042 0.305 4900 Planarity : 0.004 0.053 5160 Dihedral : 15.882 154.805 5849 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.19 % Allowed : 17.59 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3435 helix: 0.97 (0.15), residues: 1225 sheet: -1.26 (0.20), residues: 678 loop : -0.76 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 374 TYR 0.019 0.001 TYR B 48 PHE 0.037 0.002 PHE A 17 TRP 0.048 0.001 TRP I 294 HIS 0.006 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00351 (32838) covalent geometry : angle 0.58232 (45085) hydrogen bonds : bond 0.04113 ( 1261) hydrogen bonds : angle 5.17105 ( 3466) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 348 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8270 (t0) cc_final: 0.7975 (t0) REVERT: A 260 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8295 (pt0) REVERT: A 277 MET cc_start: 0.9004 (mmm) cc_final: 0.8693 (mmm) REVERT: A 291 MET cc_start: 0.8578 (tpt) cc_final: 0.8264 (tpt) REVERT: A 328 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8008 (mppt) REVERT: A 336 MET cc_start: 0.7454 (mtt) cc_final: 0.7066 (mtt) REVERT: B 103 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8235 (mmtm) REVERT: B 150 TYR cc_start: 0.8354 (t80) cc_final: 0.8120 (t80) REVERT: B 248 ILE cc_start: 0.8685 (pp) cc_final: 0.8353 (pp) REVERT: E 66 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7583 (tm-30) REVERT: E 411 VAL cc_start: 0.8733 (p) cc_final: 0.8451 (m) REVERT: F 247 LYS cc_start: 0.8974 (mttt) cc_final: 0.8708 (ttmm) REVERT: F 436 GLU cc_start: 0.9128 (mp0) cc_final: 0.8725 (mp0) REVERT: I 87 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8924 (tm-30) REVERT: I 122 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8800 (mmmt) REVERT: I 133 LYS cc_start: 0.8256 (tptm) cc_final: 0.7872 (tppt) REVERT: I 160 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.6818 (p-80) REVERT: I 219 TRP cc_start: 0.8844 (t60) cc_final: 0.8313 (t60) REVERT: I 221 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: I 268 LEU cc_start: 0.9550 (mm) cc_final: 0.9230 (mm) REVERT: I 277 MET cc_start: 0.8901 (tpp) cc_final: 0.8657 (tpp) REVERT: I 295 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: I 318 HIS cc_start: 0.7533 (m90) cc_final: 0.7200 (m-70) REVERT: I 328 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8739 (mmmt) REVERT: J 233 ASP cc_start: 0.8466 (t0) cc_final: 0.8056 (m-30) REVERT: J 327 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: J 497 LYS cc_start: 0.8523 (tppt) cc_final: 0.8309 (ttpp) REVERT: M 23 LEU cc_start: 0.8902 (mm) cc_final: 0.8591 (mm) REVERT: M 156 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6713 (mt0) REVERT: M 193 LEU cc_start: 0.8347 (mt) cc_final: 0.8040 (tt) REVERT: M 223 PHE cc_start: 0.8665 (m-80) cc_final: 0.7957 (m-80) REVERT: M 227 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8601 (tt) REVERT: M 245 GLU cc_start: 0.9133 (tt0) cc_final: 0.8825 (tp30) REVERT: M 267 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: M 271 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9090 (mmtt) REVERT: M 287 MET cc_start: 0.8422 (mmm) cc_final: 0.8123 (mmm) REVERT: M 305 PHE cc_start: 0.7675 (t80) cc_final: 0.7397 (t80) REVERT: M 315 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6335 (pttm) REVERT: M 380 PHE cc_start: 0.8416 (t80) cc_final: 0.8147 (t80) REVERT: M 394 GLU cc_start: 0.7672 (mt-10) cc_final: 0.6556 (pp20) REVERT: M 413 LYS cc_start: 0.8059 (mttt) cc_final: 0.7538 (pttm) REVERT: N 348 GLU cc_start: 0.8338 (pp20) cc_final: 0.8009 (tm-30) REVERT: N 391 THR cc_start: 0.8741 (p) cc_final: 0.8522 (m) outliers start: 67 outliers final: 53 residues processed: 390 average time/residue: 0.1922 time to fit residues: 123.8861 Evaluate side-chains 388 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain I residue 221 TYR Chi-restraints excluded: chain I residue 225 HIS Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 327 GLU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 225 HIS Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 267 optimal weight: 10.0000 chunk 330 optimal weight: 0.0040 chunk 170 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 277 optimal weight: 0.9990 chunk 327 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 338 optimal weight: 0.0870 overall best weight: 0.6332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 225 HIS ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.118052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086442 restraints weight = 77182.048| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.49 r_work: 0.3419 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32838 Z= 0.121 Angle : 0.579 14.291 45085 Z= 0.298 Chirality : 0.042 0.329 4900 Planarity : 0.004 0.052 5160 Dihedral : 15.790 154.215 5849 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.80 % Allowed : 18.11 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3435 helix: 1.09 (0.15), residues: 1224 sheet: -1.16 (0.21), residues: 666 loop : -0.72 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 232 TYR 0.019 0.001 TYR B 48 PHE 0.032 0.001 PHE A 17 TRP 0.045 0.001 TRP I 294 HIS 0.005 0.001 HIS I 225 Details of bonding type rmsd covalent geometry : bond 0.00278 (32838) covalent geometry : angle 0.57853 (45085) hydrogen bonds : bond 0.03945 ( 1261) hydrogen bonds : angle 5.06068 ( 3466) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 362 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8988 (mt) cc_final: 0.8719 (mt) REVERT: A 46 TRP cc_start: 0.7990 (t60) cc_final: 0.7591 (t60) REVERT: A 119 ASP cc_start: 0.8273 (t0) cc_final: 0.7938 (t0) REVERT: A 203 LEU cc_start: 0.8237 (mp) cc_final: 0.7744 (tp) REVERT: A 277 MET cc_start: 0.8994 (mmm) cc_final: 0.8676 (mmm) REVERT: A 291 MET cc_start: 0.8545 (tpt) cc_final: 0.8265 (tpt) REVERT: A 328 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7991 (mppt) REVERT: A 336 MET cc_start: 0.7472 (mtt) cc_final: 0.7073 (mtt) REVERT: B 103 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8245 (mmtm) REVERT: B 248 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (pp) REVERT: E 66 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 224 MET cc_start: 0.7909 (mmm) cc_final: 0.7679 (mmm) REVERT: E 402 TYR cc_start: 0.8188 (m-80) cc_final: 0.7624 (m-80) REVERT: E 411 VAL cc_start: 0.8739 (p) cc_final: 0.8478 (m) REVERT: F 247 LYS cc_start: 0.8960 (mttt) cc_final: 0.8694 (ttmm) REVERT: F 303 MET cc_start: 0.8646 (tmm) cc_final: 0.8115 (ttm) REVERT: F 436 GLU cc_start: 0.9122 (mp0) cc_final: 0.8712 (mp0) REVERT: I 87 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8963 (tm-30) REVERT: I 122 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8779 (mmmt) REVERT: I 133 LYS cc_start: 0.8228 (tptm) cc_final: 0.7931 (tppt) REVERT: I 153 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6938 (mm) REVERT: I 160 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6838 (p-80) REVERT: I 219 TRP cc_start: 0.8883 (t60) cc_final: 0.8420 (t60) REVERT: I 221 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: I 268 LEU cc_start: 0.9532 (mm) cc_final: 0.9229 (mm) REVERT: I 277 MET cc_start: 0.8873 (tpp) cc_final: 0.8597 (tpp) REVERT: I 295 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: I 318 HIS cc_start: 0.7559 (m90) cc_final: 0.7334 (m-70) REVERT: I 328 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8682 (mmmt) REVERT: J 150 TYR cc_start: 0.8794 (m-10) cc_final: 0.8579 (m-10) REVERT: J 497 LYS cc_start: 0.8510 (tppt) cc_final: 0.8291 (ttpp) REVERT: M 156 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6693 (mt0) REVERT: M 193 LEU cc_start: 0.8391 (mt) cc_final: 0.8106 (tt) REVERT: M 223 PHE cc_start: 0.8659 (m-80) cc_final: 0.7952 (m-80) REVERT: M 227 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8622 (tt) REVERT: M 245 GLU cc_start: 0.9068 (tt0) cc_final: 0.8718 (tp30) REVERT: M 287 MET cc_start: 0.8419 (mmm) cc_final: 0.8082 (mmm) REVERT: M 305 PHE cc_start: 0.7702 (t80) cc_final: 0.7451 (t80) REVERT: M 380 PHE cc_start: 0.8382 (t80) cc_final: 0.8115 (t80) REVERT: M 394 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6577 (pp20) REVERT: M 413 LYS cc_start: 0.8067 (mttt) cc_final: 0.7532 (pttm) REVERT: N 348 GLU cc_start: 0.8292 (pp20) cc_final: 0.7940 (tm-30) REVERT: N 391 THR cc_start: 0.8712 (p) cc_final: 0.8509 (m) outliers start: 55 outliers final: 39 residues processed: 398 average time/residue: 0.2030 time to fit residues: 132.1837 Evaluate side-chains 379 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain I residue 221 TYR Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 339 SER Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 332 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 325 optimal weight: 0.7980 chunk 266 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN E 15 ASN E 225 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.118251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.086784 restraints weight = 77445.337| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.48 r_work: 0.3425 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32838 Z= 0.124 Angle : 0.586 13.413 45085 Z= 0.303 Chirality : 0.042 0.337 4900 Planarity : 0.004 0.079 5160 Dihedral : 15.750 154.196 5849 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.70 % Allowed : 18.44 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3435 helix: 1.10 (0.15), residues: 1229 sheet: -1.11 (0.21), residues: 634 loop : -0.72 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 232 TYR 0.023 0.001 TYR N 48 PHE 0.040 0.001 PHE A 17 TRP 0.044 0.001 TRP I 294 HIS 0.010 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00285 (32838) covalent geometry : angle 0.58585 (45085) hydrogen bonds : bond 0.03953 ( 1261) hydrogen bonds : angle 5.03136 ( 3466) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8970 (mt) cc_final: 0.8698 (mt) REVERT: A 46 TRP cc_start: 0.7996 (t60) cc_final: 0.7594 (t60) REVERT: A 119 ASP cc_start: 0.8284 (t0) cc_final: 0.7987 (t0) REVERT: A 155 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: A 203 LEU cc_start: 0.8292 (mp) cc_final: 0.7824 (tp) REVERT: A 260 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8279 (pt0) REVERT: A 277 MET cc_start: 0.8980 (mmm) cc_final: 0.8670 (mmm) REVERT: A 291 MET cc_start: 0.8527 (tpt) cc_final: 0.8243 (tpt) REVERT: A 328 LYS cc_start: 0.8552 (mmmt) cc_final: 0.7986 (mppt) REVERT: A 336 MET cc_start: 0.7469 (mtt) cc_final: 0.7078 (mtt) REVERT: B 248 ILE cc_start: 0.8591 (pp) cc_final: 0.8254 (pp) REVERT: E 66 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7540 (tm-30) REVERT: E 224 MET cc_start: 0.7823 (mmm) cc_final: 0.7593 (mmm) REVERT: E 324 SER cc_start: 0.8494 (m) cc_final: 0.8014 (p) REVERT: E 411 VAL cc_start: 0.8757 (p) cc_final: 0.8488 (m) REVERT: F 247 LYS cc_start: 0.8959 (mttt) cc_final: 0.8696 (ttmm) REVERT: F 303 MET cc_start: 0.8635 (tmm) cc_final: 0.8195 (ttm) REVERT: F 436 GLU cc_start: 0.9128 (mp0) cc_final: 0.8742 (mp0) REVERT: I 87 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8968 (tm-30) REVERT: I 122 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8750 (mmmt) REVERT: I 133 LYS cc_start: 0.8222 (tptm) cc_final: 0.7926 (tppt) REVERT: I 153 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6761 (mm) REVERT: I 160 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.6831 (p-80) REVERT: I 219 TRP cc_start: 0.8890 (t60) cc_final: 0.8491 (t60) REVERT: I 221 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: I 268 LEU cc_start: 0.9527 (mm) cc_final: 0.9234 (mm) REVERT: I 277 MET cc_start: 0.8877 (tpp) cc_final: 0.8591 (tpp) REVERT: I 295 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: I 318 HIS cc_start: 0.7561 (m90) cc_final: 0.7331 (m-70) REVERT: I 328 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8718 (mmmt) REVERT: J 232 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8196 (mpt-90) REVERT: J 497 LYS cc_start: 0.8523 (tppt) cc_final: 0.8296 (ttpp) REVERT: M 156 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6671 (mt0) REVERT: M 193 LEU cc_start: 0.8352 (mt) cc_final: 0.8114 (tt) REVERT: M 223 PHE cc_start: 0.8646 (m-80) cc_final: 0.7944 (m-80) REVERT: M 227 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8583 (tt) REVERT: M 305 PHE cc_start: 0.7731 (t80) cc_final: 0.7495 (t80) REVERT: M 380 PHE cc_start: 0.8397 (t80) cc_final: 0.8191 (t80) REVERT: M 394 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6606 (pp20) REVERT: M 413 LYS cc_start: 0.8064 (mttt) cc_final: 0.7525 (pttm) REVERT: N 348 GLU cc_start: 0.8289 (pp20) cc_final: 0.7925 (tm-30) REVERT: N 391 THR cc_start: 0.8720 (p) cc_final: 0.8516 (m) outliers start: 52 outliers final: 38 residues processed: 390 average time/residue: 0.1966 time to fit residues: 126.8775 Evaluate side-chains 385 residues out of total 3059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 160 HIS Chi-restraints excluded: chain I residue 161 ASN Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain I residue 221 TYR Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 356 GLU Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 405 ILE Chi-restraints excluded: chain N residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 24 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 265 optimal weight: 0.0030 chunk 251 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN E 225 HIS E 267 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.113511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.081403 restraints weight = 78784.468| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.47 r_work: 0.3324 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 32838 Z= 0.278 Angle : 0.696 14.790 45085 Z= 0.360 Chirality : 0.046 0.318 4900 Planarity : 0.005 0.074 5160 Dihedral : 16.063 155.528 5849 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.03 % Allowed : 18.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3435 helix: 0.80 (0.15), residues: 1203 sheet: -1.47 (0.20), residues: 677 loop : -0.80 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 283 TYR 0.023 0.002 TYR N 48 PHE 0.047 0.002 PHE A 17 TRP 0.061 0.002 TRP I 294 HIS 0.010 0.002 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00639 (32838) covalent geometry : angle 0.69577 (45085) hydrogen bonds : bond 0.04602 ( 1261) hydrogen bonds : angle 5.41958 ( 3466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9772.54 seconds wall clock time: 168 minutes 11.71 seconds (10091.71 seconds total)