Starting phenix.real_space_refine on Sat Aug 8 23:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2026/8ifl_35420.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 160 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 19506 2.51 5 N 5195 2.21 5 O 6027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30976 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3475 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 12, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3442 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain breaks: 4 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "F" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3450 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 14, 'TRANS': 397} Chain breaks: 2 Chain: "G" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3449 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 24, 'TRANS': 403} Chain breaks: 4 Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "I" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3475 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 12, 'TRANS': 402} Chain breaks: 1 Chain: "K" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3442 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain breaks: 4 Chain: "L" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "M" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "N" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3450 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 14, 'TRANS': 397} Chain breaks: 2 Chain: "O" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3445 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 24, 'TRANS': 402} Chain breaks: 4 Chain: "P" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "Q" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" 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: 5.73, per 1000 atoms: 0.18 Number of scatterers: 30976 At special positions: 0 Unit cell: (151.8, 206.8, 168.3, 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 160 15.00 Mg 4 11.99 O 6027 8.00 N 5195 7.00 C 19506 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6380 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 40 sheets defined 36.8% alpha, 23.4% beta 62 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 3.819A pdb=" N THR A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.477A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 148 through 160 removed outlier: 4.059A pdb=" N LEU A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.804A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 removed outlier: 4.113A pdb=" N ALA B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.635A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 113 through 131 removed outlier: 3.799A pdb=" N PHE B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 4.270A pdb=" N GLU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.601A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) No H-bonds generated for '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 377 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 493 removed outlier: 4.094A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'F' and resid 10 through 29 removed outlier: 5.742A pdb=" N ASP F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 56 removed outlier: 3.992A pdb=" N ASN F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.645A pdb=" N GLN F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.639A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 removed outlier: 4.050A pdb=" N LYS F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 157 removed outlier: 3.998A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 257 through 279 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 353 through 367 removed outlier: 3.825A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 384 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 46 through 62 removed outlier: 3.550A pdb=" N LYS G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 113 through 131 removed outlier: 3.676A pdb=" N PHE G 121 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 214 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 245 through 247 No H-bonds generated for 'chain 'G' and resid 245 through 247' Processing helix chain 'G' and resid 248 through 264 removed outlier: 3.522A pdb=" N ALA G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 351 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 451 through 463 Processing helix chain 'G' and resid 477 through 493 removed outlier: 4.221A pdb=" N SER G 493 " --> pdb=" O ILE G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'J' and resid 15 through 29 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 65 through 71 removed outlier: 4.105A pdb=" N LYS J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 89 Processing helix chain 'J' and resid 109 through 114 removed outlier: 3.505A pdb=" N VAL J 113 " --> pdb=" O ASN J 109 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 109 through 114' Processing helix chain 'J' and resid 123 through 138 Processing helix chain 'J' and resid 150 through 160 removed outlier: 3.758A pdb=" N TYR J 154 " --> pdb=" O SER J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.729A pdb=" N GLU J 231 " --> pdb=" O PRO J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 249 Processing helix chain 'J' and resid 257 through 279 Processing helix chain 'J' and resid 300 through 302 No H-bonds generated for 'chain 'J' and resid 300 through 302' Processing helix chain 'J' and resid 354 through 368 removed outlier: 4.409A pdb=" N ASN J 367 " --> pdb=" O LYS J 363 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP J 368 " --> pdb=" O GLN J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 384 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 22 through 30 Processing helix chain 'K' and resid 46 through 62 removed outlier: 3.537A pdb=" N LYS K 62 " --> pdb=" O ASP K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.941A pdb=" N PHE K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 214 Processing helix chain 'K' and resid 226 through 230 Processing helix chain 'K' and resid 245 through 247 No H-bonds generated for 'chain 'K' and resid 245 through 247' Processing helix chain 'K' and resid 248 through 263 Processing helix chain 'K' and resid 331 through 351 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 451 through 463 Processing helix chain 'K' and resid 477 through 493 removed outlier: 3.539A pdb=" N ARG K 481 " --> pdb=" O PRO K 477 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER K 493 " --> pdb=" O ILE K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 506 Processing helix chain 'N' and resid 14 through 29 Processing helix chain 'N' and resid 45 through 55 Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 123 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.488A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN N 155 " --> pdb=" O ASN N 151 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 219 through 223 removed outlier: 4.064A pdb=" N PHE N 223 " --> pdb=" O GLU N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 248 Processing helix chain 'N' and resid 257 through 280 removed outlier: 3.786A pdb=" N LYS N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 367 removed outlier: 4.179A pdb=" N ASN N 367 " --> pdb=" O LYS N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 385 Processing helix chain 'O' and resid 15 through 17 No H-bonds generated for 'chain 'O' and resid 15 through 17' Processing helix chain 'O' and resid 22 through 30 Processing helix chain 'O' and resid 46 through 62 removed outlier: 3.658A pdb=" N GLN O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 83 Processing helix chain 'O' and resid 113 through 131 removed outlier: 3.850A pdb=" N PHE O 121 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 216 removed outlier: 3.749A pdb=" N GLN O 209 " --> pdb=" O GLN O 205 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU O 216 " --> pdb=" O ALA O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 230 removed outlier: 3.766A pdb=" N ALA O 230 " --> pdb=" O GLU O 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 226 through 230' Processing helix chain 'O' and resid 248 through 264 removed outlier: 3.562A pdb=" N SER O 257 " --> pdb=" O ALA O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 331 through 351 Processing helix chain 'O' and resid 366 through 377 removed outlier: 3.956A pdb=" N TRP O 370 " --> pdb=" O ASN O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 463 Processing helix chain 'O' and resid 477 through 493 removed outlier: 3.508A pdb=" N ARG O 481 " --> pdb=" O PRO O 477 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER O 493 " --> pdb=" O ILE O 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.461A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 7.340A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR B 6 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 446 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL B 278 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 305 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 7.340A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR B 6 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 446 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL B 278 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 305 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN B 296 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TRP B 320 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.383A pdb=" N PHE A 291 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA A 325 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.383A pdb=" N PHE A 291 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA A 325 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 402 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 210 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 92 through 95 removed outlier: 7.023A pdb=" N SER B 41 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 425 through 426 Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 33 removed outlier: 5.995A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS F 4 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU F 61 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE F 6 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 63 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER F 8 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.552A pdb=" N GLY G 385 " --> pdb=" O ASN G 446 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL G 357 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL G 386 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE G 359 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 388 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA G 361 " --> pdb=" O ILE G 388 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS G 279 " --> pdb=" O PHE G 358 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS G 360 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU G 281 " --> pdb=" O HIS G 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.552A pdb=" N GLY G 385 " --> pdb=" O ASN G 446 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL G 357 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL G 386 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE G 359 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 388 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA G 361 " --> pdb=" O ILE G 388 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS G 279 " --> pdb=" O PHE G 358 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS G 360 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU G 281 " --> pdb=" O HIS G 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 283 through 286 removed outlier: 6.766A pdb=" N PHE F 291 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA F 325 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 283 through 286 removed outlier: 6.766A pdb=" N PHE F 291 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA F 325 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 184 through 187 Processing sheet with id=AC1, first strand: chain 'F' and resid 304 through 305 Processing sheet with id=AC2, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AC3, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.365A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP G 139 " --> pdb=" O GLN G 222 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU G 224 " --> pdb=" O TRP G 139 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL G 141 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 425 through 426 Processing sheet with id=AC5, first strand: chain 'J' and resid 32 through 33 removed outlier: 6.910A pdb=" N ILE J 5 " --> pdb=" O TRP J 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE J 6 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL J 63 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER J 8 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE J 60 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE J 118 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 169 through 172 removed outlier: 3.599A pdb=" N LEU K 4 " --> pdb=" O PHE J 411 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE K 443 " --> pdb=" O THR K 389 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR K 389 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE K 445 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR K 387 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS K 279 " --> pdb=" O PHE K 358 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N HIS K 360 " --> pdb=" O CYS K 279 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU K 281 " --> pdb=" O HIS K 360 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL K 278 " --> pdb=" O LEU K 305 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU K 305 " --> pdb=" O VAL K 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 169 through 172 removed outlier: 3.599A pdb=" N LEU K 4 " --> pdb=" O PHE J 411 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE K 443 " --> pdb=" O THR K 389 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR K 389 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE K 445 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR K 387 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS K 279 " --> pdb=" O PHE K 358 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N HIS K 360 " --> pdb=" O CYS K 279 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU K 281 " --> pdb=" O HIS K 360 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL K 278 " --> pdb=" O LEU K 305 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU K 305 " --> pdb=" O VAL K 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 283 through 286 removed outlier: 6.852A pdb=" N PHE J 291 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA J 325 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 283 through 286 removed outlier: 6.852A pdb=" N PHE J 291 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA J 325 " --> pdb=" O PHE J 291 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU J 402 " --> pdb=" O ILE J 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 215 through 216 Processing sheet with id=AD2, first strand: chain 'J' and resid 304 through 305 Processing sheet with id=AD3, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD4, first strand: chain 'K' and resid 92 through 95 removed outlier: 6.969A pdb=" N GLY K 42 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE K 142 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL K 44 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TRP K 139 " --> pdb=" O GLN K 222 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU K 224 " --> pdb=" O TRP K 139 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL K 141 " --> pdb=" O LEU K 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 32 through 33 removed outlier: 3.611A pdb=" N TRP N 33 " --> pdb=" O ILE N 5 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE N 6 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL N 63 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER N 8 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE N 60 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU N 97 " --> pdb=" O PHE N 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE N 62 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE N 118 " --> pdb=" O ILE N 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 165 through 172 removed outlier: 5.694A pdb=" N LYS N 167 " --> pdb=" O MET N 414 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS N 409 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU O 4 " --> pdb=" O LYS N 409 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE N 411 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR O 6 " --> pdb=" O PHE N 411 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LYS N 413 " --> pdb=" O TYR O 6 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN O 446 " --> pdb=" O GLY O 385 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY O 385 " --> pdb=" O ASN O 446 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY O 448 " --> pdb=" O LEU O 383 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU O 383 " --> pdb=" O GLY O 448 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL O 357 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL O 386 " --> pdb=" O VAL O 357 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE O 359 " --> pdb=" O VAL O 386 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE O 388 " --> pdb=" O ILE O 359 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA O 361 " --> pdb=" O ILE O 388 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS O 279 " --> pdb=" O PHE O 358 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS O 360 " --> pdb=" O CYS O 279 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU O 281 " --> pdb=" O HIS O 360 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA O 300 " --> pdb=" O GLY O 318 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY O 318 " --> pdb=" O ALA O 300 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN O 302 " --> pdb=" O GLU O 316 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU O 316 " --> pdb=" O GLN O 302 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 283 through 287 removed outlier: 6.542A pdb=" N PHE N 291 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA N 325 " --> pdb=" O PHE N 291 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 283 through 287 removed outlier: 6.542A pdb=" N PHE N 291 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA N 325 " --> pdb=" O PHE N 291 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU N 402 " --> pdb=" O ILE N 179 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 208 through 210 Processing sheet with id=AE1, first strand: chain 'N' and resid 304 through 305 Processing sheet with id=AE2, first strand: chain 'O' and resid 12 through 13 Processing sheet with id=AE3, first strand: chain 'O' and resid 92 through 95 removed outlier: 7.001A pdb=" N SER O 41 " --> pdb=" O VAL O 92 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS O 94 " --> pdb=" O SER O 41 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL O 43 " --> pdb=" O LYS O 94 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY O 42 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE O 142 " --> pdb=" O GLY O 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL O 44 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TRP O 139 " --> pdb=" O GLN O 222 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU O 224 " --> pdb=" O TRP O 139 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL O 141 " --> pdb=" O LEU O 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'O' and resid 425 through 426 1213 hydrogen bonds defined for protein. 3384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.41 - 0.70: 1 0.70 - 0.99: 0 0.99 - 1.28: 4658 1.28 - 1.57: 26954 1.57 - 1.87: 443 Warning: very small bond lengths. Bond restraints: 32056 Sorted by residual: bond pdb=" CG PRO N 177 " pdb=" CD PRO N 177 " ideal model delta sigma weight residual 1.503 0.409 1.094 3.40e-02 8.65e+02 1.03e+03 bond pdb=" CG PRO K 220 " pdb=" CD PRO K 220 " ideal model delta sigma weight residual 1.503 1.217 0.286 3.40e-02 8.65e+02 7.06e+01 bond pdb=" CB PRO K 220 " pdb=" CG PRO K 220 " ideal model delta sigma weight residual 1.492 1.073 0.419 5.00e-02 4.00e+02 7.03e+01 bond pdb=" CB PRO N 177 " pdb=" CG PRO N 177 " ideal model delta sigma weight residual 1.492 1.866 -0.374 5.00e-02 4.00e+02 5.58e+01 bond pdb=" CG PRO N 333 " pdb=" CD PRO N 333 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.94e+01 ... (remaining 32051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.74: 44009 14.74 - 29.49: 2 29.49 - 44.23: 2 44.23 - 58.98: 1 58.98 - 73.72: 1 Bond angle restraints: 44015 Sorted by residual: angle pdb=" N PRO N 177 " pdb=" CD PRO N 177 " pdb=" CG PRO N 177 " ideal model delta sigma weight residual 103.20 47.65 55.55 1.50e+00 4.44e-01 1.37e+03 angle pdb=" CB PRO K 220 " pdb=" CG PRO K 220 " pdb=" CD PRO K 220 " ideal model delta sigma weight residual 106.10 179.82 -73.72 3.20e+00 9.77e-02 5.31e+02 angle pdb=" N PRO K 220 " pdb=" CD PRO K 220 " pdb=" CG PRO K 220 " ideal model delta sigma weight residual 103.20 73.57 29.63 1.50e+00 4.44e-01 3.90e+02 angle pdb=" CA PRO K 220 " pdb=" CB PRO K 220 " pdb=" CG PRO K 220 " ideal model delta sigma weight residual 104.50 71.33 33.17 1.90e+00 2.77e-01 3.05e+02 angle pdb=" CA PRO N 177 " pdb=" CB PRO N 177 " pdb=" CG PRO N 177 " ideal model delta sigma weight residual 104.50 79.07 25.43 1.90e+00 2.77e-01 1.79e+02 ... (remaining 44010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15188 17.98 - 35.96: 2593 35.96 - 53.94: 860 53.94 - 71.92: 213 71.92 - 89.90: 65 Dihedral angle restraints: 18919 sinusoidal: 9058 harmonic: 9861 Sorted by residual: dihedral pdb=" C4' A P 1 " pdb=" C3' A P 1 " pdb=" C2' A P 1 " pdb=" C1' A P 1 " ideal model delta sinusoidal sigma weight residual 36.35 -37.55 73.90 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' A L 1 " pdb=" C3' A L 1 " pdb=" C2' A L 1 " pdb=" C1' A L 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.89 73.23 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' G P 20 " pdb=" C3' G P 20 " pdb=" C2' G P 20 " pdb=" C1' G P 20 " ideal model delta sinusoidal sigma weight residual 36.35 -36.20 72.54 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 18916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3924 0.060 - 0.119: 728 0.119 - 0.178: 73 0.178 - 0.238: 76 0.238 - 0.297: 27 Chirality restraints: 4828 Sorted by residual: chirality pdb=" CG LEU N 132 " pdb=" CB LEU N 132 " pdb=" CD1 LEU N 132 " pdb=" CD2 LEU N 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' A P 1 " pdb=" C4' A P 1 " pdb=" O3' A P 1 " pdb=" C2' A P 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' A L 1 " pdb=" C4' A L 1 " pdb=" O3' A L 1 " pdb=" C2' A L 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4825 not shown) Planarity restraints: 4975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 219 " -0.097 5.00e-02 4.00e+02 1.38e-01 3.07e+01 pdb=" N PRO K 220 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO K 220 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO K 220 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 332 " 0.096 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO N 333 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO N 333 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO N 333 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 319 " 0.031 2.00e-02 2.50e+03 2.98e-02 2.22e+01 pdb=" CG TRP J 319 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP J 319 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP J 319 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 319 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 319 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 319 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 319 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 319 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP J 319 " 0.004 2.00e-02 2.50e+03 ... (remaining 4972 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 296 2.51 - 3.10: 22415 3.10 - 3.70: 52945 3.70 - 4.30: 76347 4.30 - 4.90: 121275 Nonbonded interactions: 273278 Sorted by model distance: nonbonded pdb=" OP1 A H 3 " pdb="MG MG H 101 " model vdw 1.907 2.170 nonbonded pdb=" O3' A P 2 " pdb="MG MG P 101 " model vdw 1.927 2.170 nonbonded pdb=" O3' A L 2 " pdb="MG MG L 101 " model vdw 1.978 2.170 nonbonded pdb=" OD1 ASN B 468 " pdb="MG MG B 601 " model vdw 1.994 2.170 nonbonded pdb=" OP2 A H 1 " pdb="MG MG H 101 " model vdw 2.008 2.170 ... (remaining 273273 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 40 or resid 45 through 420)) selection = (chain 'F' and (resid 3 through 141 or resid 146 through 420)) selection = (chain 'J' and (resid 3 through 40 or resid 45 through 420)) selection = (chain 'N' and (resid 3 through 141 or resid 146 through 420)) } ncs_group { reference = (chain 'B' and (resid 1 through 271 or resid 277 through 507)) selection = (chain 'G' and (resid 1 through 271 or resid 277 through 507)) selection = (chain 'K' and (resid 1 through 271 or resid 277 through 507)) selection = (chain 'O' and (resid 1 through 271 or resid 277 through 507)) } ncs_group { reference = chain 'C' selection = (chain 'H' and resid 1 through 20) selection = (chain 'L' and resid 1 through 20) selection = (chain 'P' and resid 1 through 20) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'M' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 30.280 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.094 32056 Z= 0.311 Angle : 0.882 73.719 44015 Z= 0.491 Chirality : 0.056 0.297 4828 Planarity : 0.006 0.138 4975 Dihedral : 20.148 89.898 12539 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 0.70 % Allowed : 31.62 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3303 helix: 0.58 (0.15), residues: 1127 sheet: -0.75 (0.21), residues: 574 loop : -1.30 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 19 TYR 0.021 0.001 TYR F 190 PHE 0.041 0.002 PHE K 75 TRP 0.079 0.002 TRP J 319 HIS 0.013 0.002 HIS O 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.31 (32056) covalent geometry : angle 0.88162 / 0.49 (44015) hydrogen bonds : bond 0.13930 / 9.04 ( 1248) hydrogen bonds : angle 6.82877 / 4.79 ( 3670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 788 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.5571 (tpp) cc_final: 0.5309 (mmt) REVERT: A 271 LYS cc_start: 0.8318 (tppt) cc_final: 0.7759 (mttp) REVERT: A 323 ILE cc_start: 0.7756 (pt) cc_final: 0.7238 (pt) REVERT: B 225 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7916 (ttp80) REVERT: B 233 ASP cc_start: 0.6986 (m-30) cc_final: 0.6301 (t0) REVERT: B 285 TYR cc_start: 0.7852 (m-80) cc_final: 0.7447 (m-80) REVERT: B 354 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.8278 (Cg_exo) REVERT: B 358 PHE cc_start: 0.8051 (t80) cc_final: 0.7796 (t80) REVERT: F 13 GLU cc_start: 0.8098 (mp0) cc_final: 0.7890 (mp0) REVERT: F 80 VAL cc_start: 0.8814 (p) cc_final: 0.8599 (m) REVERT: F 154 TYR cc_start: 0.8162 (t80) cc_final: 0.7904 (t80) REVERT: F 185 LEU cc_start: 0.7835 (tp) cc_final: 0.7632 (tp) REVERT: F 190 TYR cc_start: 0.4934 (m-10) cc_final: 0.4645 (m-80) REVERT: F 242 SER cc_start: 0.8976 (t) cc_final: 0.8605 (p) REVERT: F 276 ARG cc_start: 0.7149 (tpt170) cc_final: 0.6479 (mmm160) REVERT: F 414 MET cc_start: 0.7234 (tpp) cc_final: 0.7012 (mmm) REVERT: G 64 ILE cc_start: 0.8471 (tp) cc_final: 0.8269 (mt) REVERT: G 126 ILE cc_start: 0.7615 (mp) cc_final: 0.7291 (mp) REVERT: G 414 ASP cc_start: 0.7568 (t0) cc_final: 0.7319 (m-30) REVERT: G 420 LEU cc_start: 0.7384 (tp) cc_final: 0.7154 (tt) REVERT: G 449 GLU cc_start: 0.6374 (pm20) cc_final: 0.5657 (pp20) REVERT: G 458 ASP cc_start: 0.7336 (m-30) cc_final: 0.6860 (m-30) REVERT: J 33 TRP cc_start: 0.8336 (t60) cc_final: 0.7987 (t60) REVERT: J 160 HIS cc_start: 0.6419 (p-80) cc_final: 0.5809 (p-80) REVERT: J 181 PHE cc_start: 0.3687 (p90) cc_final: 0.1559 (p90) REVERT: J 259 TYR cc_start: 0.6899 (p90) cc_final: 0.6340 (p90) REVERT: J 260 GLU cc_start: 0.6575 (tm-30) cc_final: 0.5699 (mm-30) REVERT: J 263 ARG cc_start: 0.6114 (ttp80) cc_final: 0.5903 (mmt90) REVERT: J 287 MET cc_start: 0.7283 (mmm) cc_final: 0.6752 (mtt) REVERT: K 2 LYS cc_start: 0.7484 (mptt) cc_final: 0.7271 (mmmt) REVERT: K 79 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: K 213 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.7173 (mtp180) REVERT: K 225 ARG cc_start: 0.5312 (mtp-110) cc_final: 0.5070 (ttp-170) REVERT: K 328 TYR cc_start: 0.6660 (m-80) cc_final: 0.6450 (m-80) REVERT: K 387 THR cc_start: 0.5161 (m) cc_final: 0.4396 (p) REVERT: N 169 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6194 (tt0) REVERT: N 345 MET cc_start: 0.4396 (mmm) cc_final: 0.4190 (ptp) REVERT: N 401 ILE cc_start: 0.8057 (mt) cc_final: 0.7760 (mt) REVERT: N 406 LYS cc_start: 0.6524 (mmtt) cc_final: 0.6142 (mmtm) REVERT: N 414 MET cc_start: 0.6581 (mmt) cc_final: 0.5949 (mmt) REVERT: O 24 ARG cc_start: 0.7328 (mpp80) cc_final: 0.6894 (mtt180) REVERT: O 85 LYS cc_start: 0.8418 (tppt) cc_final: 0.8055 (mtpp) REVERT: O 390 LYS cc_start: 0.5398 (pptt) cc_final: 0.4932 (mmmt) REVERT: O 458 ASP cc_start: 0.5851 (m-30) cc_final: 0.5280 (m-30) REVERT: O 497 LYS cc_start: 0.8759 (tptt) cc_final: 0.8535 (tptp) outliers start: 21 outliers final: 3 residues processed: 797 average time/residue: 0.2223 time to fit residues: 273.8771 Evaluate side-chains 537 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 533 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 223 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN G 61 GLN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 HIS ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 ASN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 468 ASN N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 HIS N 234 ASN N 314 GLN N 364 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 GLN ** O 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 484 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.193537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.150677 restraints weight = 54009.320| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.96 r_work: 0.3924 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32056 Z= 0.177 Angle : 0.778 14.233 44015 Z= 0.384 Chirality : 0.056 1.392 4828 Planarity : 0.005 0.066 4975 Dihedral : 15.913 128.009 5600 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 4.00 % Allowed : 28.62 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3303 helix: 0.71 (0.15), residues: 1134 sheet: -0.67 (0.21), residues: 570 loop : -1.33 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 407 TYR 0.023 0.002 TYR J 318 PHE 0.036 0.002 PHE A 343 TRP 0.024 0.002 TRP J 319 HIS 0.012 0.001 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (32056) covalent geometry : angle 0.77798 / 0.38 (44015) hydrogen bonds : bond 0.04537 / 2.95 ( 1248) hydrogen bonds : angle 5.41375 / 3.81 ( 3670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 577 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.5924 (tpp) cc_final: 0.5637 (mmt) REVERT: A 100 ASP cc_start: 0.8486 (t70) cc_final: 0.7951 (t0) REVERT: A 262 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: A 271 LYS cc_start: 0.8257 (tppt) cc_final: 0.7609 (mttp) REVERT: A 289 LYS cc_start: 0.8165 (tptt) cc_final: 0.7392 (mtpt) REVERT: A 323 ILE cc_start: 0.7805 (pt) cc_final: 0.7335 (pt) REVERT: B 225 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8027 (ttp80) REVERT: B 233 ASP cc_start: 0.7283 (m-30) cc_final: 0.6448 (t0) REVERT: B 285 TYR cc_start: 0.7917 (m-80) cc_final: 0.7639 (m-80) REVERT: B 354 PRO cc_start: 0.8596 (Cg_endo) cc_final: 0.8339 (Cg_exo) REVERT: B 358 PHE cc_start: 0.7892 (t80) cc_final: 0.7590 (t80) REVERT: B 397 TYR cc_start: 0.7762 (m-80) cc_final: 0.7519 (m-10) REVERT: F 80 VAL cc_start: 0.8876 (p) cc_final: 0.8674 (m) REVERT: F 114 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8247 (mtp85) REVERT: F 242 SER cc_start: 0.8959 (t) cc_final: 0.8616 (p) REVERT: F 276 ARG cc_start: 0.7245 (tpt170) cc_final: 0.6660 (mmm160) REVERT: F 314 GLN cc_start: 0.4721 (OUTLIER) cc_final: 0.4113 (pp30) REVERT: F 414 MET cc_start: 0.7154 (tpp) cc_final: 0.6748 (mmt) REVERT: G 19 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (ptpt) REVERT: G 231 TRP cc_start: 0.7421 (p-90) cc_final: 0.7109 (p-90) REVERT: G 449 GLU cc_start: 0.6371 (pm20) cc_final: 0.5541 (pp20) REVERT: G 458 ASP cc_start: 0.6813 (m-30) cc_final: 0.6355 (m-30) REVERT: J 33 TRP cc_start: 0.8353 (t60) cc_final: 0.7867 (t60) REVERT: J 69 ASN cc_start: 0.7506 (m-40) cc_final: 0.7287 (m-40) REVERT: J 160 HIS cc_start: 0.5892 (p-80) cc_final: 0.5394 (p-80) REVERT: J 170 THR cc_start: 0.7659 (m) cc_final: 0.7317 (p) REVERT: J 181 PHE cc_start: 0.4443 (p90) cc_final: 0.2193 (p90) REVERT: J 243 THR cc_start: 0.5084 (OUTLIER) cc_final: 0.3682 (t) REVERT: J 260 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6326 (mm-30) REVERT: J 377 LEU cc_start: 0.1687 (OUTLIER) cc_final: 0.1461 (tp) REVERT: K 79 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: K 217 HIS cc_start: 0.5120 (OUTLIER) cc_final: 0.4348 (p90) REVERT: K 225 ARG cc_start: 0.5187 (mtp-110) cc_final: 0.4776 (ttp-170) REVERT: K 324 GLU cc_start: 0.3886 (mp0) cc_final: 0.3680 (mp0) REVERT: K 328 TYR cc_start: 0.6685 (m-80) cc_final: 0.6477 (m-80) REVERT: K 369 GLU cc_start: 0.7340 (pt0) cc_final: 0.6791 (pp20) REVERT: K 370 TRP cc_start: 0.6250 (t60) cc_final: 0.5643 (t60) REVERT: K 387 THR cc_start: 0.4595 (m) cc_final: 0.3783 (p) REVERT: N 19 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7271 (ptp90) REVERT: N 169 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6279 (tt0) REVERT: N 345 MET cc_start: 0.4829 (mmm) cc_final: 0.4280 (ptp) REVERT: N 406 LYS cc_start: 0.6112 (mmtt) cc_final: 0.5810 (mmtm) REVERT: N 414 MET cc_start: 0.6270 (mmt) cc_final: 0.5556 (mmt) REVERT: O 6 TYR cc_start: 0.6753 (t80) cc_final: 0.6258 (t80) REVERT: O 24 ARG cc_start: 0.7214 (mpp80) cc_final: 0.6576 (mtt180) REVERT: O 85 LYS cc_start: 0.8420 (tppt) cc_final: 0.7898 (mtpp) REVERT: O 94 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7194 (mmmt) REVERT: O 95 GLU cc_start: 0.7763 (pp20) cc_final: 0.7492 (pp20) REVERT: O 210 LEU cc_start: 0.8371 (tt) cc_final: 0.7637 (mt) REVERT: O 390 LYS cc_start: 0.5543 (pptt) cc_final: 0.4840 (mmmt) REVERT: O 406 MET cc_start: 0.7160 (ppp) cc_final: 0.6732 (ppp) REVERT: O 434 SER cc_start: 0.7267 (p) cc_final: 0.7046 (t) REVERT: O 497 LYS cc_start: 0.8856 (tptt) cc_final: 0.8641 (tptp) outliers start: 120 outliers final: 67 residues processed: 662 average time/residue: 0.2063 time to fit residues: 219.3795 Evaluate side-chains 592 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 518 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 147 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 373 TRP Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 63 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 HIS ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** 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 = 0.4566 r_free = 0.4566 target = 0.191974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.148881 restraints weight = 54125.504| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.97 r_work: 0.3901 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 32056 Z= 0.183 Angle : 0.722 12.739 44015 Z= 0.360 Chirality : 0.051 0.843 4828 Planarity : 0.005 0.051 4975 Dihedral : 15.792 109.017 5596 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 4.50 % Allowed : 28.35 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3303 helix: 0.75 (0.15), residues: 1126 sheet: -0.80 (0.21), residues: 586 loop : -1.33 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.020 0.002 TYR B 65 PHE 0.027 0.002 PHE B 238 TRP 0.033 0.002 TRP F 20 HIS 0.013 0.001 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (32056) covalent geometry : angle 0.72216 / 0.36 (44015) hydrogen bonds : bond 0.04260 / 2.79 ( 1248) hydrogen bonds : angle 5.22881 / 3.69 ( 3670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 539 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7487 (t0) cc_final: 0.6927 (t0) REVERT: A 92 MET cc_start: 0.5965 (tpp) cc_final: 0.5678 (mmt) REVERT: A 100 ASP cc_start: 0.8554 (t70) cc_final: 0.8008 (t0) REVERT: A 179 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.5724 (tp) REVERT: A 262 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: A 271 LYS cc_start: 0.8288 (tppt) cc_final: 0.7657 (mttp) REVERT: A 289 LYS cc_start: 0.8100 (tptt) cc_final: 0.7316 (mtpt) REVERT: A 291 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 225 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.8058 (ttp80) REVERT: B 233 ASP cc_start: 0.7381 (m-30) cc_final: 0.6557 (t0) REVERT: B 321 TYR cc_start: 0.7361 (m-80) cc_final: 0.6807 (m-80) REVERT: B 354 PRO cc_start: 0.8598 (Cg_endo) cc_final: 0.8336 (Cg_exo) REVERT: B 358 PHE cc_start: 0.7945 (t80) cc_final: 0.7670 (t80) REVERT: B 397 TYR cc_start: 0.8023 (m-80) cc_final: 0.7801 (m-10) REVERT: F 80 VAL cc_start: 0.8905 (p) cc_final: 0.8702 (m) REVERT: F 114 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8418 (mtp85) REVERT: F 165 ILE cc_start: 0.6614 (pt) cc_final: 0.6322 (pt) REVERT: F 242 SER cc_start: 0.8947 (t) cc_final: 0.8599 (p) REVERT: F 270 ASN cc_start: 0.8384 (t0) cc_final: 0.8090 (m-40) REVERT: F 276 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6707 (mmm160) REVERT: F 314 GLN cc_start: 0.4931 (OUTLIER) cc_final: 0.4288 (pp30) REVERT: F 414 MET cc_start: 0.7331 (tpp) cc_final: 0.6891 (mmt) REVERT: G 356 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7195 (tm-30) REVERT: G 449 GLU cc_start: 0.6377 (pm20) cc_final: 0.5546 (pp20) REVERT: G 458 ASP cc_start: 0.6838 (m-30) cc_final: 0.6392 (m-30) REVERT: J 33 TRP cc_start: 0.8349 (t60) cc_final: 0.7867 (t60) REVERT: J 151 ASN cc_start: 0.7548 (m-40) cc_final: 0.7046 (p0) REVERT: J 160 HIS cc_start: 0.6019 (p-80) cc_final: 0.5418 (p-80) REVERT: J 170 THR cc_start: 0.7800 (m) cc_final: 0.7526 (p) REVERT: J 181 PHE cc_start: 0.4443 (p90) cc_final: 0.2744 (p90) REVERT: J 243 THR cc_start: 0.5268 (OUTLIER) cc_final: 0.4085 (t) REVERT: J 260 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6275 (mm-30) REVERT: J 271 LYS cc_start: 0.7282 (tptp) cc_final: 0.6376 (mmmm) REVERT: J 340 HIS cc_start: 0.5933 (p90) cc_final: 0.4827 (p90) REVERT: J 354 LYS cc_start: 0.4008 (OUTLIER) cc_final: 0.3674 (tptt) REVERT: J 377 LEU cc_start: 0.1727 (OUTLIER) cc_final: 0.1525 (tp) REVERT: K 7 ILE cc_start: 0.4107 (pt) cc_final: 0.3724 (mp) REVERT: K 79 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: K 225 ARG cc_start: 0.5423 (mtp-110) cc_final: 0.4820 (ttp-170) REVERT: K 324 GLU cc_start: 0.4311 (mp0) cc_final: 0.4002 (mp0) REVERT: K 369 GLU cc_start: 0.7343 (pt0) cc_final: 0.6671 (pp20) REVERT: K 387 THR cc_start: 0.4395 (m) cc_final: 0.3644 (p) REVERT: N 19 ARG cc_start: 0.7393 (ptp90) cc_final: 0.7115 (ptp90) REVERT: N 28 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (mm) REVERT: N 169 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6394 (tt0) REVERT: N 215 CYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5596 (t) REVERT: N 283 ARG cc_start: 0.3679 (tpp-160) cc_final: 0.2048 (mtp85) REVERT: N 345 MET cc_start: 0.5055 (mmm) cc_final: 0.4496 (ptp) REVERT: N 406 LYS cc_start: 0.6330 (mmtt) cc_final: 0.6036 (mmtm) REVERT: N 414 MET cc_start: 0.5860 (mmt) cc_final: 0.5480 (mmm) REVERT: O 6 TYR cc_start: 0.6978 (t80) cc_final: 0.6622 (t80) REVERT: O 24 ARG cc_start: 0.7309 (mpp80) cc_final: 0.6664 (mtt180) REVERT: O 85 LYS cc_start: 0.8525 (tppt) cc_final: 0.8010 (mtpp) REVERT: O 94 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7296 (mmmt) REVERT: O 95 GLU cc_start: 0.7894 (pp20) cc_final: 0.7573 (pp20) REVERT: O 210 LEU cc_start: 0.8406 (tt) cc_final: 0.7682 (mt) REVERT: O 303 MET cc_start: 0.7177 (ptp) cc_final: 0.6824 (ptp) REVERT: O 390 LYS cc_start: 0.5396 (pptt) cc_final: 0.4818 (mmmt) REVERT: O 406 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6790 (ppp) REVERT: O 428 LYS cc_start: 0.8168 (tmtt) cc_final: 0.7965 (tmtt) REVERT: O 434 SER cc_start: 0.7422 (p) cc_final: 0.7159 (t) REVERT: O 497 LYS cc_start: 0.8887 (tptt) cc_final: 0.8569 (tptp) outliers start: 135 outliers final: 89 residues processed: 624 average time/residue: 0.1926 time to fit residues: 193.9779 Evaluate side-chains 601 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 501 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 489 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 232 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 314 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 HIS N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN O 322 ASN O 380 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.187967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144363 restraints weight = 54194.117| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.94 r_work: 0.3837 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 32056 Z= 0.247 Angle : 0.758 13.119 44015 Z= 0.381 Chirality : 0.052 0.672 4828 Planarity : 0.005 0.072 4975 Dihedral : 15.807 88.489 5596 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 5.94 % Allowed : 28.49 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3303 helix: 0.61 (0.15), residues: 1108 sheet: -1.12 (0.20), residues: 640 loop : -1.43 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 250 TYR 0.022 0.002 TYR B 285 PHE 0.042 0.002 PHE F 17 TRP 0.030 0.002 TRP N 20 HIS 0.011 0.002 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (32056) covalent geometry : angle 0.75825 / 0.38 (44015) hydrogen bonds : bond 0.04442 / 2.91 ( 1248) hydrogen bonds : angle 5.22393 / 3.68 ( 3670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 521 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7658 (t0) cc_final: 0.7261 (t0) REVERT: A 50 GLU cc_start: 0.7511 (tt0) cc_final: 0.7210 (tt0) REVERT: A 92 MET cc_start: 0.5986 (tpp) cc_final: 0.5656 (mmt) REVERT: A 100 ASP cc_start: 0.8620 (t70) cc_final: 0.8108 (t0) REVERT: A 149 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8633 (mtmm) REVERT: A 179 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5705 (tp) REVERT: A 262 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 271 LYS cc_start: 0.8368 (tppt) cc_final: 0.7645 (mttp) REVERT: A 289 LYS cc_start: 0.8201 (tptt) cc_final: 0.7510 (mtpt) REVERT: B 74 MET cc_start: 0.6141 (tpp) cc_final: 0.5766 (ttt) REVERT: B 225 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8137 (ttp80) REVERT: B 233 ASP cc_start: 0.7572 (m-30) cc_final: 0.6776 (t0) REVERT: B 283 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7493 (pp) REVERT: B 321 TYR cc_start: 0.7552 (m-80) cc_final: 0.7022 (m-80) REVERT: B 358 PHE cc_start: 0.7952 (t80) cc_final: 0.7696 (t80) REVERT: F 114 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8445 (mtp85) REVERT: F 160 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6709 (p-80) REVERT: F 242 SER cc_start: 0.8956 (t) cc_final: 0.8602 (p) REVERT: F 270 ASN cc_start: 0.8424 (t0) cc_final: 0.8223 (m-40) REVERT: F 276 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6714 (mmm160) REVERT: F 295 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (pt) REVERT: F 314 GLN cc_start: 0.5130 (OUTLIER) cc_final: 0.4339 (pp30) REVERT: G 137 ASP cc_start: 0.7787 (m-30) cc_final: 0.7470 (m-30) REVERT: G 221 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8767 (t) REVERT: G 285 TYR cc_start: 0.8547 (m-80) cc_final: 0.8191 (m-80) REVERT: G 449 GLU cc_start: 0.6474 (pm20) cc_final: 0.5487 (pp20) REVERT: G 458 ASP cc_start: 0.6956 (m-30) cc_final: 0.6391 (m-30) REVERT: J 46 TRP cc_start: 0.6190 (OUTLIER) cc_final: 0.4895 (m-90) REVERT: J 151 ASN cc_start: 0.7372 (m-40) cc_final: 0.6942 (p0) REVERT: J 160 HIS cc_start: 0.6341 (p-80) cc_final: 0.5088 (p-80) REVERT: J 161 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6313 (m-30) REVERT: J 170 THR cc_start: 0.7855 (m) cc_final: 0.7649 (p) REVERT: J 181 PHE cc_start: 0.4219 (p90) cc_final: 0.2545 (p90) REVERT: J 243 THR cc_start: 0.5472 (OUTLIER) cc_final: 0.4264 (t) REVERT: J 250 ARG cc_start: 0.7746 (ttm110) cc_final: 0.6813 (mmt-90) REVERT: J 260 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6348 (mm-30) REVERT: J 354 LYS cc_start: 0.4094 (OUTLIER) cc_final: 0.3692 (tptt) REVERT: J 372 LYS cc_start: 0.5809 (ttmt) cc_final: 0.5579 (mptt) REVERT: K 217 HIS cc_start: 0.5322 (OUTLIER) cc_final: 0.4523 (p90) REVERT: K 225 ARG cc_start: 0.5743 (mtp-110) cc_final: 0.5169 (ttp-170) REVERT: K 285 TYR cc_start: 0.6129 (m-10) cc_final: 0.5644 (m-10) REVERT: K 286 LYS cc_start: 0.8429 (mmpt) cc_final: 0.7448 (mmpt) REVERT: K 324 GLU cc_start: 0.4478 (mp0) cc_final: 0.4154 (mp0) REVERT: K 460 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6453 (mp) REVERT: N 28 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8145 (mm) REVERT: N 130 ASP cc_start: 0.8126 (m-30) cc_final: 0.7834 (m-30) REVERT: N 162 LYS cc_start: 0.7990 (mttp) cc_final: 0.7776 (mttp) REVERT: N 215 CYS cc_start: 0.6545 (OUTLIER) cc_final: 0.5897 (t) REVERT: N 283 ARG cc_start: 0.3725 (tpp-160) cc_final: 0.2127 (ttt180) REVERT: N 345 MET cc_start: 0.5568 (mmm) cc_final: 0.4986 (ptp) REVERT: N 382 ARG cc_start: 0.2711 (mmt-90) cc_final: 0.2394 (tpp80) REVERT: N 407 PRO cc_start: 0.6927 (Cg_endo) cc_final: 0.6552 (Cg_exo) REVERT: O 6 TYR cc_start: 0.7126 (t80) cc_final: 0.6807 (t80) REVERT: O 85 LYS cc_start: 0.8664 (tppt) cc_final: 0.8020 (mtpp) REVERT: O 390 LYS cc_start: 0.5625 (pptt) cc_final: 0.5125 (mmmt) REVERT: O 406 MET cc_start: 0.7363 (ppp) cc_final: 0.6767 (ppp) REVERT: O 434 SER cc_start: 0.7725 (p) cc_final: 0.7416 (t) REVERT: O 497 LYS cc_start: 0.8982 (tptt) cc_final: 0.8647 (tptp) outliers start: 178 outliers final: 110 residues processed: 653 average time/residue: 0.1964 time to fit residues: 204.9814 Evaluate side-chains 609 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 484 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 489 ILE Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 460 LEU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 147 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 279 CYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 GLN J 267 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS K 251 HIS K 380 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 HIS N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.190434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.147493 restraints weight = 53794.807| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.96 r_work: 0.3885 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32056 Z= 0.153 Angle : 0.691 12.675 44015 Z= 0.347 Chirality : 0.049 0.502 4828 Planarity : 0.005 0.048 4975 Dihedral : 15.753 83.557 5593 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.20 % Allowed : 29.05 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3303 helix: 0.71 (0.15), residues: 1126 sheet: -0.88 (0.21), residues: 577 loop : -1.40 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 250 TYR 0.032 0.002 TYR N 293 PHE 0.023 0.002 PHE F 17 TRP 0.030 0.002 TRP N 20 HIS 0.012 0.001 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (32056) covalent geometry : angle 0.69127 / 0.35 (44015) hydrogen bonds : bond 0.04012 / 2.63 ( 1248) hydrogen bonds : angle 5.04839 / 3.55 ( 3670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 525 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7570 (t0) cc_final: 0.7156 (t0) REVERT: A 50 GLU cc_start: 0.7527 (tt0) cc_final: 0.7294 (tt0) REVERT: A 92 MET cc_start: 0.6039 (tpp) cc_final: 0.5620 (mmt) REVERT: A 100 ASP cc_start: 0.8612 (t70) cc_final: 0.8108 (t0) REVERT: A 149 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8582 (mtmm) REVERT: A 179 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.5826 (tp) REVERT: A 262 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: A 271 LYS cc_start: 0.8328 (tppt) cc_final: 0.7607 (mttp) REVERT: A 330 TYR cc_start: 0.7810 (t80) cc_final: 0.7561 (t80) REVERT: B 74 MET cc_start: 0.6164 (tpp) cc_final: 0.5831 (ttt) REVERT: B 225 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8128 (ttp80) REVERT: B 233 ASP cc_start: 0.7529 (m-30) cc_final: 0.6688 (t0) REVERT: B 283 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7186 (pp) REVERT: B 321 TYR cc_start: 0.7456 (m-80) cc_final: 0.7060 (m-80) REVERT: B 354 PRO cc_start: 0.8658 (Cg_endo) cc_final: 0.8397 (Cg_exo) REVERT: B 358 PHE cc_start: 0.7967 (t80) cc_final: 0.7727 (t80) REVERT: B 397 TYR cc_start: 0.8025 (m-80) cc_final: 0.7693 (m-80) REVERT: F 242 SER cc_start: 0.8936 (t) cc_final: 0.8589 (p) REVERT: F 295 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7859 (pt) REVERT: F 302 LYS cc_start: 0.8376 (tptm) cc_final: 0.8062 (tmtt) REVERT: F 314 GLN cc_start: 0.5214 (OUTLIER) cc_final: 0.4393 (pp30) REVERT: F 329 LEU cc_start: 0.8011 (mt) cc_final: 0.7606 (mt) REVERT: G 137 ASP cc_start: 0.7746 (m-30) cc_final: 0.7430 (m-30) REVERT: G 221 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8728 (t) REVERT: G 449 GLU cc_start: 0.6471 (pm20) cc_final: 0.5464 (pp20) REVERT: G 458 ASP cc_start: 0.6775 (m-30) cc_final: 0.6366 (m-30) REVERT: J 33 TRP cc_start: 0.8386 (t60) cc_final: 0.7960 (t60) REVERT: J 46 TRP cc_start: 0.6146 (OUTLIER) cc_final: 0.4781 (m-90) REVERT: J 137 LYS cc_start: 0.6766 (pptt) cc_final: 0.6063 (ptpt) REVERT: J 151 ASN cc_start: 0.7437 (m-40) cc_final: 0.6938 (p0) REVERT: J 161 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5162 (p0) REVERT: J 181 PHE cc_start: 0.4512 (p90) cc_final: 0.3009 (p90) REVERT: J 213 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: J 243 THR cc_start: 0.5388 (OUTLIER) cc_final: 0.4187 (t) REVERT: J 260 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6388 (mm-30) REVERT: J 261 CYS cc_start: 0.7582 (t) cc_final: 0.7322 (p) REVERT: J 271 LYS cc_start: 0.7194 (tptp) cc_final: 0.6338 (mmmm) REVERT: J 323 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6257 (pp) REVERT: J 354 LYS cc_start: 0.4151 (OUTLIER) cc_final: 0.3720 (tptt) REVERT: J 372 LYS cc_start: 0.5818 (ttmt) cc_final: 0.5607 (mptt) REVERT: K 57 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6149 (tp) REVERT: K 215 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7549 (mt) REVERT: K 217 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.4362 (p90) REVERT: K 225 ARG cc_start: 0.5767 (mtp-110) cc_final: 0.5205 (ttp-170) REVERT: K 256 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8097 (mm) REVERT: K 285 TYR cc_start: 0.5978 (m-10) cc_final: 0.5416 (m-10) REVERT: K 286 LYS cc_start: 0.8283 (mmpt) cc_final: 0.7304 (mmpt) REVERT: K 324 GLU cc_start: 0.4570 (mp0) cc_final: 0.4196 (mp0) REVERT: K 328 TYR cc_start: 0.7079 (m-80) cc_final: 0.6580 (m-80) REVERT: K 470 CYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7368 (m) REVERT: N 28 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8183 (mm) REVERT: N 61 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.7984 (mt) REVERT: N 126 LYS cc_start: 0.7930 (pttt) cc_final: 0.7679 (pttp) REVERT: N 154 TYR cc_start: 0.7917 (t80) cc_final: 0.7375 (t80) REVERT: N 283 ARG cc_start: 0.4288 (tpp-160) cc_final: 0.2876 (ttt180) REVERT: N 345 MET cc_start: 0.5612 (mmm) cc_final: 0.5017 (ptt) REVERT: N 382 ARG cc_start: 0.2477 (mmt-90) cc_final: 0.2273 (tpp80) REVERT: N 407 PRO cc_start: 0.6779 (Cg_endo) cc_final: 0.6399 (Cg_exo) REVERT: O 24 ARG cc_start: 0.7384 (mpp80) cc_final: 0.6693 (mtt180) REVERT: O 85 LYS cc_start: 0.8634 (tppt) cc_final: 0.8035 (mtpp) REVERT: O 390 LYS cc_start: 0.5764 (pptt) cc_final: 0.5346 (mmtt) REVERT: O 406 MET cc_start: 0.7242 (ppp) cc_final: 0.6719 (ppp) REVERT: O 434 SER cc_start: 0.7620 (p) cc_final: 0.7279 (t) REVERT: O 497 LYS cc_start: 0.8967 (tptt) cc_final: 0.8633 (tptp) outliers start: 156 outliers final: 101 residues processed: 635 average time/residue: 0.1883 time to fit residues: 191.4639 Evaluate side-chains 617 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 497 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 213 TYR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 443 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 303 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN K 251 HIS ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 HIS N 281 ASN N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.182202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.138683 restraints weight = 55063.261| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.93 r_work: 0.3765 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 32056 Z= 0.382 Angle : 0.925 15.291 44015 Z= 0.465 Chirality : 0.058 0.693 4828 Planarity : 0.007 0.088 4975 Dihedral : 16.003 89.622 5593 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 6.74 % Allowed : 28.05 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3303 helix: -0.03 (0.14), residues: 1106 sheet: -1.45 (0.20), residues: 634 loop : -1.71 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 240 TYR 0.026 0.003 TYR A 171 PHE 0.034 0.003 PHE B 419 TRP 0.050 0.003 TRP N 20 HIS 0.016 0.002 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.38 (32056) covalent geometry : angle 0.92544 / 0.46 (44015) hydrogen bonds : bond 0.05365 / 3.51 ( 1248) hydrogen bonds : angle 5.54817 / 3.91 ( 3670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 498 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7795 (t0) cc_final: 0.7514 (t0) REVERT: A 92 MET cc_start: 0.5895 (tpp) cc_final: 0.5420 (mmt) REVERT: A 149 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8506 (mtmm) REVERT: A 179 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5740 (tp) REVERT: A 262 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: A 263 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7767 (ttp80) REVERT: A 267 GLN cc_start: 0.7890 (pt0) cc_final: 0.7215 (tp40) REVERT: A 271 LYS cc_start: 0.8581 (tppt) cc_final: 0.8344 (tptp) REVERT: A 275 LEU cc_start: 0.7868 (pp) cc_final: 0.7555 (pp) REVERT: A 330 TYR cc_start: 0.7793 (t80) cc_final: 0.7566 (t80) REVERT: B 65 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: B 137 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: B 207 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7695 (t-90) REVERT: B 225 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8083 (ttp80) REVERT: B 233 ASP cc_start: 0.7711 (m-30) cc_final: 0.6867 (t0) REVERT: B 283 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7295 (pp) REVERT: B 321 TYR cc_start: 0.7694 (m-80) cc_final: 0.7185 (m-80) REVERT: B 354 PRO cc_start: 0.8782 (Cg_endo) cc_final: 0.8521 (Cg_exo) REVERT: B 358 PHE cc_start: 0.8246 (t80) cc_final: 0.7979 (t80) REVERT: F 114 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8463 (mtp85) REVERT: F 160 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.6879 (p-80) REVERT: F 242 SER cc_start: 0.8990 (t) cc_final: 0.8623 (p) REVERT: F 276 ARG cc_start: 0.7532 (tpt170) cc_final: 0.6694 (mmm160) REVERT: F 295 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7885 (pt) REVERT: F 302 LYS cc_start: 0.8383 (tptm) cc_final: 0.8086 (tmmt) REVERT: F 314 GLN cc_start: 0.5607 (OUTLIER) cc_final: 0.4627 (pp30) REVERT: G 3 GLU cc_start: 0.7287 (tp30) cc_final: 0.7063 (tt0) REVERT: G 221 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8729 (t) REVERT: G 226 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6400 (mt-10) REVERT: G 231 TRP cc_start: 0.7590 (p-90) cc_final: 0.7269 (p-90) REVERT: G 285 TYR cc_start: 0.8658 (m-80) cc_final: 0.8261 (m-80) REVERT: G 449 GLU cc_start: 0.6394 (pm20) cc_final: 0.5496 (pp20) REVERT: J 46 TRP cc_start: 0.6609 (OUTLIER) cc_final: 0.6177 (m100) REVERT: J 137 LYS cc_start: 0.7015 (pptt) cc_final: 0.6264 (ptpt) REVERT: J 161 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.5491 (p0) REVERT: J 170 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7531 (t) REVERT: J 181 PHE cc_start: 0.4380 (p90) cc_final: 0.2925 (p90) REVERT: J 213 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: J 243 THR cc_start: 0.5608 (OUTLIER) cc_final: 0.4577 (t) REVERT: J 259 TYR cc_start: 0.6713 (p90) cc_final: 0.6509 (p90) REVERT: J 260 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6415 (mm-30) REVERT: J 354 LYS cc_start: 0.4079 (OUTLIER) cc_final: 0.3711 (tptt) REVERT: J 372 LYS cc_start: 0.5991 (ttmt) cc_final: 0.5733 (mptt) REVERT: K 57 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6306 (tp) REVERT: K 79 GLU cc_start: 0.7539 (mp0) cc_final: 0.6920 (mp0) REVERT: K 85 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8066 (mtmm) REVERT: K 215 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7669 (mt) REVERT: K 217 HIS cc_start: 0.5454 (OUTLIER) cc_final: 0.4576 (p90) REVERT: K 225 ARG cc_start: 0.6074 (mtp-110) cc_final: 0.5642 (ttp-170) REVERT: K 256 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8170 (mm) REVERT: K 285 TYR cc_start: 0.6302 (m-10) cc_final: 0.5894 (m-10) REVERT: K 286 LYS cc_start: 0.8641 (mmpt) cc_final: 0.7674 (mmpt) REVERT: K 324 GLU cc_start: 0.4707 (mp0) cc_final: 0.4320 (mp0) REVERT: K 460 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6569 (mp) REVERT: K 470 CYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8069 (m) REVERT: N 19 ARG cc_start: 0.7414 (ptp-170) cc_final: 0.6967 (ptp-170) REVERT: N 28 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (mm) REVERT: N 128 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7944 (tt) REVERT: N 215 CYS cc_start: 0.6645 (OUTLIER) cc_final: 0.6115 (t) REVERT: N 283 ARG cc_start: 0.5028 (tpp-160) cc_final: 0.3253 (ttt180) REVERT: N 285 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.3474 (t80) REVERT: N 345 MET cc_start: 0.5563 (mmm) cc_final: 0.4967 (ptp) REVERT: N 407 PRO cc_start: 0.7265 (Cg_endo) cc_final: 0.6849 (Cg_exo) REVERT: O 6 TYR cc_start: 0.7038 (t80) cc_final: 0.6485 (t80) REVERT: O 85 LYS cc_start: 0.8779 (tppt) cc_final: 0.8171 (mtpp) REVERT: O 94 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7684 (mttt) REVERT: O 390 LYS cc_start: 0.5837 (pptt) cc_final: 0.5318 (mmmt) REVERT: O 434 SER cc_start: 0.7862 (p) cc_final: 0.7487 (t) REVERT: O 497 LYS cc_start: 0.9039 (tptt) cc_final: 0.8740 (tptp) outliers start: 202 outliers final: 132 residues processed: 646 average time/residue: 0.1965 time to fit residues: 203.6450 Evaluate side-chains 629 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 471 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 470 CYS Chi-restraints excluded: chain G residue 489 ILE Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 213 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 311 THR Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 460 LEU Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 364 ARG Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Chi-restraints excluded: chain O residue 486 ILE Chi-restraints excluded: chain O residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 0.0870 chunk 60 optimal weight: 0.5980 chunk 258 optimal weight: 10.0000 chunk 320 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.186918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143334 restraints weight = 54172.413| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.96 r_work: 0.3864 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32056 Z= 0.150 Angle : 0.719 13.693 44015 Z= 0.360 Chirality : 0.050 0.442 4828 Planarity : 0.005 0.051 4975 Dihedral : 15.842 84.346 5593 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.74 % Allowed : 29.99 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3303 helix: 0.61 (0.15), residues: 1113 sheet: -1.31 (0.21), residues: 582 loop : -1.48 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 72 TYR 0.024 0.002 TYR G 472 PHE 0.026 0.002 PHE F 135 TRP 0.047 0.002 TRP N 20 HIS 0.010 0.001 HIS J 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (32056) covalent geometry : angle 0.71893 / 0.36 (44015) hydrogen bonds : bond 0.04116 / 2.68 ( 1248) hydrogen bonds : angle 5.03449 / 3.55 ( 3670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 523 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7642 (t0) cc_final: 0.7308 (t0) REVERT: A 71 ARG cc_start: 0.7189 (tpp-160) cc_final: 0.6866 (ttm110) REVERT: A 92 MET cc_start: 0.5970 (tpp) cc_final: 0.5496 (mmt) REVERT: A 100 ASP cc_start: 0.8564 (t70) cc_final: 0.8054 (t0) REVERT: A 149 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8543 (mtmm) REVERT: A 179 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.5776 (tp) REVERT: A 262 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: A 263 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7779 (ttp80) REVERT: A 267 GLN cc_start: 0.7895 (pt0) cc_final: 0.7243 (tp40) REVERT: A 330 TYR cc_start: 0.7758 (t80) cc_final: 0.7547 (t80) REVERT: B 74 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.6001 (ttt) REVERT: B 225 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7827 (ttm170) REVERT: B 233 ASP cc_start: 0.7590 (m-30) cc_final: 0.6740 (t0) REVERT: B 283 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7200 (pp) REVERT: B 321 TYR cc_start: 0.7726 (m-80) cc_final: 0.7354 (m-80) REVERT: B 358 PHE cc_start: 0.7919 (t80) cc_final: 0.7689 (t80) REVERT: B 397 TYR cc_start: 0.7888 (m-80) cc_final: 0.7643 (m-80) REVERT: F 160 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.6642 (p-80) REVERT: F 242 SER cc_start: 0.8961 (t) cc_final: 0.8593 (p) REVERT: F 276 ARG cc_start: 0.7529 (tpt170) cc_final: 0.6666 (mmm160) REVERT: F 295 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7789 (pt) REVERT: F 302 LYS cc_start: 0.8316 (tptm) cc_final: 0.8000 (tmmt) REVERT: F 314 GLN cc_start: 0.5590 (OUTLIER) cc_final: 0.4661 (pp30) REVERT: G 3 GLU cc_start: 0.7291 (tp30) cc_final: 0.7041 (tt0) REVERT: G 221 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8697 (t) REVERT: G 226 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6143 (mt-10) REVERT: G 327 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7881 (mm-30) REVERT: G 356 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6859 (tm-30) REVERT: G 449 GLU cc_start: 0.6248 (pm20) cc_final: 0.5418 (pp20) REVERT: J 46 TRP cc_start: 0.6246 (OUTLIER) cc_final: 0.5037 (m-90) REVERT: J 137 LYS cc_start: 0.6895 (pptt) cc_final: 0.6235 (ptpt) REVERT: J 169 GLU cc_start: 0.4831 (tp30) cc_final: 0.4487 (tp30) REVERT: J 170 THR cc_start: 0.7561 (p) cc_final: 0.7292 (t) REVERT: J 181 PHE cc_start: 0.4830 (p90) cc_final: 0.3851 (p90) REVERT: J 213 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: J 243 THR cc_start: 0.5335 (OUTLIER) cc_final: 0.4187 (t) REVERT: J 260 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6391 (mm-30) REVERT: J 261 CYS cc_start: 0.7602 (t) cc_final: 0.7344 (p) REVERT: J 271 LYS cc_start: 0.7212 (tptp) cc_final: 0.6382 (mmmm) REVERT: K 54 LYS cc_start: 0.6650 (ptpt) cc_final: 0.6418 (pttt) REVERT: K 217 HIS cc_start: 0.5316 (OUTLIER) cc_final: 0.4478 (p90) REVERT: K 225 ARG cc_start: 0.6036 (mtp-110) cc_final: 0.5612 (ttp-170) REVERT: K 256 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8071 (mm) REVERT: K 303 MET cc_start: 0.5994 (tmm) cc_final: 0.5473 (tmm) REVERT: K 324 GLU cc_start: 0.5111 (mp0) cc_final: 0.4742 (mp0) REVERT: K 328 TYR cc_start: 0.7179 (m-80) cc_final: 0.6503 (m-10) REVERT: N 130 ASP cc_start: 0.8206 (m-30) cc_final: 0.8000 (m-30) REVERT: N 154 TYR cc_start: 0.7905 (t80) cc_final: 0.7364 (t80) REVERT: N 215 CYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6024 (t) REVERT: N 283 ARG cc_start: 0.4622 (tpp-160) cc_final: 0.3330 (mtp180) REVERT: N 345 MET cc_start: 0.5531 (mmm) cc_final: 0.4982 (ptt) REVERT: N 407 PRO cc_start: 0.6827 (Cg_endo) cc_final: 0.6439 (Cg_exo) REVERT: O 6 TYR cc_start: 0.6660 (t80) cc_final: 0.6234 (t80) REVERT: O 24 ARG cc_start: 0.7303 (mpp80) cc_final: 0.6653 (mtt180) REVERT: O 85 LYS cc_start: 0.8629 (tppt) cc_final: 0.7933 (mtpp) REVERT: O 94 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7487 (mttt) REVERT: O 302 GLN cc_start: 0.6014 (pt0) cc_final: 0.5639 (pt0) REVERT: O 328 TYR cc_start: 0.7734 (m-80) cc_final: 0.7438 (m-10) REVERT: O 390 LYS cc_start: 0.5936 (pptt) cc_final: 0.5445 (mmmt) REVERT: O 406 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6584 (ppp) REVERT: O 497 LYS cc_start: 0.9007 (tptt) cc_final: 0.8704 (tptp) outliers start: 142 outliers final: 96 residues processed: 619 average time/residue: 0.1909 time to fit residues: 189.3678 Evaluate side-chains 591 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 480 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 213 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 431 SER Chi-restraints excluded: chain K residue 435 MET Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 188 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 340 HIS Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 319 optimal weight: 0.0970 chunk 194 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 331 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 HIS F 340 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** 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 = 0.4509 r_free = 0.4509 target = 0.188329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144911 restraints weight = 54202.459| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.97 r_work: 0.3885 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32056 Z= 0.144 Angle : 0.701 14.883 44015 Z= 0.349 Chirality : 0.049 0.365 4828 Planarity : 0.005 0.060 4975 Dihedral : 15.756 87.419 5593 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.34 % Allowed : 30.62 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3303 helix: 0.70 (0.15), residues: 1126 sheet: -1.16 (0.21), residues: 596 loop : -1.48 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 72 TYR 0.018 0.001 TYR O 115 PHE 0.027 0.002 PHE F 158 TRP 0.046 0.002 TRP O 370 HIS 0.011 0.001 HIS K 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (32056) covalent geometry : angle 0.70109 / 0.35 (44015) hydrogen bonds : bond 0.03866 / 2.53 ( 1248) hydrogen bonds : angle 4.97734 / 3.49 ( 3670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 498 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7683 (t0) cc_final: 0.7330 (t0) REVERT: A 71 ARG cc_start: 0.7274 (tpp-160) cc_final: 0.6683 (tpp80) REVERT: A 92 MET cc_start: 0.5992 (tpp) cc_final: 0.5531 (mmt) REVERT: A 100 ASP cc_start: 0.8543 (t70) cc_final: 0.7959 (t0) REVERT: A 149 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8540 (mtmm) REVERT: A 179 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.5730 (tp) REVERT: A 260 GLU cc_start: 0.8588 (tp30) cc_final: 0.8370 (tp30) REVERT: A 262 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 263 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7154 (mtm110) REVERT: A 267 GLN cc_start: 0.7915 (pt0) cc_final: 0.7207 (tp40) REVERT: A 271 LYS cc_start: 0.8668 (tptp) cc_final: 0.8463 (tptp) REVERT: B 74 MET cc_start: 0.6244 (tpp) cc_final: 0.5932 (ttt) REVERT: B 225 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8066 (ttp80) REVERT: B 233 ASP cc_start: 0.7596 (m-30) cc_final: 0.6744 (t0) REVERT: B 283 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7209 (pp) REVERT: B 321 TYR cc_start: 0.7646 (m-80) cc_final: 0.7246 (m-80) REVERT: B 358 PHE cc_start: 0.7895 (t80) cc_final: 0.7641 (t80) REVERT: F 114 ARG cc_start: 0.8427 (mtp85) cc_final: 0.8182 (mtp85) REVERT: F 160 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6620 (p-80) REVERT: F 242 SER cc_start: 0.8970 (t) cc_final: 0.8613 (p) REVERT: F 276 ARG cc_start: 0.7521 (tpt170) cc_final: 0.6621 (mmm160) REVERT: F 295 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7893 (pt) REVERT: F 302 LYS cc_start: 0.8280 (tptm) cc_final: 0.8019 (tmmt) REVERT: F 314 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.4482 (pp30) REVERT: G 3 GLU cc_start: 0.7429 (tp30) cc_final: 0.7041 (tt0) REVERT: G 221 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8705 (t) REVERT: G 231 TRP cc_start: 0.7368 (p-90) cc_final: 0.7150 (p-90) REVERT: G 283 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8224 (pp) REVERT: G 356 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6733 (tm-30) REVERT: G 449 GLU cc_start: 0.6307 (pm20) cc_final: 0.5496 (pp20) REVERT: J 46 TRP cc_start: 0.6219 (OUTLIER) cc_final: 0.4821 (m-90) REVERT: J 137 LYS cc_start: 0.6857 (pptt) cc_final: 0.6265 (ptpt) REVERT: J 160 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.4990 (p-80) REVERT: J 161 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.5311 (p0) REVERT: J 181 PHE cc_start: 0.4783 (p90) cc_final: 0.3828 (p90) REVERT: J 213 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: J 243 THR cc_start: 0.5260 (OUTLIER) cc_final: 0.4011 (t) REVERT: J 260 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6427 (mm-30) REVERT: J 261 CYS cc_start: 0.7588 (t) cc_final: 0.7337 (p) REVERT: J 271 LYS cc_start: 0.7159 (tptp) cc_final: 0.6261 (mmmm) REVERT: J 354 LYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3754 (tptt) REVERT: K 217 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4280 (p90) REVERT: K 225 ARG cc_start: 0.6064 (mtp-110) cc_final: 0.5473 (ttp-170) REVERT: K 303 MET cc_start: 0.5932 (tmm) cc_final: 0.5403 (tmm) REVERT: K 324 GLU cc_start: 0.5061 (mp0) cc_final: 0.4680 (mp0) REVERT: K 328 TYR cc_start: 0.7285 (m-80) cc_final: 0.6776 (m-80) REVERT: N 126 LYS cc_start: 0.7900 (pttt) cc_final: 0.7666 (pttp) REVERT: N 215 CYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5888 (t) REVERT: N 283 ARG cc_start: 0.4325 (tpp-160) cc_final: 0.2912 (ttt180) REVERT: N 345 MET cc_start: 0.5594 (mmm) cc_final: 0.5055 (ptt) REVERT: N 407 PRO cc_start: 0.6710 (Cg_endo) cc_final: 0.6316 (Cg_exo) REVERT: O 6 TYR cc_start: 0.6638 (t80) cc_final: 0.6189 (t80) REVERT: O 24 ARG cc_start: 0.7250 (mpp80) cc_final: 0.6696 (mtt180) REVERT: O 85 LYS cc_start: 0.8532 (tppt) cc_final: 0.7888 (mtpp) REVERT: O 94 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7494 (mttt) REVERT: O 252 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6203 (tp) REVERT: O 328 TYR cc_start: 0.7687 (m-80) cc_final: 0.7484 (m-10) REVERT: O 390 LYS cc_start: 0.5971 (pptt) cc_final: 0.5622 (mmmt) REVERT: O 406 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6557 (ppp) REVERT: O 430 GLN cc_start: 0.8165 (mt0) cc_final: 0.7963 (mm-40) REVERT: O 497 LYS cc_start: 0.9025 (tptt) cc_final: 0.8710 (tptp) outliers start: 130 outliers final: 91 residues processed: 585 average time/residue: 0.2074 time to fit residues: 194.8417 Evaluate side-chains 576 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 467 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 160 HIS Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 213 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 435 MET Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 188 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 252 LEU Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Chi-restraints excluded: chain O residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 334 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 285 optimal weight: 9.9990 chunk 308 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 GLN ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 ASN ** N 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.188436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145021 restraints weight = 54261.806| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.96 r_work: 0.3888 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32056 Z= 0.150 Angle : 0.711 13.984 44015 Z= 0.351 Chirality : 0.049 0.331 4828 Planarity : 0.005 0.066 4975 Dihedral : 15.716 84.530 5593 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.04 % Allowed : 31.12 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3303 helix: 0.75 (0.15), residues: 1128 sheet: -1.15 (0.21), residues: 600 loop : -1.46 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 72 TYR 0.019 0.001 TYR F 285 PHE 0.032 0.002 PHE F 158 TRP 0.030 0.002 TRP O 370 HIS 0.019 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (32056) covalent geometry : angle 0.71143 / 0.35 (44015) hydrogen bonds : bond 0.03837 / 2.51 ( 1248) hydrogen bonds : angle 4.94595 / 3.46 ( 3670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 486 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7661 (t0) cc_final: 0.7349 (t0) REVERT: A 71 ARG cc_start: 0.7254 (tpp-160) cc_final: 0.6691 (tpp80) REVERT: A 92 MET cc_start: 0.5866 (tpp) cc_final: 0.5400 (mmt) REVERT: A 100 ASP cc_start: 0.8541 (t70) cc_final: 0.8020 (t0) REVERT: A 149 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8531 (mtmm) REVERT: A 179 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.5734 (tp) REVERT: A 260 GLU cc_start: 0.8575 (tp30) cc_final: 0.8373 (tp30) REVERT: A 262 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: A 263 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7266 (mtm110) REVERT: A 267 GLN cc_start: 0.7925 (pt0) cc_final: 0.7221 (tp40) REVERT: A 271 LYS cc_start: 0.8640 (tptp) cc_final: 0.8395 (tptp) REVERT: B 74 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5938 (ttt) REVERT: B 225 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8066 (ttp80) REVERT: B 233 ASP cc_start: 0.7589 (m-30) cc_final: 0.6741 (t0) REVERT: B 283 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7334 (pp) REVERT: B 321 TYR cc_start: 0.7645 (m-80) cc_final: 0.7254 (m-80) REVERT: B 358 PHE cc_start: 0.7901 (t80) cc_final: 0.7627 (t80) REVERT: F 114 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8197 (mtp85) REVERT: F 160 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.6650 (p-80) REVERT: F 242 SER cc_start: 0.9028 (t) cc_final: 0.8763 (p) REVERT: F 276 ARG cc_start: 0.7514 (tpt170) cc_final: 0.6615 (mmm160) REVERT: F 295 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7839 (pt) REVERT: F 302 LYS cc_start: 0.8226 (tptm) cc_final: 0.7971 (tmmt) REVERT: F 314 GLN cc_start: 0.5372 (OUTLIER) cc_final: 0.4479 (pp30) REVERT: G 3 GLU cc_start: 0.7430 (tp30) cc_final: 0.7057 (tt0) REVERT: G 113 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.3563 (pmt170) REVERT: G 221 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (t) REVERT: G 231 TRP cc_start: 0.7405 (p-90) cc_final: 0.7192 (p-90) REVERT: G 283 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8317 (pp) REVERT: G 327 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7842 (mm-30) REVERT: G 449 GLU cc_start: 0.6292 (pm20) cc_final: 0.5472 (pp20) REVERT: J 33 TRP cc_start: 0.8356 (t60) cc_final: 0.7949 (t60) REVERT: J 46 TRP cc_start: 0.6211 (OUTLIER) cc_final: 0.4791 (m-90) REVERT: J 137 LYS cc_start: 0.6855 (pptt) cc_final: 0.6254 (ptpt) REVERT: J 160 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.4969 (p-80) REVERT: J 161 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.5307 (p0) REVERT: J 181 PHE cc_start: 0.4629 (p90) cc_final: 0.3874 (p90) REVERT: J 189 ARG cc_start: 0.6032 (ttt-90) cc_final: 0.5416 (ttt-90) REVERT: J 213 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: J 243 THR cc_start: 0.5211 (OUTLIER) cc_final: 0.3978 (t) REVERT: J 260 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6483 (mm-30) REVERT: J 261 CYS cc_start: 0.7586 (t) cc_final: 0.7334 (p) REVERT: J 271 LYS cc_start: 0.7155 (tptp) cc_final: 0.6260 (mmmm) REVERT: J 354 LYS cc_start: 0.4094 (OUTLIER) cc_final: 0.3773 (tptt) REVERT: K 54 LYS cc_start: 0.6690 (pttt) cc_final: 0.6475 (ptpt) REVERT: K 217 HIS cc_start: 0.5207 (OUTLIER) cc_final: 0.4304 (p90) REVERT: K 225 ARG cc_start: 0.6115 (mtp-110) cc_final: 0.5726 (ttp-170) REVERT: K 303 MET cc_start: 0.5986 (tmm) cc_final: 0.5455 (tmm) REVERT: K 324 GLU cc_start: 0.5007 (mp0) cc_final: 0.4610 (mp0) REVERT: K 328 TYR cc_start: 0.7342 (m-80) cc_final: 0.6848 (m-80) REVERT: K 374 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7832 (m110) REVERT: N 126 LYS cc_start: 0.7839 (pttt) cc_final: 0.7629 (pttp) REVERT: N 128 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7642 (tt) REVERT: N 136 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6878 (mt-10) REVERT: N 154 TYR cc_start: 0.7890 (t80) cc_final: 0.7377 (t80) REVERT: N 215 CYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5888 (t) REVERT: N 283 ARG cc_start: 0.4496 (tpp-160) cc_final: 0.3342 (mtp180) REVERT: N 345 MET cc_start: 0.5601 (mmm) cc_final: 0.5039 (ptt) REVERT: N 407 PRO cc_start: 0.6686 (Cg_endo) cc_final: 0.6289 (Cg_exo) REVERT: O 6 TYR cc_start: 0.6643 (t80) cc_final: 0.6141 (t80) REVERT: O 24 ARG cc_start: 0.7232 (mpp80) cc_final: 0.6690 (mtt180) REVERT: O 85 LYS cc_start: 0.8424 (tppt) cc_final: 0.7823 (mtpp) REVERT: O 94 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7514 (mttt) REVERT: O 328 TYR cc_start: 0.7685 (m-80) cc_final: 0.7483 (m-10) REVERT: O 390 LYS cc_start: 0.5993 (pptt) cc_final: 0.5603 (mmmt) REVERT: O 406 MET cc_start: 0.6942 (ppp) cc_final: 0.6716 (ppp) REVERT: O 497 LYS cc_start: 0.9020 (tptt) cc_final: 0.8704 (tptp) outliers start: 121 outliers final: 95 residues processed: 571 average time/residue: 0.2030 time to fit residues: 185.2854 Evaluate side-chains 578 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 463 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 160 HIS Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 213 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 374 ASN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 435 MET Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 188 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 286 GLN Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Chi-restraints excluded: chain O residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 343 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.189340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146377 restraints weight = 54406.905| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.96 r_work: 0.3871 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32056 Z= 0.181 Angle : 0.726 14.036 44015 Z= 0.360 Chirality : 0.049 0.336 4828 Planarity : 0.005 0.052 4975 Dihedral : 15.710 84.351 5593 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.20 % Allowed : 30.95 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3303 helix: 0.70 (0.15), residues: 1128 sheet: -1.13 (0.21), residues: 596 loop : -1.50 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 72 TYR 0.026 0.002 TYR N 285 PHE 0.036 0.002 PHE F 17 TRP 0.080 0.002 TRP F 20 HIS 0.011 0.001 HIS K 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (32056) covalent geometry : angle 0.72567 / 0.36 (44015) hydrogen bonds : bond 0.03956 / 2.58 ( 1248) hydrogen bonds : angle 4.98727 / 3.48 ( 3670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 487 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7650 (t0) cc_final: 0.7389 (t0) REVERT: A 92 MET cc_start: 0.5890 (tpp) cc_final: 0.5475 (mmt) REVERT: A 100 ASP cc_start: 0.8553 (t70) cc_final: 0.8051 (t0) REVERT: A 149 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8443 (mtmm) REVERT: A 179 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.5694 (tp) REVERT: A 260 GLU cc_start: 0.8568 (tp30) cc_final: 0.8357 (tp30) REVERT: A 262 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: A 263 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7160 (mtm110) REVERT: A 267 GLN cc_start: 0.7918 (pt0) cc_final: 0.7210 (tp40) REVERT: A 271 LYS cc_start: 0.8671 (tptp) cc_final: 0.8444 (tptp) REVERT: B 225 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8094 (ttp80) REVERT: B 233 ASP cc_start: 0.7522 (m-30) cc_final: 0.6719 (t0) REVERT: B 283 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7431 (pp) REVERT: B 321 TYR cc_start: 0.7798 (m-80) cc_final: 0.7392 (m-80) REVERT: B 358 PHE cc_start: 0.8012 (t80) cc_final: 0.7726 (t80) REVERT: F 114 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8286 (mtp85) REVERT: F 160 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6876 (p-80) REVERT: F 242 SER cc_start: 0.9072 (t) cc_final: 0.8819 (p) REVERT: F 276 ARG cc_start: 0.7509 (tpt170) cc_final: 0.6619 (mmm160) REVERT: F 295 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7837 (pt) REVERT: F 302 LYS cc_start: 0.8228 (tptm) cc_final: 0.7967 (tmmt) REVERT: F 314 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.4522 (pp30) REVERT: F 336 MET cc_start: 0.8105 (ptp) cc_final: 0.7669 (ptp) REVERT: F 398 GLU cc_start: 0.6377 (pm20) cc_final: 0.6173 (pm20) REVERT: G 3 GLU cc_start: 0.7412 (tp30) cc_final: 0.7040 (tt0) REVERT: G 113 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.3650 (pmt170) REVERT: G 221 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8717 (t) REVERT: G 226 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6350 (mt-10) REVERT: G 231 TRP cc_start: 0.7477 (p-90) cc_final: 0.7218 (p-90) REVERT: G 283 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8362 (pp) REVERT: G 327 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7847 (mm-30) REVERT: G 449 GLU cc_start: 0.6300 (pm20) cc_final: 0.5490 (pp20) REVERT: J 46 TRP cc_start: 0.6308 (OUTLIER) cc_final: 0.4898 (m-90) REVERT: J 137 LYS cc_start: 0.6899 (pptt) cc_final: 0.6291 (ptpt) REVERT: J 160 HIS cc_start: 0.6427 (OUTLIER) cc_final: 0.5001 (p-80) REVERT: J 161 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.5185 (p0) REVERT: J 181 PHE cc_start: 0.4576 (p90) cc_final: 0.3803 (p90) REVERT: J 189 ARG cc_start: 0.6099 (ttt-90) cc_final: 0.5462 (ttt-90) REVERT: J 213 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: J 243 THR cc_start: 0.5235 (OUTLIER) cc_final: 0.4038 (t) REVERT: J 260 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6482 (mm-30) REVERT: J 261 CYS cc_start: 0.7605 (t) cc_final: 0.7340 (p) REVERT: J 323 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6212 (pp) REVERT: J 354 LYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3764 (tptt) REVERT: K 217 HIS cc_start: 0.5252 (OUTLIER) cc_final: 0.4336 (p90) REVERT: K 225 ARG cc_start: 0.6128 (mtp-110) cc_final: 0.5699 (ttp-170) REVERT: K 303 MET cc_start: 0.6035 (tmm) cc_final: 0.5487 (tmm) REVERT: K 324 GLU cc_start: 0.5036 (mp0) cc_final: 0.4627 (mp0) REVERT: K 328 TYR cc_start: 0.7366 (m-80) cc_final: 0.6882 (m-80) REVERT: K 374 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7860 (m110) REVERT: N 119 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7574 (t0) REVERT: N 136 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6913 (mt-10) REVERT: N 154 TYR cc_start: 0.7908 (t80) cc_final: 0.7398 (t80) REVERT: N 215 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.5955 (t) REVERT: N 283 ARG cc_start: 0.4415 (tpp-160) cc_final: 0.3173 (mtp180) REVERT: N 286 GLN cc_start: 0.3769 (OUTLIER) cc_final: 0.3195 (pp30) REVERT: N 345 MET cc_start: 0.5569 (mmm) cc_final: 0.5054 (ptt) REVERT: N 407 PRO cc_start: 0.6718 (Cg_endo) cc_final: 0.6332 (Cg_exo) REVERT: N 411 PHE cc_start: 0.7016 (p90) cc_final: 0.6596 (p90) REVERT: O 6 TYR cc_start: 0.6673 (t80) cc_final: 0.6170 (t80) REVERT: O 24 ARG cc_start: 0.7362 (mpp80) cc_final: 0.6748 (mtt180) REVERT: O 85 LYS cc_start: 0.8460 (tppt) cc_final: 0.7875 (mtpp) REVERT: O 217 HIS cc_start: 0.5252 (OUTLIER) cc_final: 0.4239 (p-80) REVERT: O 390 LYS cc_start: 0.6015 (pptt) cc_final: 0.5629 (mmmt) REVERT: O 406 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6787 (ppp) REVERT: O 497 LYS cc_start: 0.9012 (tptt) cc_final: 0.8709 (tptp) outliers start: 126 outliers final: 95 residues processed: 573 average time/residue: 0.2077 time to fit residues: 190.6537 Evaluate side-chains 589 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 471 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 46 TRP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 160 HIS Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 213 TYR Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 374 ASN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 399 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 435 MET Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 188 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 286 GLN Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Chi-restraints excluded: chain O residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 297 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 310 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 264 optimal weight: 0.0970 chunk 286 optimal weight: 3.9990 chunk 131 optimal weight: 0.0870 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.189521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146535 restraints weight = 54604.183| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.97 r_work: 0.3870 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.407 32056 Z= 0.264 Angle : 0.881 59.200 44015 Z= 0.489 Chirality : 0.049 0.402 4828 Planarity : 0.005 0.082 4975 Dihedral : 15.709 84.367 5593 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.07 % Allowed : 31.12 % Favored : 64.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3303 helix: 0.71 (0.15), residues: 1128 sheet: -1.12 (0.21), residues: 596 loop : -1.50 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 72 TYR 0.037 0.002 TYR B 65 PHE 0.031 0.002 PHE F 17 TRP 0.066 0.002 TRP F 20 HIS 0.011 0.001 HIS K 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.26 (32056) covalent geometry : angle 0.88133 / 0.49 (44015) hydrogen bonds : bond 0.03940 / 2.57 ( 1248) hydrogen bonds : angle 4.98487 / 3.48 ( 3670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9585.08 seconds wall clock time: 164 minutes 49.94 seconds (9889.94 seconds total)