Starting phenix.real_space_refine on Mon Aug 25 21:28:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i87_35240/08_2025/8i87_35240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i87_35240/08_2025/8i87_35240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2025/8i87_35240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2025/8i87_35240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2025/8i87_35240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2025/8i87_35240.map" } resolution = 3.1 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= 0.003 sd= 0.051 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 143 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 19624 2.51 5 N 5205 2.21 5 O 6006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31066 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3264 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3758 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3306 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "D" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3782 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3762 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3203 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 394} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "O" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3292 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "T" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3782 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 362 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "I" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 343 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 324 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "S" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "U" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 324 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 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: "D" 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: "H" 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: 7.86, per 1000 atoms: 0.25 Number of scatterers: 31066 At special positions: 0 Unit cell: (121.6, 166.25, 214.7, 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 84 16.00 P 143 15.00 Mg 4 11.99 O 6006 8.00 N 5205 7.00 C 19624 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6710 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 33 sheets defined 38.4% alpha, 19.4% beta 53 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.540A pdb=" N ARG A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.936A pdb=" N THR A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 296 through 300 removed outlier: 4.093A pdb=" N LEU A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 368 through 385 removed outlier: 3.879A pdb=" N THR A 372 " --> pdb=" O TRP A 368 " (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 28 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.831A pdb=" N GLN B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.868A pdb=" N GLY B 90 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.944A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 4.119A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 226 through 230 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 375 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.558A pdb=" N ILE B 489 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.748A pdb=" N TYR B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 removed outlier: 3.560A pdb=" N TRP C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.769A pdb=" N ASN C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 4.667A pdb=" N GLN C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.251A pdb=" N SER C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.843A pdb=" N ARG C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.664A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.890A pdb=" N THR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 257 through 280 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 353 through 365 removed outlier: 3.776A pdb=" N GLN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 removed outlier: 3.986A pdb=" N THR C 372 " --> pdb=" O TRP C 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 22 through 30 Processing helix chain 'D' and resid 46 through 62 removed outlier: 3.812A pdb=" N GLN D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.656A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.745A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 331 through 351 Processing helix chain 'D' and resid 366 through 375 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 477 through 491 removed outlier: 3.676A pdb=" N ILE D 489 " --> pdb=" O LYS D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.788A pdb=" N TYR D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) 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 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.599A pdb=" N GLN F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 97 through 106 removed outlier: 3.971A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR F 106 " --> pdb=" O GLY F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 131 removed outlier: 3.742A pdb=" N THR F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'F' and resid 215 through 218 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 231 through 234 Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 350 Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.711A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 477 through 491 Processing helix chain 'G' and resid 14 through 28 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 71 through 89 Processing helix chain 'G' and resid 109 through 114 removed outlier: 4.293A pdb=" N ARG G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'G' and resid 148 through 160 Processing helix chain 'G' and resid 192 through 198 Processing helix chain 'G' and resid 242 through 248 removed outlier: 3.673A pdb=" N SER G 248 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 279 removed outlier: 3.726A pdb=" N MET G 277 " --> pdb=" O PHE G 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 279 " --> pdb=" O LEU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 300 removed outlier: 4.067A pdb=" N LEU G 300 " --> pdb=" O LYS G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 365 Processing helix chain 'G' and resid 368 through 384 removed outlier: 3.792A pdb=" N THR G 372 " --> pdb=" O TRP G 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 28 Processing helix chain 'O' and resid 45 through 56 Processing helix chain 'O' and resid 71 through 89 Processing helix chain 'O' and resid 109 through 113 Processing helix chain 'O' and resid 123 through 138 Processing helix chain 'O' and resid 146 through 159 removed outlier: 4.187A pdb=" N SER O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU O 159 " --> pdb=" O GLN O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 197 removed outlier: 3.979A pdb=" N ARG O 197 " --> pdb=" O MET O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 219 through 225 removed outlier: 4.134A pdb=" N TYR O 225 " --> pdb=" O ASP O 222 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 232 Processing helix chain 'O' and resid 242 through 247 Processing helix chain 'O' and resid 257 through 280 Processing helix chain 'O' and resid 304 through 308 Processing helix chain 'O' and resid 353 through 365 Processing helix chain 'O' and resid 368 through 385 removed outlier: 3.985A pdb=" N THR O 372 " --> pdb=" O TRP O 368 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 17 No H-bonds generated for 'chain 'T' and resid 15 through 17' Processing helix chain 'T' and resid 22 through 30 Processing helix chain 'T' and resid 46 through 60 Processing helix chain 'T' and resid 77 through 83 Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.763A pdb=" N GLY T 90 " --> pdb=" O GLU T 87 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE T 91 " --> pdb=" O SER T 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 87 through 91' Processing helix chain 'T' and resid 97 through 106 removed outlier: 3.626A pdb=" N PHE T 104 " --> pdb=" O ASP T 100 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR T 106 " --> pdb=" O GLY T 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 131 removed outlier: 3.690A pdb=" N LYS T 124 " --> pdb=" O LEU T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 151 Processing helix chain 'T' and resid 205 through 214 Processing helix chain 'T' and resid 215 through 218 Processing helix chain 'T' and resid 226 through 230 Processing helix chain 'T' and resid 248 through 264 Processing helix chain 'T' and resid 331 through 351 Processing helix chain 'T' and resid 366 through 375 Processing helix chain 'T' and resid 451 through 463 Processing helix chain 'T' and resid 477 through 491 removed outlier: 3.692A pdb=" N ILE T 489 " --> pdb=" O LYS T 485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.800A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 311 through 322 removed outlier: 6.303A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TRP B 320 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASN B 296 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE B 419 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLU B 3 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.811A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.811A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.512A pdb=" N ILE A 241 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 187 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE A 239 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.466A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 34 removed outlier: 5.977A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LYS C 4 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 60 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE C 6 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU C 62 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER C 8 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER C 64 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'C' and resid 178 through 180 removed outlier: 3.650A pdb=" N LEU C 179 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 207 through 209 Processing sheet with id=AB3, first strand: chain 'C' and resid 283 through 286 removed outlier: 6.809A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 283 through 286 removed outlier: 6.809A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 6 removed outlier: 5.053A pdb=" N VAL D 412 " --> pdb=" O PHE D 419 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE D 419 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY D 385 " --> pdb=" O ASN D 446 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL D 357 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL D 386 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE D 359 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 388 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ALA D 361 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D 278 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU D 305 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D 295 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN D 296 " --> pdb=" O TRP D 320 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TRP D 320 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS D 298 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY D 318 " --> pdb=" O CYS D 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.689A pdb=" N GLY D 45 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP D 139 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE D 224 " --> pdb=" O TRP D 139 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL D 141 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 425 through 426 removed outlier: 3.543A pdb=" N THR D 431 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 311 through 322 removed outlier: 6.069A pdb=" N GLY F 318 " --> pdb=" O CYS F 298 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS F 298 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TRP F 320 " --> pdb=" O ASN F 296 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN F 296 " --> pdb=" O TRP F 320 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL F 357 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL F 386 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE F 359 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE F 388 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ALA F 361 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY F 385 " --> pdb=" O ASN F 446 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER F 417 " --> pdb=" O VAL F 413 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL F 412 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU F 3 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS F 2 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.905A pdb=" N SER F 41 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 425 through 426 removed outlier: 4.172A pdb=" N VAL F 426 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.151A pdb=" N ILE G 5 " --> pdb=" O TRP G 33 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS G 4 " --> pdb=" O CYS G 58 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE G 60 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE G 6 " --> pdb=" O PHE G 60 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU G 62 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER G 8 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER G 64 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ILE G 95 " --> pdb=" O CYS G 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE G 60 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU G 97 " --> pdb=" O PHE G 60 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G 62 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.656A pdb=" N THR G 291 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY G 325 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.656A pdb=" N THR G 291 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY G 325 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER G 177 " --> pdb=" O SER G 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 404 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE G 402 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 186 through 188 removed outlier: 3.536A pdb=" N VAL G 208 " --> pdb=" O CYS G 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 31 through 33 removed outlier: 5.948A pdb=" N ILE O 5 " --> pdb=" O TRP O 33 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS O 4 " --> pdb=" O LYS O 59 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU O 61 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE O 6 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL O 63 " --> pdb=" O PHE O 6 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER O 8 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE O 95 " --> pdb=" O CYS O 58 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE O 60 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU O 97 " --> pdb=" O PHE O 60 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU O 62 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 311 through 322 removed outlier: 6.102A pdb=" N GLY T 318 " --> pdb=" O CYS T 298 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS T 298 " --> pdb=" O GLY T 318 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TRP T 320 " --> pdb=" O ASN T 296 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN T 296 " --> pdb=" O TRP T 320 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG T 295 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA T 301 " --> pdb=" O GLY T 282 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU T 305 " --> pdb=" O VAL T 278 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL T 278 " --> pdb=" O LEU T 305 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS T 279 " --> pdb=" O PHE T 358 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N HIS T 360 " --> pdb=" O CYS T 279 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU T 281 " --> pdb=" O HIS T 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL T 357 " --> pdb=" O VAL T 384 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL T 386 " --> pdb=" O VAL T 357 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE T 359 " --> pdb=" O VAL T 386 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE T 388 " --> pdb=" O ILE T 359 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA T 361 " --> pdb=" O ILE T 388 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY T 385 " --> pdb=" O ASN T 446 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER T 417 " --> pdb=" O ASN T 414 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE T 419 " --> pdb=" O VAL T 412 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL T 412 " --> pdb=" O PHE T 419 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL T 412 " --> pdb=" O GLU T 3 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU T 3 " --> pdb=" O VAL T 412 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS T 2 " --> pdb=" O LYS O 409 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN O 413 " --> pdb=" O LEU T 4 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR T 6 " --> pdb=" O ASN O 413 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N SER O 415 " --> pdb=" O TYR T 6 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS O 167 " --> pdb=" O VAL O 414 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 283 through 286 removed outlier: 6.570A pdb=" N THR O 291 " --> pdb=" O GLY O 325 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY O 325 " --> pdb=" O THR O 291 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 283 through 286 removed outlier: 6.570A pdb=" N THR O 291 " --> pdb=" O GLY O 325 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY O 325 " --> pdb=" O THR O 291 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER O 180 " --> pdb=" O PHE O 402 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE O 402 " --> pdb=" O SER O 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 208 through 209 Processing sheet with id=AD4, first strand: chain 'T' and resid 19 through 20 Processing sheet with id=AD5, first strand: chain 'T' and resid 92 through 95 removed outlier: 7.076A pdb=" N SER T 41 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS T 94 " --> pdb=" O SER T 41 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL T 43 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY T 42 " --> pdb=" O PHE T 140 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE T 142 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE T 44 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TRP T 139 " --> pdb=" O GLN T 222 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE T 224 " --> pdb=" O TRP T 139 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL T 141 " --> pdb=" O PHE T 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'T' and resid 425 through 426 removed outlier: 3.516A pdb=" N THR T 431 " --> pdb=" O VAL T 426 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9074 1.34 - 1.46: 6771 1.46 - 1.58: 15847 1.58 - 1.70: 278 1.70 - 1.82: 125 Bond restraints: 32095 Sorted by residual: bond pdb=" CB PRO O 242 " pdb=" CG PRO O 242 " ideal model delta sigma weight residual 1.492 1.724 -0.232 5.00e-02 4.00e+02 2.16e+01 bond pdb=" CG PRO O 242 " pdb=" CD PRO O 242 " ideal model delta sigma weight residual 1.503 1.361 0.142 3.40e-02 8.65e+02 1.74e+01 bond pdb=" N PRO O 242 " pdb=" CD PRO O 242 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CA LEU A 194 " pdb=" CB LEU A 194 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.62e+00 bond pdb=" C ILE O 241 " pdb=" O ILE O 241 " ideal model delta sigma weight residual 1.240 1.225 0.015 1.26e-02 6.30e+03 1.35e+00 ... (remaining 32090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 43972 3.47 - 6.93: 87 6.93 - 10.40: 10 10.40 - 13.87: 2 13.87 - 17.34: 1 Bond angle restraints: 44072 Sorted by residual: angle pdb=" CA PRO O 242 " pdb=" N PRO O 242 " pdb=" CD PRO O 242 " ideal model delta sigma weight residual 112.00 94.66 17.34 1.40e+00 5.10e-01 1.53e+02 angle pdb=" N PRO A 195 " pdb=" CA PRO A 195 " pdb=" CB PRO A 195 " ideal model delta sigma weight residual 103.25 111.72 -8.47 1.05e+00 9.07e-01 6.50e+01 angle pdb=" N PRO C 195 " pdb=" CA PRO C 195 " pdb=" CB PRO C 195 " ideal model delta sigma weight residual 103.25 111.63 -8.38 1.05e+00 9.07e-01 6.37e+01 angle pdb=" N PRO O 195 " pdb=" CA PRO O 195 " pdb=" CB PRO O 195 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.26e+01 angle pdb=" N PRO G 195 " pdb=" CA PRO G 195 " pdb=" CB PRO G 195 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 ... (remaining 44067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.16: 17252 28.16 - 56.32: 1598 56.32 - 84.48: 218 84.48 - 112.64: 6 112.64 - 140.79: 4 Dihedral angle restraints: 19078 sinusoidal: 8713 harmonic: 10365 Sorted by residual: dihedral pdb=" CA MET G 277 " pdb=" C MET G 277 " pdb=" N LYS G 278 " pdb=" CA LYS G 278 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" N PRO A 195 " pdb=" C PRO A 195 " pdb=" CA PRO A 195 " pdb=" CB PRO A 195 " ideal model delta harmonic sigma weight residual 115.10 125.38 -10.28 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" N PRO O 195 " pdb=" C PRO O 195 " pdb=" CA PRO O 195 " pdb=" CB PRO O 195 " ideal model delta harmonic sigma weight residual 115.10 125.12 -10.02 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 19075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4609 0.080 - 0.160: 308 0.160 - 0.240: 1 0.240 - 0.321: 5 0.321 - 0.401: 2 Chirality restraints: 4925 Sorted by residual: chirality pdb=" CB ILE B 147 " pdb=" CA ILE B 147 " pdb=" CG1 ILE B 147 " pdb=" CG2 ILE B 147 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CG LEU G 269 " pdb=" CB LEU G 269 " pdb=" CD1 LEU G 269 " pdb=" CD2 LEU G 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA PRO A 195 " pdb=" N PRO A 195 " pdb=" C PRO A 195 " pdb=" CB PRO A 195 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4922 not shown) Planarity restraints: 5044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE O 241 " -0.094 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO O 242 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO O 242 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO O 242 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 319 " -0.015 2.00e-02 2.50e+03 1.67e-02 7.00e+00 pdb=" CG TRP C 319 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 319 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 319 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 319 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 319 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 319 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 319 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 319 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 319 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 83 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ASP T 83 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP T 83 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS T 84 " 0.011 2.00e-02 2.50e+03 ... (remaining 5041 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 315 2.60 - 3.17: 24261 3.17 - 3.75: 48708 3.75 - 4.32: 69220 4.32 - 4.90: 114312 Nonbonded interactions: 256816 Sorted by model distance: nonbonded pdb=" OD1 ASN F 468 " pdb="MG MG F 601 " model vdw 2.023 2.170 nonbonded pdb=" OD1 ASN B 468 " pdb="MG MG B 601 " model vdw 2.077 2.170 nonbonded pdb=" OP1 U H 1 " pdb="MG MG H 101 " model vdw 2.088 2.170 nonbonded pdb=" OG SER A 173 " pdb=" O VAL A 408 " model vdw 2.170 3.040 nonbonded pdb=" O ASP O 14 " pdb=" OG1 THR O 18 " model vdw 2.176 3.040 ... (remaining 256811 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 3 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 42 or (resid 43 through 45 and (nam \ e N or name CA or name C or name O or name CB )) or resid 46 through 227 or resi \ d 235 through 418)) selection = (chain 'C' and (resid 3 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 42 or (resid 43 through 45 and (nam \ e N or name CA or name C or name O or name CB )) or resid 46 through 88 or (resi \ d 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throug \ h 100 or (resid 101 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 105 or (resid 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 125 or (resid 126 and (name N or n \ ame CA or name C or name O or name CB )) or resid 127 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 13 \ 8 or (resid 139 and (name N or name CA or name C or name O or name CB )) or resi \ d 140 through 142 or (resid 143 and (name N or name CA or name C or name O or na \ me CB )) or resid 144 through 145 or resid 148 through 160 or (resid 161 and (na \ me N or name CA or name C or name O or name CB )) or resid 162 through 227 or re \ sid 235 through 236 or (resid 237 and (name N or name CA or name C or name O or \ name CB )) or resid 238 through 418)) selection = (chain 'G' and (resid 3 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 42 or (resid 43 through 45 and (nam \ e N or name CA or name C or name O or name CB )) or resid 46 through 418)) selection = (chain 'O' and (resid 3 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB )) or resid 90 through 100 or (resid 101 through 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ through 125 or (resid 126 and (name N or name CA or name C or name O or name CB \ )) or resid 127 through 135 or (resid 136 and (name N or name CA or name C or n \ ame O or name CB )) or resid 137 through 138 or (resid 139 and (name N or name C \ A or name C or name O or name CB )) or resid 140 through 142 or (resid 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 145 or \ resid 148 through 160 or (resid 161 and (name N or name CA or name C or name O o \ r name CB )) or resid 162 through 227 or resid 235 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB )) or resid 238 through 418)) \ } ncs_group { reference = (chain 'B' and (resid 1 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 507)) selection = (chain 'D' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 160 or resid 201 through 237 or \ (resid 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 434 or (resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 436 through 507)) selection = (chain 'F' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 289 or (resid 290 and (name N or \ name CA or name C or name O or name CB )) or resid 291 through 507)) selection = (chain 'T' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 160 or resid 201 through 237 or \ (resid 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 434 or (resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 436 through 507)) } ncs_group { reference = (chain 'E' and resid 2 through 17) selection = (chain 'J' and resid 2 through 17) selection = (chain 'K' and resid 2 through 17) selection = (chain 'U' and resid 2 through 17) } ncs_group { reference = (chain 'H' and resid 1 through 18) selection = chain 'I' selection = chain 'L' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 33.490 Find NCS groups from input model: 0.860 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.232 32095 Z= 0.117 Angle : 0.526 17.335 44072 Z= 0.289 Chirality : 0.041 0.401 4925 Planarity : 0.004 0.128 5044 Dihedral : 19.601 140.794 12368 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.99 % Favored : 95.72 % Rotamer: Outliers : 4.16 % Allowed : 28.88 % Favored : 66.96 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.14), residues: 3481 helix: 1.60 (0.16), residues: 1198 sheet: -0.32 (0.20), residues: 698 loop : -1.41 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 152 TYR 0.017 0.001 TYR F 411 PHE 0.015 0.001 PHE T 304 TRP 0.046 0.001 TRP C 319 HIS 0.003 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00286 (32095) covalent geometry : angle 0.52577 (44072) hydrogen bonds : bond 0.12813 ( 1295) hydrogen bonds : angle 5.90525 ( 3585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 219 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.6689 (mptt) cc_final: 0.6043 (ptpt) REVERT: C 186 ARG cc_start: 0.5486 (mpt-90) cc_final: 0.4735 (mtt180) REVERT: C 274 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6625 (pt0) REVERT: C 415 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8239 (m) REVERT: D 371 ASP cc_start: 0.7855 (m-30) cc_final: 0.7507 (m-30) REVERT: F 132 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: G 332 PHE cc_start: 0.5542 (p90) cc_final: 0.5185 (p90) REVERT: O 299 LYS cc_start: 0.6163 (mmpt) cc_final: 0.5438 (mtmt) outliers start: 124 outliers final: 113 residues processed: 336 average time/residue: 0.1869 time to fit residues: 104.2293 Evaluate side-chains 317 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 202 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 354 SER Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 408 VAL Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain T residue 233 ASP Chi-restraints excluded: chain T residue 246 SER Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 348 GLU Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain T residue 437 VAL Chi-restraints excluded: chain T residue 478 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 370 ASN C 234 HIS C 320 HIS F 68 ASN F 329 HIS G 283 GLN O 226 HIS ** T 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110525 restraints weight = 41660.256| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.76 r_work: 0.2941 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 32095 Z= 0.346 Angle : 0.651 8.355 44072 Z= 0.338 Chirality : 0.047 0.280 4925 Planarity : 0.005 0.054 5044 Dihedral : 16.662 145.019 5848 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.63 % Favored : 94.00 % Rotamer: Outliers : 5.74 % Allowed : 25.86 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3481 helix: 1.15 (0.15), residues: 1223 sheet: -0.49 (0.20), residues: 698 loop : -1.63 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 54 TYR 0.017 0.002 TYR A 154 PHE 0.020 0.002 PHE A 45 TRP 0.020 0.002 TRP C 319 HIS 0.008 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00852 (32095) covalent geometry : angle 0.65056 (44072) hydrogen bonds : bond 0.05312 ( 1295) hydrogen bonds : angle 5.02844 ( 3585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 205 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7335 (p0) REVERT: A 278 LYS cc_start: 0.6961 (mptt) cc_final: 0.6210 (ptpt) REVERT: A 286 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: B 145 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: B 281 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7939 (tt) REVERT: D 29 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8835 (mp) REVERT: F 295 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6643 (ttp-170) REVERT: F 327 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: F 396 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8352 (mp) REVERT: G 149 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6469 (tmmm) REVERT: G 309 MET cc_start: 0.6325 (mtp) cc_final: 0.5584 (tpt) REVERT: G 328 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8691 (mmtm) REVERT: T 149 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7709 (tppt) REVERT: T 205 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: T 222 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8199 (tp-100) outliers start: 171 outliers final: 111 residues processed: 354 average time/residue: 0.1689 time to fit residues: 98.0257 Evaluate side-chains 322 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 198 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 288 SER Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 328 LYS Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 144 VAL Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 313 LYS Chi-restraints excluded: chain O residue 337 ILE Chi-restraints excluded: chain O residue 356 VAL Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 408 VAL Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 98 ASN Chi-restraints excluded: chain T residue 149 LYS Chi-restraints excluded: chain T residue 205 GLN Chi-restraints excluded: chain T residue 222 GLN Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 389 SER Chi-restraints excluded: chain T residue 437 VAL Chi-restraints excluded: chain T residue 460 LEU Chi-restraints excluded: chain T residue 478 VAL Chi-restraints excluded: chain T residue 498 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 129 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 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 226 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN O 226 HIS O 364 GLN ** T 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115860 restraints weight = 41490.815| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.67 r_work: 0.3007 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32095 Z= 0.120 Angle : 0.499 10.120 44072 Z= 0.266 Chirality : 0.040 0.337 4925 Planarity : 0.003 0.054 5044 Dihedral : 16.226 141.737 5776 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.99 % Favored : 95.69 % Rotamer: Outliers : 4.47 % Allowed : 26.90 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3481 helix: 1.54 (0.15), residues: 1224 sheet: -0.29 (0.20), residues: 673 loop : -1.55 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 152 TYR 0.010 0.001 TYR A 233 PHE 0.014 0.001 PHE T 78 TRP 0.016 0.001 TRP C 319 HIS 0.005 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00274 (32095) covalent geometry : angle 0.49945 (44072) hydrogen bonds : bond 0.03732 ( 1295) hydrogen bonds : angle 4.65848 ( 3585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 219 time to evaluate : 1.089 Fit side-chains REVERT: A 16 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 278 LYS cc_start: 0.6775 (mptt) cc_final: 0.6278 (ptpt) REVERT: B 152 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6019 (mtp85) REVERT: C 274 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6660 (pt0) REVERT: C 395 MET cc_start: 0.5876 (mmp) cc_final: 0.4970 (mmm) REVERT: D 29 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8825 (mp) REVERT: D 222 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8178 (tp-100) REVERT: D 430 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: D 486 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8303 (mt) REVERT: F 132 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: F 396 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8402 (mp) REVERT: G 142 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8118 (ttmt) REVERT: G 283 GLN cc_start: 0.5601 (OUTLIER) cc_final: 0.5374 (pp30) REVERT: G 309 MET cc_start: 0.6215 (mtp) cc_final: 0.5460 (tpt) REVERT: O 287 MET cc_start: 0.8865 (mtp) cc_final: 0.8528 (mtp) REVERT: O 299 LYS cc_start: 0.6229 (mmpt) cc_final: 0.5698 (mtmt) REVERT: O 313 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6285 (tttt) REVERT: T 1 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6855 (ptp) REVERT: T 149 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8034 (tppt) REVERT: T 205 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: T 428 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7921 (ttpt) outliers start: 133 outliers final: 75 residues processed: 327 average time/residue: 0.1702 time to fit residues: 91.8267 Evaluate side-chains 290 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 200 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 288 SER Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 313 LYS Chi-restraints excluded: chain O residue 337 ILE Chi-restraints excluded: chain O residue 356 VAL Chi-restraints excluded: chain O residue 418 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 84 CYS Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 149 LYS Chi-restraints excluded: chain T residue 205 GLN Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 389 SER Chi-restraints excluded: chain T residue 428 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 204 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 322 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN F 68 ASN G 283 GLN O 226 HIS ** T 209 GLN ** 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 = 0.3899 r_free = 0.3899 target = 0.154483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115836 restraints weight = 41184.263| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.62 r_work: 0.3015 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32095 Z= 0.130 Angle : 0.492 11.119 44072 Z= 0.261 Chirality : 0.040 0.338 4925 Planarity : 0.003 0.054 5044 Dihedral : 16.081 141.153 5733 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.83 % Favored : 94.86 % Rotamer: Outliers : 4.77 % Allowed : 26.86 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3481 helix: 1.70 (0.15), residues: 1208 sheet: -0.31 (0.20), residues: 683 loop : -1.48 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 152 TYR 0.015 0.001 TYR A 210 PHE 0.012 0.001 PHE T 210 TRP 0.011 0.001 TRP C 319 HIS 0.005 0.001 HIS O 320 Details of bonding type rmsd covalent geometry : bond 0.00305 (32095) covalent geometry : angle 0.49195 (44072) hydrogen bonds : bond 0.03645 ( 1295) hydrogen bonds : angle 4.53272 ( 3585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 205 time to evaluate : 1.072 Fit side-chains REVERT: A 16 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7285 (p0) REVERT: A 336 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.6537 (mpt) REVERT: B 72 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6874 (mpp80) REVERT: B 152 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6130 (mtp85) REVERT: B 233 ASP cc_start: 0.8328 (m-30) cc_final: 0.8070 (m-30) REVERT: B 281 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7596 (tt) REVERT: B 383 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8310 (mp) REVERT: C 186 ARG cc_start: 0.5422 (mpt-90) cc_final: 0.4678 (mtt180) REVERT: C 274 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6588 (pt0) REVERT: C 415 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8533 (m) REVERT: D 29 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8791 (mp) REVERT: D 430 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: F 132 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: F 396 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8418 (mp) REVERT: G 142 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8094 (ttmt) REVERT: G 149 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6468 (tmmm) REVERT: G 158 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: G 309 MET cc_start: 0.6172 (mtp) cc_final: 0.5474 (tpt) REVERT: O 287 MET cc_start: 0.8894 (mtp) cc_final: 0.8586 (mtp) REVERT: O 299 LYS cc_start: 0.6167 (mmpt) cc_final: 0.5768 (mtmt) REVERT: O 310 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7301 (mp) REVERT: O 313 LYS cc_start: 0.6587 (OUTLIER) cc_final: 0.6289 (tttt) REVERT: T 1 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6768 (ptp) REVERT: T 149 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8124 (tppt) REVERT: T 205 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: T 222 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8221 (tp-100) REVERT: T 229 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8955 (mt) REVERT: T 283 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8880 (mp) REVERT: T 428 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7962 (ttpt) outliers start: 142 outliers final: 87 residues processed: 323 average time/residue: 0.1675 time to fit residues: 88.7600 Evaluate side-chains 302 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 192 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 288 SER Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 144 VAL Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 313 LYS Chi-restraints excluded: chain O residue 337 ILE Chi-restraints excluded: chain O residue 356 VAL Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 408 VAL Chi-restraints excluded: chain O residue 418 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 84 CYS Chi-restraints excluded: chain T residue 98 ASN Chi-restraints excluded: chain T residue 149 LYS Chi-restraints excluded: chain T residue 205 GLN Chi-restraints excluded: chain T residue 222 GLN Chi-restraints excluded: chain T residue 229 LEU Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 389 SER Chi-restraints excluded: chain T residue 428 LYS Chi-restraints excluded: chain T residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 300 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 143 optimal weight: 0.0060 chunk 253 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN F 68 ASN G 138 GLN G 283 GLN O 160 HIS O 364 GLN T 209 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116420 restraints weight = 41452.939| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.68 r_work: 0.3013 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32095 Z= 0.126 Angle : 0.489 11.692 44072 Z= 0.258 Chirality : 0.040 0.353 4925 Planarity : 0.003 0.057 5044 Dihedral : 15.941 140.888 5718 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.32 % Rotamer: Outliers : 5.00 % Allowed : 26.23 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3481 helix: 1.75 (0.15), residues: 1208 sheet: -0.25 (0.20), residues: 683 loop : -1.46 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 152 TYR 0.010 0.001 TYR F 56 PHE 0.012 0.001 PHE T 210 TRP 0.021 0.001 TRP A 319 HIS 0.004 0.001 HIS O 320 Details of bonding type rmsd covalent geometry : bond 0.00296 (32095) covalent geometry : angle 0.48924 (44072) hydrogen bonds : bond 0.03539 ( 1295) hydrogen bonds : angle 4.46892 ( 3585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 212 time to evaluate : 1.023 Fit side-chains REVERT: A 16 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7271 (p0) REVERT: A 336 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.6496 (mpt) REVERT: B 152 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6023 (mtp85) REVERT: B 233 ASP cc_start: 0.8316 (m-30) cc_final: 0.8066 (m-30) REVERT: B 281 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7594 (tt) REVERT: B 383 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 186 ARG cc_start: 0.5443 (mpt-90) cc_final: 0.4715 (mtt180) REVERT: C 274 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6573 (pt0) REVERT: C 395 MET cc_start: 0.5586 (mmp) cc_final: 0.5136 (mmm) REVERT: C 415 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8528 (m) REVERT: D 29 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8782 (mp) REVERT: D 222 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8158 (tp-100) REVERT: D 430 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: D 486 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8258 (mt) REVERT: F 132 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: F 248 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8246 (mm) REVERT: F 396 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8418 (mp) REVERT: G 142 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8095 (ttmt) REVERT: G 149 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6478 (tmmm) REVERT: G 158 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: G 309 MET cc_start: 0.6145 (mtp) cc_final: 0.5384 (tpt) REVERT: O 264 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8272 (mp) REVERT: O 287 MET cc_start: 0.8875 (mtp) cc_final: 0.8583 (mtp) REVERT: O 299 LYS cc_start: 0.6082 (mmpt) cc_final: 0.5742 (mtmt) REVERT: O 313 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6315 (tttt) REVERT: T 1 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6751 (ptp) REVERT: T 149 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8222 (tppt) REVERT: T 205 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: T 222 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8223 (tp-100) REVERT: T 229 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8959 (mt) REVERT: T 283 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8919 (mp) REVERT: T 428 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7944 (ttpt) outliers start: 149 outliers final: 95 residues processed: 338 average time/residue: 0.1623 time to fit residues: 89.6805 Evaluate side-chains 312 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 192 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 288 SER Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 144 VAL Chi-restraints excluded: chain O residue 264 LEU Chi-restraints excluded: chain O residue 313 LYS Chi-restraints excluded: chain O residue 337 ILE Chi-restraints excluded: chain O residue 356 VAL Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 408 VAL Chi-restraints excluded: chain O residue 418 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 84 CYS Chi-restraints excluded: chain T residue 98 ASN Chi-restraints excluded: chain T residue 149 LYS Chi-restraints excluded: chain T residue 205 GLN Chi-restraints excluded: chain T residue 222 GLN Chi-restraints excluded: chain T residue 229 LEU Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 389 SER Chi-restraints excluded: chain T residue 428 LYS Chi-restraints excluded: chain T residue 437 VAL Chi-restraints excluded: chain T residue 498 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 264 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 324 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN F 68 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114295 restraints weight = 41419.066| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.73 r_work: 0.2985 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32095 Z= 0.180 Angle : 0.523 12.364 44072 Z= 0.273 Chirality : 0.041 0.336 4925 Planarity : 0.004 0.056 5044 Dihedral : 15.964 141.990 5712 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.83 % Rotamer: Outliers : 4.90 % Allowed : 26.16 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.14), residues: 3481 helix: 1.67 (0.15), residues: 1208 sheet: -0.29 (0.20), residues: 687 loop : -1.50 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 152 TYR 0.011 0.001 TYR A 154 PHE 0.014 0.001 PHE A 45 TRP 0.015 0.001 TRP A 319 HIS 0.005 0.001 HIS T 59 Details of bonding type rmsd covalent geometry : bond 0.00437 (32095) covalent geometry : angle 0.52250 (44072) hydrogen bonds : bond 0.03909 ( 1295) hydrogen bonds : angle 4.50378 ( 3585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 204 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7330 (p0) REVERT: A 336 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.6509 (mpp) REVERT: B 72 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6931 (mpp80) REVERT: B 152 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6163 (mtp85) REVERT: B 281 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7771 (tt) REVERT: B 383 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 186 ARG cc_start: 0.5415 (mpt-90) cc_final: 0.4667 (mtt180) REVERT: C 274 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6559 (pt0) REVERT: C 395 MET cc_start: 0.5657 (mmp) cc_final: 0.5012 (mmm) REVERT: D 29 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 222 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8103 (tp-100) REVERT: D 430 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: F 132 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: F 295 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6672 (ttp-170) REVERT: F 327 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: F 396 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8409 (mp) REVERT: G 142 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8141 (ttmt) REVERT: G 149 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6492 (tmmm) REVERT: G 158 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: G 309 MET cc_start: 0.6258 (mtp) cc_final: 0.5487 (tpt) REVERT: O 287 MET cc_start: 0.8906 (mtp) cc_final: 0.8628 (mtp) REVERT: O 299 LYS cc_start: 0.6081 (mmpt) cc_final: 0.5777 (mtmt) REVERT: O 310 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7300 (mp) REVERT: O 313 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6351 (tttt) REVERT: O 336 MET cc_start: 0.8481 (mtp) cc_final: 0.8274 (mtm) REVERT: T 1 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6918 (ptp) REVERT: T 149 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8212 (tppt) REVERT: T 205 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: T 222 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8245 (tp-100) REVERT: T 229 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8956 (mt) REVERT: T 283 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8860 (mp) REVERT: T 428 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7840 (ttpt) REVERT: T 441 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8115 (mp) outliers start: 146 outliers final: 97 residues processed: 327 average time/residue: 0.1714 time to fit residues: 91.5474 Evaluate side-chains 315 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 192 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 295 ARG Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 288 SER Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 144 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 313 LYS Chi-restraints excluded: chain O residue 337 ILE Chi-restraints excluded: chain O residue 356 VAL Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 408 VAL Chi-restraints excluded: chain O residue 418 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 84 CYS Chi-restraints excluded: chain T residue 98 ASN Chi-restraints excluded: chain T residue 149 LYS Chi-restraints excluded: chain T residue 205 GLN Chi-restraints excluded: chain T residue 222 GLN Chi-restraints excluded: chain T residue 229 LEU Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 389 SER Chi-restraints excluded: chain T residue 428 LYS Chi-restraints excluded: chain T residue 437 VAL Chi-restraints excluded: chain T residue 441 LEU Chi-restraints excluded: chain T residue 498 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.9792 > 50: distance: 1 - 30: 8.743 distance: 22 - 30: 6.954 distance: 31 - 32: 18.176 distance: 31 - 34: 9.648 distance: 32 - 33: 12.384 distance: 32 - 38: 12.531 distance: 34 - 35: 14.982 distance: 34 - 36: 12.398 distance: 35 - 37: 6.732 distance: 38 - 39: 17.896 distance: 39 - 40: 16.562 distance: 39 - 42: 9.873 distance: 40 - 41: 12.754 distance: 40 - 47: 7.137 distance: 42 - 43: 12.481 distance: 43 - 44: 8.087 distance: 44 - 45: 8.542 distance: 44 - 46: 7.380 distance: 47 - 48: 4.514 distance: 48 - 49: 8.732 distance: 48 - 51: 4.439 distance: 49 - 50: 7.649 distance: 49 - 56: 15.347 distance: 51 - 52: 5.523 distance: 52 - 53: 6.314 distance: 53 - 54: 3.467 distance: 54 - 55: 4.485 distance: 56 - 57: 13.933 distance: 56 - 62: 12.622 distance: 57 - 58: 9.981 distance: 57 - 60: 5.543 distance: 58 - 59: 5.238 distance: 58 - 63: 12.324 distance: 63 - 64: 12.214 distance: 64 - 65: 16.232 distance: 64 - 67: 9.771 distance: 65 - 66: 12.246 distance: 65 - 71: 11.895 distance: 67 - 68: 18.727 distance: 67 - 69: 19.328 distance: 68 - 70: 3.457 distance: 72 - 73: 4.339 distance: 72 - 75: 6.428 distance: 73 - 74: 8.000 distance: 73 - 83: 12.196 distance: 75 - 76: 3.340 distance: 76 - 77: 9.077 distance: 77 - 79: 11.562 distance: 78 - 80: 6.686 distance: 79 - 81: 3.669 distance: 80 - 81: 7.854 distance: 81 - 82: 13.895 distance: 83 - 84: 9.688 distance: 84 - 85: 13.673 distance: 84 - 87: 3.060 distance: 85 - 86: 13.723 distance: 85 - 91: 39.185 distance: 88 - 90: 8.665 distance: 91 - 92: 7.488 distance: 92 - 93: 17.220 distance: 93 - 94: 10.605 distance: 93 - 97: 10.882 distance: 95 - 96: 3.829 distance: 98 - 99: 6.737 distance: 98 - 101: 6.874 distance: 99 - 100: 6.817 distance: 99 - 105: 6.459 distance: 101 - 102: 9.214 distance: 102 - 103: 11.495 distance: 102 - 104: 12.146 distance: 105 - 106: 7.454 distance: 106 - 107: 9.684 distance: 106 - 109: 16.842 distance: 107 - 108: 9.092 distance: 107 - 111: 9.179 distance: 109 - 110: 22.211