Starting phenix.real_space_refine on Mon Aug 25 22:08:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifl_35420/08_2025/8ifl_35420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifl_35420/08_2025/8ifl_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2025/8ifl_35420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2025/8ifl_35420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2025/8ifl_35420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifl_35420/08_2025/8ifl_35420.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 6.93, per 1000 atoms: 0.22 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: 2.56 Conformation dependent library (CDL) restraints added in 972.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.14 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: 6.81 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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 - 18.90: 15527 18.90 - 37.80: 2490 37.80 - 56.71: 778 56.71 - 75.61: 182 75.61 - 94.51: 38 Dihedral angle restraints: 19015 sinusoidal: 9154 harmonic: 9861 Sorted by residual: dihedral pdb=" CA PHE F 135 " pdb=" C PHE F 135 " pdb=" N GLU F 136 " pdb=" CA GLU F 136 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" N PRO N 177 " pdb=" CG PRO N 177 " pdb=" CD PRO N 177 " pdb=" CB PRO N 177 " ideal model delta sinusoidal sigma weight residual -30.00 -89.78 59.78 1 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" CA PRO N 177 " pdb=" CB PRO N 177 " pdb=" CG PRO N 177 " pdb=" CD PRO N 177 " ideal model delta sinusoidal sigma weight residual -38.00 -121.14 83.14 1 2.00e+01 2.50e-03 2.11e+01 ... (remaining 19012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4101 0.059 - 0.119: 649 0.119 - 0.178: 70 0.178 - 0.238: 5 0.238 - 0.297: 3 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=" CB ILE O 486 " pdb=" CA ILE O 486 " pdb=" CG1 ILE O 486 " pdb=" CG2 ILE O 486 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU K 50 " pdb=" CB LEU K 50 " pdb=" CD1 LEU K 50 " pdb=" CD2 LEU K 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.62e+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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 30.040 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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= 0.267 Angle : 0.841 73.719 44015 Z= 0.439 Chirality : 0.044 0.297 4828 Planarity : 0.006 0.138 4975 Dihedral : 19.935 94.510 12635 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 aren 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 covalent geometry : bond 0.00828 (32056) covalent geometry : angle 0.84069 (44015) hydrogen bonds : bond 0.13930 ( 1248) hydrogen bonds : angle 6.82877 ( 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 : 0.932 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: 0.5160 (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: 0.2097 time to fit residues: 255.7909 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 : 0.797 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 349 GLN ** 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 446 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 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 = 0.4564 r_free = 0.4564 target = 0.193823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.150843 restraints weight = 54687.937| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.01 r_work: 0.3916 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32056 Z= 0.154 Angle : 0.652 12.304 44015 Z= 0.338 Chirality : 0.044 0.289 4828 Planarity : 0.005 0.067 4975 Dihedral : 16.270 93.567 5696 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 4.24 % Allowed : 28.45 % Favored : 67.31 % 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 aren not related in a simple way. whole: -0.66 (0.14), residues: 3303 helix: 0.84 (0.15), residues: 1126 sheet: -0.61 (0.21), residues: 570 loop : -1.30 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 283 TYR 0.021 0.001 TYR F 330 PHE 0.037 0.002 PHE A 343 TRP 0.030 0.002 TRP J 319 HIS 0.014 0.001 HIS J 340 Details of bonding type rmsd covalent geometry : bond 0.00351 (32056) covalent geometry : angle 0.65181 (44015) hydrogen bonds : bond 0.04210 ( 1248) hydrogen bonds : angle 5.23796 ( 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 713 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 586 time to evaluate : 1.146 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: 0.7470 (t0) cc_final: 0.7139 (t0) REVERT: A 92 MET cc_start: 0.6007 (tpp) cc_final: 0.5604 (mmt) REVERT: A 100 ASP cc_start: 0.8522 (t70) cc_final: 0.7943 (t0) REVERT: A 262 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: A 271 LYS cc_start: 0.8273 (tppt) cc_final: 0.7615 (mttp) REVERT: A 289 LYS cc_start: 0.8152 (tptt) cc_final: 0.7395 (mtpt) REVERT: A 323 ILE cc_start: 0.7838 (pt) cc_final: 0.7390 (pt) REVERT: B 225 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.7961 (ttp80) REVERT: B 233 ASP cc_start: 0.7270 (m-30) cc_final: 0.6407 (t0) REVERT: B 354 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8338 (Cg_exo) REVERT: B 358 PHE cc_start: 0.7916 (t80) cc_final: 0.7644 (t80) REVERT: B 397 TYR cc_start: 0.7777 (m-80) cc_final: 0.7515 (m-10) REVERT: F 80 VAL cc_start: 0.8911 (p) cc_final: 0.8706 (m) REVERT: F 114 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8402 (mtp85) REVERT: F 165 ILE cc_start: 0.6567 (pt) cc_final: 0.6264 (pt) REVERT: F 242 SER cc_start: 0.8951 (t) cc_final: 0.8607 (p) REVERT: F 276 ARG cc_start: 0.7221 (tpt170) cc_final: 0.6741 (mmm160) REVERT: F 414 MET cc_start: 0.7175 (tpp) cc_final: 0.6882 (tpp) REVERT: G 231 TRP cc_start: 0.7415 (p-90) cc_final: 0.7115 (p-90) REVERT: G 449 GLU cc_start: 0.6500 (pm20) cc_final: 0.5623 (pp20) REVERT: G 458 ASP cc_start: 0.6795 (m-30) cc_final: 0.6336 (m-30) REVERT: J 33 TRP cc_start: 0.8322 (t60) cc_final: 0.7835 (t60) REVERT: J 69 ASN cc_start: 0.7562 (m-40) cc_final: 0.7326 (m-40) REVERT: J 133 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: J 160 HIS cc_start: 0.5931 (p-80) cc_final: 0.5386 (p-80) REVERT: J 170 THR cc_start: 0.7752 (m) cc_final: 0.7419 (p) REVERT: J 181 PHE cc_start: 0.4414 (p90) cc_final: 0.2241 (p90) REVERT: J 243 THR cc_start: 0.5241 (OUTLIER) cc_final: 0.3767 (t) REVERT: J 260 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6324 (mm-30) REVERT: J 323 ILE cc_start: 0.6426 (pp) cc_final: 0.5995 (pp) REVERT: J 377 LEU cc_start: 0.1630 (OUTLIER) cc_final: 0.1429 (tp) REVERT: K 79 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: K 217 HIS cc_start: 0.5110 (OUTLIER) cc_final: 0.4364 (p90) REVERT: K 324 GLU cc_start: 0.4108 (mp0) cc_final: 0.3882 (mp0) REVERT: N 19 ARG cc_start: 0.7383 (ptp90) cc_final: 0.7116 (ptp90) REVERT: N 126 LYS cc_start: 0.8100 (pttt) cc_final: 0.7885 (pttt) REVERT: N 169 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6280 (tt0) REVERT: N 345 MET cc_start: 0.5071 (mmm) cc_final: 0.4488 (ptt) REVERT: N 406 LYS cc_start: 0.6118 (mmtt) cc_final: 0.5798 (mmtm) REVERT: O 24 ARG cc_start: 0.7184 (mpp80) cc_final: 0.6559 (mtt180) REVERT: O 68 ASN cc_start: 0.7200 (OUTLIER) cc_final: 0.6915 (t0) REVERT: O 85 LYS cc_start: 0.8467 (tppt) cc_final: 0.7992 (mtpp) REVERT: O 94 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7364 (mmmt) REVERT: O 95 GLU cc_start: 0.7899 (pp20) cc_final: 0.7599 (pp20) REVERT: O 210 LEU cc_start: 0.8388 (tt) cc_final: 0.7675 (mt) REVERT: O 298 CYS cc_start: 0.7497 (p) cc_final: 0.7295 (p) REVERT: O 390 LYS cc_start: 0.5352 (pptt) cc_final: 0.4879 (mmmt) REVERT: O 406 MET cc_start: 0.7285 (ppp) cc_final: 0.6734 (ppp) REVERT: O 434 SER cc_start: 0.7333 (p) cc_final: 0.7103 (t) REVERT: O 497 LYS cc_start: 0.8855 (tptt) cc_final: 0.8642 (tptp) outliers start: 127 outliers final: 65 residues processed: 671 average time/residue: 0.2000 time to fit residues: 212.6441 Evaluate side-chains 578 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 506 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 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 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 295 ILE 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 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 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 377 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 120 LEU 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 112 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 210 TYR 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 68 ASN 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 317 VAL Chi-restraints excluded: chain O residue 405 ILE 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: 0.9980 chunk 275 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 F 156 GLN G 329 HIS ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS K 380 ASN N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 HIS N 188 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.190273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146749 restraints weight = 54774.769| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.00 r_work: 0.3862 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32056 Z= 0.192 Angle : 0.651 13.046 44015 Z= 0.337 Chirality : 0.044 0.222 4828 Planarity : 0.005 0.055 4975 Dihedral : 16.274 94.813 5692 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.47 % Allowed : 27.92 % Favored : 66.61 % 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 aren not related in a simple way. whole: -0.79 (0.14), residues: 3303 helix: 0.82 (0.15), residues: 1114 sheet: -0.86 (0.21), residues: 595 loop : -1.35 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 114 TYR 0.021 0.002 TYR F 330 PHE 0.019 0.002 PHE F 135 TRP 0.025 0.002 TRP O 231 HIS 0.013 0.001 HIS J 340 Details of bonding type rmsd covalent geometry : bond 0.00437 (32056) covalent geometry : angle 0.65135 (44015) hydrogen bonds : bond 0.04106 ( 1248) hydrogen bonds : angle 5.06777 ( 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 709 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 545 time to evaluate : 1.064 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 92 MET cc_start: 0.6024 (tpp) cc_final: 0.5586 (mmt) REVERT: A 100 ASP cc_start: 0.8618 (t70) cc_final: 0.8132 (t0) REVERT: A 149 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8650 (mtmm) REVERT: A 179 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.5770 (tp) REVERT: A 262 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: A 271 LYS cc_start: 0.8360 (tppt) cc_final: 0.7655 (mttp) REVERT: A 289 LYS cc_start: 0.8145 (tptt) cc_final: 0.7444 (mtpt) REVERT: B 216 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 225 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.8085 (ttp80) REVERT: B 233 ASP cc_start: 0.7572 (m-30) cc_final: 0.6721 (t0) REVERT: B 321 TYR cc_start: 0.7494 (m-80) cc_final: 0.7068 (m-80) REVERT: B 358 PHE cc_start: 0.8038 (t80) cc_final: 0.7768 (t80) REVERT: F 15 ASP cc_start: 0.5079 (OUTLIER) cc_final: 0.4857 (m-30) REVERT: F 114 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8343 (mtp85) REVERT: F 242 SER cc_start: 0.8954 (t) cc_final: 0.8610 (p) REVERT: F 295 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (pt) REVERT: F 314 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4456 (pp30) REVERT: F 330 TYR cc_start: 0.5401 (t80) cc_final: 0.5174 (t80) REVERT: G 137 ASP cc_start: 0.7714 (m-30) cc_final: 0.7411 (m-30) REVERT: G 221 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8733 (t) REVERT: G 285 TYR cc_start: 0.8551 (m-80) cc_final: 0.8206 (m-80) REVERT: G 449 GLU cc_start: 0.6455 (pm20) cc_final: 0.5466 (pp20) REVERT: G 458 ASP cc_start: 0.6896 (m-30) cc_final: 0.6376 (m-30) REVERT: J 33 TRP cc_start: 0.8373 (t60) cc_final: 0.7877 (t60) REVERT: J 46 TRP cc_start: 0.6051 (OUTLIER) cc_final: 0.4636 (m-90) REVERT: J 69 ASN cc_start: 0.7590 (m-40) cc_final: 0.7347 (m-40) REVERT: J 133 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: J 161 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.5250 (p0) REVERT: J 170 THR cc_start: 0.7876 (m) cc_final: 0.7622 (p) REVERT: J 181 PHE cc_start: 0.4738 (p90) cc_final: 0.3242 (p90) REVERT: J 243 THR cc_start: 0.5293 (OUTLIER) cc_final: 0.4043 (t) REVERT: J 260 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6298 (mm-30) REVERT: J 271 LYS cc_start: 0.7322 (tptp) cc_final: 0.6390 (mmmm) REVERT: J 354 LYS cc_start: 0.4143 (OUTLIER) cc_final: 0.3710 (tptt) REVERT: J 372 LYS cc_start: 0.5829 (ttmt) cc_final: 0.5583 (mptt) REVERT: J 377 LEU cc_start: 0.1854 (OUTLIER) cc_final: 0.1629 (tp) REVERT: K 324 GLU cc_start: 0.4361 (mp0) cc_final: 0.4032 (mp0) REVERT: N 28 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8114 (mm) REVERT: N 162 LYS cc_start: 0.7801 (mttp) cc_final: 0.7532 (mttp) REVERT: N 283 ARG cc_start: 0.3820 (tpp-160) cc_final: 0.3203 (tpp-160) REVERT: N 345 MET cc_start: 0.5431 (mmm) cc_final: 0.4879 (ptt) REVERT: N 382 ARG cc_start: 0.2618 (mmt-90) cc_final: 0.2393 (tpp80) REVERT: N 407 PRO cc_start: 0.6831 (Cg_endo) cc_final: 0.6482 (Cg_exo) REVERT: N 414 MET cc_start: 0.5757 (mmt) cc_final: 0.5351 (mmm) REVERT: O 6 TYR cc_start: 0.7156 (t80) cc_final: 0.6477 (t80) REVERT: O 24 ARG cc_start: 0.7357 (mpp80) cc_final: 0.6720 (mtt180) REVERT: O 85 LYS cc_start: 0.8638 (tppt) cc_final: 0.8021 (mtpp) REVERT: O 210 LEU cc_start: 0.8402 (tt) cc_final: 0.7673 (mt) REVERT: O 390 LYS cc_start: 0.5428 (pptt) cc_final: 0.5080 (mmmt) REVERT: O 434 SER cc_start: 0.7635 (p) cc_final: 0.7279 (t) REVERT: O 497 LYS cc_start: 0.8976 (tptt) cc_final: 0.8648 (tptp) outliers start: 164 outliers final: 99 residues processed: 658 average time/residue: 0.2042 time to fit residues: 214.5231 Evaluate side-chains 615 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 503 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 143 VAL 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 330 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 498 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 47 SER 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 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 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 12 ILE 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 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 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 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 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 270 ASN 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 377 LEU Chi-restraints excluded: chain K residue 1 MET 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 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 478 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 147 HIS Chi-restraints excluded: chain N residue 210 TYR 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 138 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 233 ASP 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 367 ASP 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: 0.3980 chunk 174 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 312 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 314 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 F 147 HIS ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS ** K 430 GLN ** 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 90 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.191323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.147951 restraints weight = 53887.302| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.96 r_work: 0.3919 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32056 Z= 0.127 Angle : 0.605 12.546 44015 Z= 0.312 Chirality : 0.043 0.279 4828 Planarity : 0.004 0.054 4975 Dihedral : 16.178 94.276 5689 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.14 % Allowed : 29.32 % Favored : 66.54 % 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 aren not related in a simple way. whole: -0.66 (0.14), residues: 3303 helix: 0.99 (0.15), residues: 1126 sheet: -0.80 (0.21), residues: 587 loop : -1.34 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 225 TYR 0.025 0.001 TYR F 285 PHE 0.033 0.002 PHE F 17 TRP 0.026 0.001 TRP O 370 HIS 0.021 0.001 HIS N 147 Details of bonding type rmsd covalent geometry : bond 0.00289 (32056) covalent geometry : angle 0.60454 (44015) hydrogen bonds : bond 0.03643 ( 1248) hydrogen bonds : angle 4.85877 ( 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 672 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 548 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7694 (t0) cc_final: 0.7151 (t0) REVERT: A 71 ARG cc_start: 0.7351 (tpp-160) cc_final: 0.6955 (ttm110) REVERT: A 92 MET cc_start: 0.6069 (tpp) cc_final: 0.5616 (mmt) REVERT: A 100 ASP cc_start: 0.8579 (t70) cc_final: 0.8043 (t0) REVERT: A 179 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.5928 (tp) REVERT: A 262 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: A 271 LYS cc_start: 0.8332 (tppt) cc_final: 0.7636 (mttp) REVERT: A 291 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7505 (t80) REVERT: A 414 MET cc_start: 0.8172 (mmm) cc_final: 0.7603 (mmm) REVERT: B 217 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6842 (p-80) REVERT: B 225 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8064 (ttp80) REVERT: B 233 ASP cc_start: 0.7411 (m-30) cc_final: 0.6545 (t0) REVERT: B 321 TYR cc_start: 0.7415 (m-80) cc_final: 0.7047 (m-80) REVERT: B 354 PRO cc_start: 0.8644 (Cg_endo) cc_final: 0.8416 (Cg_exo) REVERT: B 358 PHE cc_start: 0.7889 (t80) cc_final: 0.7642 (t80) REVERT: B 397 TYR cc_start: 0.7977 (m-80) cc_final: 0.7775 (m-80) REVERT: B 504 LYS cc_start: 0.7412 (ptmt) cc_final: 0.7131 (pttt) REVERT: F 15 ASP cc_start: 0.5184 (OUTLIER) cc_final: 0.4941 (m-30) REVERT: F 160 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6626 (p-80) REVERT: F 242 SER cc_start: 0.8953 (t) cc_final: 0.8632 (p) REVERT: F 276 ARG cc_start: 0.7268 (tpt170) cc_final: 0.6642 (mmm160) REVERT: F 295 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7788 (pt) REVERT: F 314 GLN cc_start: 0.4993 (OUTLIER) cc_final: 0.4549 (pp30) REVERT: F 414 MET cc_start: 0.7136 (mmm) cc_final: 0.6915 (mmt) REVERT: G 231 TRP cc_start: 0.7331 (p-90) cc_final: 0.7098 (p-90) REVERT: G 449 GLU cc_start: 0.6399 (pm20) cc_final: 0.5376 (pp20) REVERT: G 458 ASP cc_start: 0.6793 (m-30) cc_final: 0.6371 (m-30) REVERT: J 33 TRP cc_start: 0.8268 (t60) cc_final: 0.7885 (t60) REVERT: J 133 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: J 137 LYS cc_start: 0.6797 (pptt) cc_final: 0.6106 (ptpt) REVERT: J 151 ASN cc_start: 0.7542 (m-40) cc_final: 0.7017 (p0) REVERT: J 161 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.5175 (p0) REVERT: J 170 THR cc_start: 0.7809 (m) cc_final: 0.7588 (p) REVERT: J 181 PHE cc_start: 0.4723 (p90) cc_final: 0.3608 (p90) REVERT: J 243 THR cc_start: 0.5045 (OUTLIER) cc_final: 0.3542 (t) REVERT: J 260 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6342 (mm-30) REVERT: J 323 ILE cc_start: 0.6450 (pp) cc_final: 0.6235 (pp) REVERT: J 377 LEU cc_start: 0.1888 (OUTLIER) cc_final: 0.1586 (tp) REVERT: K 217 HIS cc_start: 0.4837 (OUTLIER) cc_final: 0.3760 (p90) REVERT: K 286 LYS cc_start: 0.8391 (mmpt) cc_final: 0.8008 (mmmt) REVERT: K 324 GLU cc_start: 0.4358 (mp0) cc_final: 0.4010 (mp0) REVERT: K 328 TYR cc_start: 0.7058 (m-80) cc_final: 0.6402 (m-80) REVERT: K 369 GLU cc_start: 0.7296 (pt0) cc_final: 0.6607 (pp20) REVERT: K 406 MET cc_start: 0.6450 (ttp) cc_final: 0.6221 (ttp) REVERT: K 467 TYR cc_start: 0.8222 (m-80) cc_final: 0.7740 (m-80) REVERT: N 19 ARG cc_start: 0.7393 (ptp90) cc_final: 0.7130 (ptp90) REVERT: N 28 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8219 (mm) REVERT: N 126 LYS cc_start: 0.7784 (pttt) cc_final: 0.7518 (pttp) REVERT: N 162 LYS cc_start: 0.7667 (mttp) cc_final: 0.7299 (mtmm) REVERT: N 215 CYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5726 (t) REVERT: N 345 MET cc_start: 0.5460 (mmm) cc_final: 0.4967 (ptt) REVERT: N 407 PRO cc_start: 0.6663 (Cg_endo) cc_final: 0.6305 (Cg_exo) REVERT: N 414 MET cc_start: 0.5814 (mmt) cc_final: 0.5466 (mmm) REVERT: O 24 ARG cc_start: 0.7042 (mpp80) cc_final: 0.6519 (mtt180) REVERT: O 85 LYS cc_start: 0.8590 (tppt) cc_final: 0.7961 (mtpp) REVERT: O 210 LEU cc_start: 0.8339 (tt) cc_final: 0.7711 (mt) REVERT: O 225 ARG cc_start: 0.5769 (mtm180) cc_final: 0.5527 (mtm180) REVERT: O 390 LYS cc_start: 0.5658 (pptt) cc_final: 0.5313 (mmmt) REVERT: O 406 MET cc_start: 0.7201 (ppp) cc_final: 0.6928 (ppp) REVERT: O 497 LYS cc_start: 0.8950 (tptt) cc_final: 0.8616 (tptp) outliers start: 124 outliers final: 79 residues processed: 631 average time/residue: 0.1837 time to fit residues: 184.7676 Evaluate side-chains 589 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 495 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 282 VAL Chi-restraints excluded: chain A residue 291 PHE 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 217 HIS 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 399 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 498 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 47 SER 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 160 HIS Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 296 GLU 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 12 ILE Chi-restraints excluded: chain G residue 66 ASN 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 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 103 LEU 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 179 ILE 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 377 LEU Chi-restraints excluded: chain J residue 392 TYR 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 120 LEU Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 340 HIS Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 12 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 138 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 233 ASP 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 383 LEU 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: 6.9990 chunk 273 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 313 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS G 349 GLN J 267 GLN ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.189129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145565 restraints weight = 54196.618| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.95 r_work: 0.3889 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32056 Z= 0.156 Angle : 0.616 13.128 44015 Z= 0.319 Chirality : 0.043 0.313 4828 Planarity : 0.004 0.046 4975 Dihedral : 16.135 94.707 5689 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.07 % Allowed : 28.75 % Favored : 66.18 % 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 aren not related in a simple way. whole: -0.68 (0.14), residues: 3303 helix: 0.99 (0.15), residues: 1126 sheet: -0.79 (0.21), residues: 603 loop : -1.38 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 481 TYR 0.026 0.001 TYR N 285 PHE 0.036 0.002 PHE B 238 TRP 0.026 0.002 TRP O 231 HIS 0.009 0.001 HIS J 340 Details of bonding type rmsd covalent geometry : bond 0.00357 (32056) covalent geometry : angle 0.61554 (44015) hydrogen bonds : bond 0.03680 ( 1248) hydrogen bonds : angle 4.82351 ( 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 673 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 521 time to evaluate : 1.146 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: 0.7676 (t0) cc_final: 0.7090 (t0) REVERT: A 71 ARG cc_start: 0.7260 (tpp-160) cc_final: 0.6955 (ttm110) REVERT: A 92 MET cc_start: 0.6084 (tpp) cc_final: 0.5586 (mmt) REVERT: A 100 ASP cc_start: 0.8593 (t70) cc_final: 0.8086 (t0) REVERT: A 179 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.5965 (tp) REVERT: A 262 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: A 271 LYS cc_start: 0.8415 (tppt) cc_final: 0.7658 (mttp) REVERT: A 291 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7616 (t80) REVERT: B 217 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6898 (p-80) REVERT: B 225 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.8032 (ttp80) REVERT: B 233 ASP cc_start: 0.7482 (m-30) cc_final: 0.6667 (t0) REVERT: B 321 TYR cc_start: 0.7548 (m-80) cc_final: 0.7186 (m-80) REVERT: B 358 PHE cc_start: 0.8021 (t80) cc_final: 0.7738 (t80) REVERT: B 504 LYS cc_start: 0.7525 (ptmt) cc_final: 0.7164 (pttt) REVERT: F 15 ASP cc_start: 0.5048 (OUTLIER) cc_final: 0.4807 (m-30) REVERT: F 160 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.6685 (p-80) REVERT: F 242 SER cc_start: 0.9037 (t) cc_final: 0.8728 (p) REVERT: F 276 ARG cc_start: 0.7339 (tpt170) cc_final: 0.6723 (mmm160) REVERT: F 295 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7851 (pt) REVERT: F 314 GLN cc_start: 0.5059 (OUTLIER) cc_final: 0.4395 (pp30) REVERT: G 3 GLU cc_start: 0.7148 (tp30) cc_final: 0.6599 (tt0) REVERT: G 137 ASP cc_start: 0.7784 (m-30) cc_final: 0.7411 (m-30) REVERT: G 231 TRP cc_start: 0.7445 (p-90) cc_final: 0.7184 (p-90) REVERT: G 349 GLN cc_start: 0.5942 (OUTLIER) cc_final: 0.5726 (mt0) REVERT: G 449 GLU cc_start: 0.6320 (pm20) cc_final: 0.5310 (pp20) REVERT: J 33 TRP cc_start: 0.8378 (t60) cc_final: 0.7958 (t60) REVERT: J 46 TRP cc_start: 0.6169 (OUTLIER) cc_final: 0.4619 (m-90) REVERT: J 137 LYS cc_start: 0.6804 (pptt) cc_final: 0.6153 (ptpt) REVERT: J 151 ASN cc_start: 0.7538 (m-40) cc_final: 0.7019 (p0) REVERT: J 161 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.5232 (p0) REVERT: J 181 PHE cc_start: 0.4760 (p90) cc_final: 0.3897 (p90) REVERT: J 213 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: J 243 THR cc_start: 0.5176 (OUTLIER) cc_final: 0.3855 (t) REVERT: J 260 GLU cc_start: 0.6641 (tm-30) cc_final: 0.6423 (mm-30) REVERT: J 323 ILE cc_start: 0.6536 (pp) cc_final: 0.6310 (pp) REVERT: J 354 LYS cc_start: 0.3987 (OUTLIER) cc_final: 0.3702 (tptt) REVERT: J 377 LEU cc_start: 0.2119 (OUTLIER) cc_final: 0.1767 (tp) REVERT: K 217 HIS cc_start: 0.4923 (OUTLIER) cc_final: 0.3823 (p90) REVERT: K 285 TYR cc_start: 0.6014 (m-10) cc_final: 0.5741 (m-10) REVERT: K 286 LYS cc_start: 0.8457 (mmpt) cc_final: 0.8117 (mmmt) REVERT: K 324 GLU cc_start: 0.4848 (mp0) cc_final: 0.4462 (mp0) REVERT: K 328 TYR cc_start: 0.7166 (m-80) cc_final: 0.6548 (m-80) REVERT: K 369 GLU cc_start: 0.7310 (pt0) cc_final: 0.6627 (pp20) REVERT: K 370 TRP cc_start: 0.6601 (t60) cc_final: 0.6174 (t60) REVERT: K 467 TYR cc_start: 0.8266 (m-80) cc_final: 0.7990 (m-80) REVERT: K 470 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7668 (m) REVERT: N 19 ARG cc_start: 0.7369 (ptp90) cc_final: 0.7116 (ptp90) REVERT: N 28 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8166 (mm) REVERT: N 126 LYS cc_start: 0.7749 (pttt) cc_final: 0.7523 (pttp) REVERT: N 128 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7636 (tt) REVERT: N 162 LYS cc_start: 0.7844 (mttp) cc_final: 0.7481 (mtmm) REVERT: N 215 CYS cc_start: 0.6402 (OUTLIER) cc_final: 0.5806 (t) REVERT: N 283 ARG cc_start: 0.3836 (tpp-160) cc_final: 0.3209 (tpp-160) REVERT: N 345 MET cc_start: 0.5572 (mmm) cc_final: 0.4878 (ptp) REVERT: N 407 PRO cc_start: 0.6770 (Cg_endo) cc_final: 0.6415 (Cg_exo) REVERT: N 414 MET cc_start: 0.5835 (mmt) cc_final: 0.5486 (mmm) REVERT: O 24 ARG cc_start: 0.7075 (mpp80) cc_final: 0.6579 (mtt180) REVERT: O 85 LYS cc_start: 0.8639 (tppt) cc_final: 0.7962 (mtpp) REVERT: O 94 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7569 (mttt) REVERT: O 210 LEU cc_start: 0.8343 (tt) cc_final: 0.7677 (mt) REVERT: O 217 HIS cc_start: 0.4314 (OUTLIER) cc_final: 0.3135 (p-80) REVERT: O 347 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7839 (tmmt) REVERT: O 390 LYS cc_start: 0.5724 (pptt) cc_final: 0.5417 (mmmt) REVERT: O 497 LYS cc_start: 0.8987 (tptt) cc_final: 0.8645 (tptp) outliers start: 152 outliers final: 103 residues processed: 629 average time/residue: 0.1910 time to fit residues: 191.8498 Evaluate side-chains 606 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 481 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 356 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 LEU 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 217 HIS 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 399 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 498 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 47 SER 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 160 HIS Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 296 GLU 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 12 ILE 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 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 349 GLN 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 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 161 ASP 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 329 LEU 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 377 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 39 ILE 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 283 LEU Chi-restraints excluded: chain K residue 383 LEU 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 470 CYS 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 99 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 107 ASP 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 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 393 LEU 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 138 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 208 ASP 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 347 LYS 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 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU 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: 0.0670 chunk 236 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 238 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 HIS N 281 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.190230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146792 restraints weight = 54180.066| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.96 r_work: 0.3909 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32056 Z= 0.136 Angle : 0.604 12.909 44015 Z= 0.311 Chirality : 0.043 0.232 4828 Planarity : 0.004 0.044 4975 Dihedral : 16.105 94.323 5689 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.00 % Allowed : 29.39 % Favored : 65.61 % 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 aren not related in a simple way. whole: -0.62 (0.14), residues: 3303 helix: 1.09 (0.15), residues: 1126 sheet: -0.79 (0.21), residues: 599 loop : -1.37 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 114 TYR 0.023 0.001 TYR N 285 PHE 0.028 0.002 PHE K 206 TRP 0.026 0.001 TRP O 231 HIS 0.007 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00311 (32056) covalent geometry : angle 0.60384 (44015) hydrogen bonds : bond 0.03590 ( 1248) hydrogen bonds : angle 4.72753 ( 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 658 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 508 time to evaluate : 1.092 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: 0.7591 (t0) cc_final: 0.7124 (t0) REVERT: A 71 ARG cc_start: 0.7215 (tpp-160) cc_final: 0.6932 (ttm110) REVERT: A 92 MET cc_start: 0.5924 (tpp) cc_final: 0.5475 (mmt) REVERT: A 100 ASP cc_start: 0.8565 (t70) cc_final: 0.8040 (t0) REVERT: A 179 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.5858 (tp) REVERT: A 262 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: A 271 LYS cc_start: 0.8411 (tppt) cc_final: 0.7652 (mttp) REVERT: A 291 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 217 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6787 (p-80) REVERT: B 225 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.8033 (ttp80) REVERT: B 233 ASP cc_start: 0.7434 (m-30) cc_final: 0.6637 (t0) REVERT: B 321 TYR cc_start: 0.7628 (m-80) cc_final: 0.7265 (m-80) REVERT: B 358 PHE cc_start: 0.7992 (t80) cc_final: 0.7719 (t80) REVERT: F 15 ASP cc_start: 0.5031 (OUTLIER) cc_final: 0.4787 (m-30) REVERT: F 160 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6705 (p-80) REVERT: F 242 SER cc_start: 0.9038 (t) cc_final: 0.8748 (p) REVERT: F 276 ARG cc_start: 0.7422 (tpt170) cc_final: 0.6794 (mmm160) REVERT: F 295 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7831 (pt) REVERT: F 314 GLN cc_start: 0.5043 (OUTLIER) cc_final: 0.4609 (pp30) REVERT: G 3 GLU cc_start: 0.7184 (tp30) cc_final: 0.6656 (tt0) REVERT: G 137 ASP cc_start: 0.7739 (m-30) cc_final: 0.7412 (m-30) REVERT: G 221 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8718 (t) REVERT: G 349 GLN cc_start: 0.6101 (mt0) cc_final: 0.5383 (tp40) REVERT: G 449 GLU cc_start: 0.6259 (pm20) cc_final: 0.5423 (pp20) REVERT: J 33 TRP cc_start: 0.8347 (t60) cc_final: 0.7949 (t60) REVERT: J 46 TRP cc_start: 0.6184 (OUTLIER) cc_final: 0.4742 (m-10) REVERT: J 137 LYS cc_start: 0.6831 (pptt) cc_final: 0.6189 (ptpt) REVERT: J 151 ASN cc_start: 0.7495 (m-40) cc_final: 0.6992 (p0) REVERT: J 160 HIS cc_start: 0.6348 (OUTLIER) cc_final: 0.4856 (p-80) REVERT: J 161 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.5150 (p0) REVERT: J 181 PHE cc_start: 0.4560 (p90) cc_final: 0.3960 (p90) REVERT: J 213 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: J 243 THR cc_start: 0.5181 (OUTLIER) cc_final: 0.4108 (t) REVERT: J 271 LYS cc_start: 0.7226 (tptp) cc_final: 0.7011 (tptp) REVERT: J 354 LYS cc_start: 0.3962 (OUTLIER) cc_final: 0.3684 (tptt) REVERT: J 377 LEU cc_start: 0.2120 (OUTLIER) cc_final: 0.1754 (tp) REVERT: K 57 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6031 (tp) REVERT: K 217 HIS cc_start: 0.4981 (OUTLIER) cc_final: 0.3981 (p90) REVERT: K 271 LEU cc_start: 0.5944 (pp) cc_final: 0.5327 (tp) REVERT: K 286 LYS cc_start: 0.8431 (mmpt) cc_final: 0.8163 (mmmt) REVERT: K 324 GLU cc_start: 0.4819 (mp0) cc_final: 0.4414 (mp0) REVERT: K 328 TYR cc_start: 0.7164 (m-80) cc_final: 0.6584 (m-80) REVERT: K 406 MET cc_start: 0.6720 (ttp) cc_final: 0.6281 (ttp) REVERT: K 467 TYR cc_start: 0.8247 (m-80) cc_final: 0.8021 (m-80) REVERT: K 470 CYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7722 (m) REVERT: N 14 ASP cc_start: 0.7543 (m-30) cc_final: 0.7287 (m-30) REVERT: N 19 ARG cc_start: 0.7244 (ptp90) cc_final: 0.6989 (ptp90) REVERT: N 126 LYS cc_start: 0.7717 (pttt) cc_final: 0.7496 (pttm) REVERT: N 162 LYS cc_start: 0.7939 (mttp) cc_final: 0.7388 (mtmm) REVERT: N 215 CYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5850 (t) REVERT: N 345 MET cc_start: 0.5470 (mmm) cc_final: 0.4898 (ptp) REVERT: N 407 PRO cc_start: 0.6565 (Cg_endo) cc_final: 0.6235 (Cg_exo) REVERT: N 414 MET cc_start: 0.5835 (mmt) cc_final: 0.5461 (mmm) REVERT: O 24 ARG cc_start: 0.7093 (mpp80) cc_final: 0.6714 (mtt180) REVERT: O 85 LYS cc_start: 0.8581 (tppt) cc_final: 0.7990 (mtpp) REVERT: O 95 GLU cc_start: 0.7956 (pp20) cc_final: 0.7737 (pp20) REVERT: O 210 LEU cc_start: 0.8307 (tt) cc_final: 0.7672 (mt) REVERT: O 217 HIS cc_start: 0.4290 (OUTLIER) cc_final: 0.2986 (p-80) REVERT: O 225 ARG cc_start: 0.5448 (mtm180) cc_final: 0.5075 (mtm180) REVERT: O 347 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7736 (tmmt) REVERT: O 390 LYS cc_start: 0.5823 (pptt) cc_final: 0.5517 (mmmt) REVERT: O 435 MET cc_start: 0.6122 (ptp) cc_final: 0.4337 (mmm) REVERT: O 497 LYS cc_start: 0.8981 (tptt) cc_final: 0.8639 (tptp) outliers start: 150 outliers final: 102 residues processed: 615 average time/residue: 0.1985 time to fit residues: 193.9983 Evaluate side-chains 601 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 477 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 103 LEU 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 356 ILE Chi-restraints excluded: chain B residue 57 LEU 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 217 HIS 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 399 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 498 THR Chi-restraints excluded: chain F residue 15 ASP 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 160 HIS 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 296 GLU 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 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 74 MET 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 317 VAL 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 133 ASP 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 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 370 ASN Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 392 TYR 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 57 LEU Chi-restraints excluded: chain K residue 120 LEU 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 283 LEU Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain K residue 470 CYS Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 107 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 338 SER Chi-restraints excluded: chain N residue 340 HIS Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 344 THR Chi-restraints excluded: chain N residue 354 LYS Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 12 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 138 VAL Chi-restraints excluded: chain O residue 143 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 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 347 LYS 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 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 63 optimal weight: 0.0980 chunk 140 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 320 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN ** K 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 HIS ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.191672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.148444 restraints weight = 53996.887| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.96 r_work: 0.3931 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32056 Z= 0.126 Angle : 0.613 14.116 44015 Z= 0.314 Chirality : 0.043 0.302 4828 Planarity : 0.004 0.092 4975 Dihedral : 16.063 94.074 5689 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.90 % Allowed : 29.65 % Favored : 65.44 % 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 aren not related in a simple way. whole: -0.57 (0.14), residues: 3303 helix: 1.13 (0.15), residues: 1126 sheet: -0.77 (0.21), residues: 595 loop : -1.34 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 362 TYR 0.017 0.001 TYR F 233 PHE 0.030 0.002 PHE K 206 TRP 0.028 0.002 TRP N 20 HIS 0.008 0.001 HIS J 9 Details of bonding type rmsd covalent geometry : bond 0.00283 (32056) covalent geometry : angle 0.61321 (44015) hydrogen bonds : bond 0.03514 ( 1248) hydrogen bonds : angle 4.69847 ( 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 656 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 509 time to evaluate : 0.830 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: 0.7515 (t0) cc_final: 0.7034 (t0) REVERT: A 71 ARG cc_start: 0.7188 (tpp-160) cc_final: 0.6933 (ttm110) REVERT: A 92 MET cc_start: 0.5730 (tpp) cc_final: 0.5280 (mmt) REVERT: A 100 ASP cc_start: 0.8561 (t70) cc_final: 0.8036 (t0) REVERT: A 179 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.5974 (tp) REVERT: A 262 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: A 271 LYS cc_start: 0.8408 (tppt) cc_final: 0.7652 (mttp) REVERT: A 291 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 389 ASN cc_start: 0.7542 (p0) cc_final: 0.7269 (t0) REVERT: B 132 ASP cc_start: 0.7636 (m-30) cc_final: 0.7388 (m-30) REVERT: B 217 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6762 (p-80) REVERT: B 225 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8008 (ttp80) REVERT: B 233 ASP cc_start: 0.7380 (m-30) cc_final: 0.6561 (t0) REVERT: B 321 TYR cc_start: 0.7554 (m-80) cc_final: 0.7232 (m-80) REVERT: B 358 PHE cc_start: 0.7963 (t80) cc_final: 0.7695 (t80) REVERT: F 15 ASP cc_start: 0.5113 (OUTLIER) cc_final: 0.4855 (m-30) REVERT: F 160 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6723 (p-80) REVERT: F 276 ARG cc_start: 0.7399 (tpt170) cc_final: 0.6760 (mmm160) REVERT: F 295 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7903 (pt) REVERT: F 314 GLN cc_start: 0.5176 (OUTLIER) cc_final: 0.4782 (pp30) REVERT: F 332 SER cc_start: 0.8354 (p) cc_final: 0.8153 (m) REVERT: G 3 GLU cc_start: 0.7175 (tp30) cc_final: 0.6963 (tt0) REVERT: G 137 ASP cc_start: 0.7752 (m-30) cc_final: 0.7406 (m-30) REVERT: G 349 GLN cc_start: 0.5876 (mt0) cc_final: 0.5128 (tp40) REVERT: G 449 GLU cc_start: 0.6354 (pm20) cc_final: 0.5512 (pp20) REVERT: J 33 TRP cc_start: 0.8305 (t60) cc_final: 0.7934 (t60) REVERT: J 137 LYS cc_start: 0.6832 (pptt) cc_final: 0.6181 (ptpt) REVERT: J 151 ASN cc_start: 0.7491 (m-40) cc_final: 0.7031 (p0) REVERT: J 160 HIS cc_start: 0.6307 (OUTLIER) cc_final: 0.4772 (p-80) REVERT: J 161 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.5073 (p0) REVERT: J 181 PHE cc_start: 0.4828 (p90) cc_final: 0.4556 (p90) REVERT: J 189 ARG cc_start: 0.6024 (ttt-90) cc_final: 0.5494 (ttt-90) REVERT: J 213 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: J 243 THR cc_start: 0.5206 (OUTLIER) cc_final: 0.4122 (t) REVERT: J 271 LYS cc_start: 0.7107 (tptp) cc_final: 0.6875 (tptp) REVERT: J 354 LYS cc_start: 0.4054 (OUTLIER) cc_final: 0.3706 (tptt) REVERT: J 377 LEU cc_start: 0.2051 (OUTLIER) cc_final: 0.1676 (tp) REVERT: K 57 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5881 (tp) REVERT: K 217 HIS cc_start: 0.4869 (OUTLIER) cc_final: 0.3856 (p90) REVERT: K 271 LEU cc_start: 0.5701 (pp) cc_final: 0.5096 (tt) REVERT: K 286 LYS cc_start: 0.8400 (mmpt) cc_final: 0.7461 (mmpt) REVERT: K 324 GLU cc_start: 0.4760 (mp0) cc_final: 0.4337 (mp0) REVERT: K 328 TYR cc_start: 0.7178 (m-80) cc_final: 0.6628 (m-80) REVERT: K 467 TYR cc_start: 0.8218 (m-80) cc_final: 0.8005 (m-80) REVERT: N 14 ASP cc_start: 0.7504 (m-30) cc_final: 0.7279 (m-30) REVERT: N 162 LYS cc_start: 0.7907 (mttp) cc_final: 0.7666 (mtmm) REVERT: N 215 CYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5868 (t) REVERT: N 345 MET cc_start: 0.5490 (mmm) cc_final: 0.4923 (ptp) REVERT: N 407 PRO cc_start: 0.6649 (Cg_endo) cc_final: 0.6330 (Cg_exo) REVERT: N 414 MET cc_start: 0.5702 (mmt) cc_final: 0.5369 (mmm) REVERT: O 24 ARG cc_start: 0.7017 (mpp80) cc_final: 0.6698 (mtt180) REVERT: O 85 LYS cc_start: 0.8496 (tppt) cc_final: 0.7888 (mtpp) REVERT: O 95 GLU cc_start: 0.8031 (pp20) cc_final: 0.7771 (pp20) REVERT: O 210 LEU cc_start: 0.8354 (tt) cc_final: 0.7748 (mt) REVERT: O 225 ARG cc_start: 0.5460 (mtm180) cc_final: 0.5206 (mtm180) REVERT: O 347 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7684 (tmmt) REVERT: O 390 LYS cc_start: 0.6305 (pptt) cc_final: 0.6024 (mmtt) REVERT: O 428 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7871 (tmtt) REVERT: O 435 MET cc_start: 0.6105 (ptp) cc_final: 0.4259 (mmm) REVERT: O 497 LYS cc_start: 0.8987 (tptt) cc_final: 0.8646 (tptp) outliers start: 147 outliers final: 95 residues processed: 614 average time/residue: 0.1916 time to fit residues: 187.6379 Evaluate side-chains 592 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 479 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 291 PHE 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 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 217 HIS 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 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 498 THR Chi-restraints excluded: chain F residue 15 ASP 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 225 HIS Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 296 GLU 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 74 MET Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 317 VAL 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 62 ILE Chi-restraints excluded: chain J residue 103 LEU 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 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 329 LEU 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 377 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER 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 57 LEU Chi-restraints excluded: chain K residue 120 LEU 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 305 LEU Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 132 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 338 SER Chi-restraints excluded: chain N residue 340 HIS Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 354 LYS Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 21 THR 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 138 VAL Chi-restraints excluded: chain O residue 143 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 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 389 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 319 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 GLN O 430 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.188908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145711 restraints weight = 54513.687| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.97 r_work: 0.3861 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32056 Z= 0.199 Angle : 0.668 14.749 44015 Z= 0.345 Chirality : 0.045 0.240 4828 Planarity : 0.005 0.054 4975 Dihedral : 16.091 93.564 5689 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.10 % Allowed : 29.79 % Favored : 65.11 % 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 aren not related in a simple way. whole: -0.78 (0.14), residues: 3303 helix: 0.99 (0.15), residues: 1112 sheet: -1.02 (0.21), residues: 606 loop : -1.41 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 135 TYR 0.023 0.002 TYR O 285 PHE 0.034 0.002 PHE K 206 TRP 0.050 0.002 TRP F 20 HIS 0.007 0.001 HIS J 9 Details of bonding type rmsd covalent geometry : bond 0.00465 (32056) covalent geometry : angle 0.66809 (44015) hydrogen bonds : bond 0.03895 ( 1248) hydrogen bonds : angle 4.83461 ( 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 647 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 494 time to evaluate : 1.265 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: 0.7698 (t0) cc_final: 0.7336 (t0) REVERT: A 71 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.6906 (ttm110) REVERT: A 92 MET cc_start: 0.5680 (tpp) cc_final: 0.5279 (mmt) REVERT: A 100 ASP cc_start: 0.8547 (t70) cc_final: 0.8079 (t0) REVERT: A 179 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.5911 (tp) REVERT: A 262 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: A 267 GLN cc_start: 0.7946 (pt0) cc_final: 0.7247 (tp40) REVERT: A 271 LYS cc_start: 0.8535 (tppt) cc_final: 0.8248 (tptp) REVERT: A 389 ASN cc_start: 0.7512 (p0) cc_final: 0.7248 (t0) REVERT: B 217 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.7109 (p-80) REVERT: B 233 ASP cc_start: 0.7497 (m-30) cc_final: 0.6675 (t0) REVERT: B 321 TYR cc_start: 0.7862 (m-80) cc_final: 0.7531 (m-80) REVERT: B 358 PHE cc_start: 0.7942 (t80) cc_final: 0.7644 (t80) REVERT: F 15 ASP cc_start: 0.5128 (OUTLIER) cc_final: 0.4852 (m-30) REVERT: F 160 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.6948 (p-80) REVERT: F 276 ARG cc_start: 0.7486 (tpt170) cc_final: 0.6696 (mmm160) REVERT: F 295 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7795 (pt) REVERT: F 314 GLN cc_start: 0.5452 (OUTLIER) cc_final: 0.4765 (pp30) REVERT: F 336 MET cc_start: 0.8131 (ptp) cc_final: 0.7881 (ptp) REVERT: G 3 GLU cc_start: 0.7272 (tp30) cc_final: 0.7027 (tt0) REVERT: G 226 GLU cc_start: 0.6433 (mt-10) cc_final: 0.6172 (mt-10) REVERT: G 243 ARG cc_start: 0.6553 (mtp180) cc_final: 0.6130 (mtp180) REVERT: G 449 GLU cc_start: 0.6270 (pm20) cc_final: 0.5445 (pp20) REVERT: J 46 TRP cc_start: 0.6294 (OUTLIER) cc_final: 0.4927 (m-90) REVERT: J 69 ASN cc_start: 0.7796 (m-40) cc_final: 0.7106 (p0) REVERT: J 137 LYS cc_start: 0.6863 (pptt) cc_final: 0.6242 (ptpt) REVERT: J 160 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.4989 (p-80) REVERT: J 161 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.5296 (p0) REVERT: J 181 PHE cc_start: 0.4835 (p90) cc_final: 0.4607 (p90) REVERT: J 213 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: J 243 THR cc_start: 0.5326 (OUTLIER) cc_final: 0.4323 (t) REVERT: J 354 LYS cc_start: 0.4065 (OUTLIER) cc_final: 0.3763 (tptt) REVERT: J 377 LEU cc_start: 0.2222 (OUTLIER) cc_final: 0.1835 (tp) REVERT: K 215 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7597 (mt) REVERT: K 217 HIS cc_start: 0.4987 (OUTLIER) cc_final: 0.3833 (p90) REVERT: K 271 LEU cc_start: 0.6040 (pp) cc_final: 0.5641 (tp) REVERT: K 324 GLU cc_start: 0.5052 (mp0) cc_final: 0.4557 (mp0) REVERT: K 328 TYR cc_start: 0.7222 (m-80) cc_final: 0.6663 (m-80) REVERT: N 14 ASP cc_start: 0.7559 (m-30) cc_final: 0.7329 (m-30) REVERT: N 19 ARG cc_start: 0.7354 (ptp90) cc_final: 0.7140 (ptp90) REVERT: N 122 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8339 (mmtt) REVERT: N 158 PHE cc_start: 0.8177 (m-80) cc_final: 0.7937 (m-80) REVERT: N 162 LYS cc_start: 0.7973 (mttp) cc_final: 0.7766 (mtmm) REVERT: N 295 ILE cc_start: 0.7410 (tp) cc_final: 0.6912 (pt) REVERT: N 345 MET cc_start: 0.5586 (mmm) cc_final: 0.4946 (ptp) REVERT: N 383 PHE cc_start: 0.7018 (t80) cc_final: 0.6756 (t80) REVERT: N 393 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7509 (tp) REVERT: N 407 PRO cc_start: 0.6731 (Cg_endo) cc_final: 0.6389 (Cg_exo) REVERT: N 414 MET cc_start: 0.5826 (mmt) cc_final: 0.5605 (mmm) REVERT: O 24 ARG cc_start: 0.7151 (mpp80) cc_final: 0.6686 (mtt180) REVERT: O 85 LYS cc_start: 0.8526 (tppt) cc_final: 0.7910 (mtpp) REVERT: O 210 LEU cc_start: 0.8392 (tt) cc_final: 0.7697 (mt) REVERT: O 225 ARG cc_start: 0.5505 (mtm180) cc_final: 0.5284 (mtm180) REVERT: O 390 LYS cc_start: 0.6006 (pptt) cc_final: 0.5728 (mmmt) REVERT: O 497 LYS cc_start: 0.8980 (tptt) cc_final: 0.8660 (tptp) outliers start: 153 outliers final: 106 residues processed: 601 average time/residue: 0.2237 time to fit residues: 213.0612 Evaluate side-chains 596 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 473 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 51 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 103 LEU 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 356 ILE 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 60 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 217 HIS Chi-restraints excluded: chain B residue 224 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 399 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 15 ASP 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 296 GLU 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 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 317 VAL 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 133 ASP 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 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 329 LEU Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER 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 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 283 LEU Chi-restraints excluded: chain K residue 383 LEU 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 478 VAL Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 354 LYS Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 21 THR 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 138 VAL Chi-restraints excluded: chain O residue 143 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 248 ILE Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 384 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 334 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 279 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS F 109 ASN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4530 r_free = 0.4530 target = 0.190389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.147293 restraints weight = 54613.250| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.99 r_work: 0.3881 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32056 Z= 0.165 Angle : 0.662 14.222 44015 Z= 0.339 Chirality : 0.045 0.409 4828 Planarity : 0.005 0.080 4975 Dihedral : 16.062 93.215 5687 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.44 % Allowed : 31.12 % Favored : 64.44 % 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 aren not related in a simple way. whole: -0.80 (0.14), residues: 3303 helix: 0.92 (0.15), residues: 1129 sheet: -0.97 (0.22), residues: 600 loop : -1.42 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG O 362 TYR 0.021 0.001 TYR K 280 PHE 0.037 0.002 PHE K 206 TRP 0.044 0.002 TRP N 219 HIS 0.006 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00383 (32056) covalent geometry : angle 0.66167 (44015) hydrogen bonds : bond 0.03780 ( 1248) hydrogen bonds : angle 4.79236 ( 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 639 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 506 time to evaluate : 1.134 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: 0.7687 (t0) cc_final: 0.7321 (t0) REVERT: A 92 MET cc_start: 0.5647 (tpp) cc_final: 0.5256 (mmt) REVERT: A 100 ASP cc_start: 0.8548 (t70) cc_final: 0.8050 (t0) REVERT: A 179 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.5909 (tp) REVERT: A 262 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: A 267 GLN cc_start: 0.7967 (pt0) cc_final: 0.7264 (tp40) REVERT: A 389 ASN cc_start: 0.7605 (p0) cc_final: 0.7349 (t0) REVERT: B 217 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.7000 (p-80) REVERT: B 233 ASP cc_start: 0.7492 (m-30) cc_final: 0.6625 (t0) REVERT: B 321 TYR cc_start: 0.7805 (m-80) cc_final: 0.7466 (m-80) REVERT: B 358 PHE cc_start: 0.7875 (t80) cc_final: 0.7574 (t80) REVERT: F 15 ASP cc_start: 0.5072 (OUTLIER) cc_final: 0.4793 (m-30) REVERT: F 160 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6818 (p-80) REVERT: F 295 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7827 (pt) REVERT: F 302 LYS cc_start: 0.8253 (tptm) cc_final: 0.7839 (tmtt) REVERT: F 314 GLN cc_start: 0.5578 (OUTLIER) cc_final: 0.5064 (pp30) REVERT: F 336 MET cc_start: 0.8160 (ptp) cc_final: 0.7939 (ptp) REVERT: G 3 GLU cc_start: 0.7354 (tp30) cc_final: 0.6970 (tt0) REVERT: G 243 ARG cc_start: 0.6621 (mtp180) cc_final: 0.6187 (mtp180) REVERT: G 349 GLN cc_start: 0.6209 (mt0) cc_final: 0.5258 (tp40) REVERT: G 449 GLU cc_start: 0.6295 (pm20) cc_final: 0.5477 (pp20) REVERT: J 33 TRP cc_start: 0.8397 (t60) cc_final: 0.7999 (t60) REVERT: J 46 TRP cc_start: 0.6304 (OUTLIER) cc_final: 0.4820 (m-90) REVERT: J 69 ASN cc_start: 0.7349 (m-40) cc_final: 0.7072 (p0) REVERT: J 137 LYS cc_start: 0.6920 (pptt) cc_final: 0.6311 (ptpt) REVERT: J 160 HIS cc_start: 0.6409 (OUTLIER) cc_final: 0.4956 (p-80) REVERT: J 161 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.5066 (p0) REVERT: J 213 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: J 243 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.4329 (t) REVERT: J 291 PHE cc_start: 0.6185 (t80) cc_final: 0.5945 (t80) REVERT: J 354 LYS cc_start: 0.4080 (OUTLIER) cc_final: 0.3784 (tptt) REVERT: J 377 LEU cc_start: 0.2130 (OUTLIER) cc_final: 0.1733 (tp) REVERT: K 217 HIS cc_start: 0.5004 (OUTLIER) cc_final: 0.3775 (p90) REVERT: K 324 GLU cc_start: 0.4842 (mp0) cc_final: 0.4364 (mp0) REVERT: K 328 TYR cc_start: 0.7152 (m-80) cc_final: 0.6673 (m-80) REVERT: K 419 PHE cc_start: 0.6380 (m-80) cc_final: 0.6178 (m-80) REVERT: N 14 ASP cc_start: 0.7588 (m-30) cc_final: 0.7382 (m-30) REVERT: N 19 ARG cc_start: 0.7311 (ptp90) cc_final: 0.7048 (ptp90) REVERT: N 169 GLU cc_start: 0.5759 (tm-30) cc_final: 0.5250 (tm-30) REVERT: N 215 CYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6149 (t) REVERT: N 295 ILE cc_start: 0.7429 (tp) cc_final: 0.6987 (pt) REVERT: N 345 MET cc_start: 0.5554 (mmm) cc_final: 0.4974 (ptt) REVERT: N 383 PHE cc_start: 0.7043 (t80) cc_final: 0.6801 (t80) REVERT: N 393 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7450 (tp) REVERT: N 407 PRO cc_start: 0.6674 (Cg_endo) cc_final: 0.6335 (Cg_exo) REVERT: N 414 MET cc_start: 0.5745 (mmt) cc_final: 0.5394 (mmt) REVERT: O 24 ARG cc_start: 0.7157 (mpp80) cc_final: 0.6748 (mtt180) REVERT: O 85 LYS cc_start: 0.8402 (tppt) cc_final: 0.7812 (mtpp) REVERT: O 210 LEU cc_start: 0.8385 (tt) cc_final: 0.7725 (mt) REVERT: O 217 HIS cc_start: 0.5007 (OUTLIER) cc_final: 0.3812 (p-80) REVERT: O 328 TYR cc_start: 0.7020 (m-10) cc_final: 0.6808 (m-10) REVERT: O 390 LYS cc_start: 0.6125 (pptt) cc_final: 0.5827 (mmmt) REVERT: O 497 LYS cc_start: 0.8976 (tptt) cc_final: 0.8656 (tptp) outliers start: 133 outliers final: 104 residues processed: 597 average time/residue: 0.1967 time to fit residues: 186.8894 Evaluate side-chains 605 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 483 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 51 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 103 LEU 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 291 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 60 ILE 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 208 ASP Chi-restraints excluded: chain B residue 217 HIS 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 422 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 15 ASP 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 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 296 GLU 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 74 MET Chi-restraints excluded: chain G residue 138 VAL 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 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 133 ASP 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 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 270 ASN Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER 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 120 LEU 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 283 LEU Chi-restraints excluded: chain K residue 383 LEU 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 478 VAL Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 103 LEU 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 N residue 354 LYS Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 21 THR 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 138 VAL Chi-restraints excluded: chain O residue 143 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 248 ILE Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 347 LYS Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 384 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: 0.9990 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 224 optimal weight: 0.3980 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS F 109 ASN ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4538 r_free = 0.4538 target = 0.191069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148094 restraints weight = 54373.100| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.97 r_work: 0.3886 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32056 Z= 0.156 Angle : 0.661 13.911 44015 Z= 0.339 Chirality : 0.045 0.354 4828 Planarity : 0.004 0.050 4975 Dihedral : 16.045 92.819 5687 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.97 % Allowed : 31.42 % Favored : 64.61 % 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 aren not related in a simple way. whole: -0.78 (0.14), residues: 3303 helix: 0.97 (0.15), residues: 1128 sheet: -0.97 (0.22), residues: 604 loop : -1.43 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 135 TYR 0.018 0.001 TYR O 285 PHE 0.040 0.002 PHE K 206 TRP 0.053 0.002 TRP K 370 HIS 0.006 0.001 HIS N 188 Details of bonding type rmsd covalent geometry : bond 0.00360 (32056) covalent geometry : angle 0.66083 (44015) hydrogen bonds : bond 0.03714 ( 1248) hydrogen bonds : angle 4.77277 ( 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 622 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 503 time to evaluate : 1.216 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: 0.7715 (t0) cc_final: 0.7372 (t0) REVERT: A 92 MET cc_start: 0.5653 (tpp) cc_final: 0.5216 (mmt) REVERT: A 100 ASP cc_start: 0.8508 (t70) cc_final: 0.7997 (t0) REVERT: A 122 LYS cc_start: 0.7938 (ptpt) cc_final: 0.7731 (mttm) REVERT: A 179 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.5918 (tp) REVERT: A 262 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: A 263 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7238 (mtm110) REVERT: A 267 GLN cc_start: 0.8010 (pt0) cc_final: 0.7250 (tp40) REVERT: A 271 LYS cc_start: 0.8764 (tptp) cc_final: 0.8535 (tptp) REVERT: A 389 ASN cc_start: 0.7612 (p0) cc_final: 0.7401 (t0) REVERT: A 392 TYR cc_start: 0.3736 (m-10) cc_final: 0.3404 (m-80) REVERT: B 217 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6988 (p-80) REVERT: B 233 ASP cc_start: 0.7429 (m-30) cc_final: 0.6580 (t0) REVERT: B 321 TYR cc_start: 0.7801 (m-80) cc_final: 0.7452 (m-80) REVERT: B 358 PHE cc_start: 0.7861 (t80) cc_final: 0.7561 (t80) REVERT: F 15 ASP cc_start: 0.5071 (OUTLIER) cc_final: 0.4789 (m-30) REVERT: F 160 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.6840 (p-80) REVERT: F 295 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7790 (pt) REVERT: F 314 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.4958 (pp30) REVERT: F 336 MET cc_start: 0.8110 (ptp) cc_final: 0.7863 (ptp) REVERT: F 398 GLU cc_start: 0.6440 (pm20) cc_final: 0.6215 (pm20) REVERT: G 3 GLU cc_start: 0.7402 (tp30) cc_final: 0.7048 (tt0) REVERT: G 243 ARG cc_start: 0.6636 (mtp180) cc_final: 0.6197 (mtp180) REVERT: G 349 GLN cc_start: 0.6270 (mt0) cc_final: 0.5189 (tp40) REVERT: G 449 GLU cc_start: 0.6329 (pm20) cc_final: 0.5533 (pp20) REVERT: J 33 TRP cc_start: 0.8386 (t60) cc_final: 0.7964 (t60) REVERT: J 46 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.4689 (m-90) REVERT: J 137 LYS cc_start: 0.6927 (pptt) cc_final: 0.6314 (ptpt) REVERT: J 160 HIS cc_start: 0.6385 (OUTLIER) cc_final: 0.4904 (p-80) REVERT: J 161 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.5047 (p0) REVERT: J 189 ARG cc_start: 0.6104 (ttt-90) cc_final: 0.5629 (ttt-90) REVERT: J 213 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: J 291 PHE cc_start: 0.6283 (t80) cc_final: 0.6004 (t80) REVERT: J 354 LYS cc_start: 0.4175 (OUTLIER) cc_final: 0.3890 (tptt) REVERT: J 377 LEU cc_start: 0.2275 (OUTLIER) cc_final: 0.1857 (tp) REVERT: K 216 GLU cc_start: 0.5907 (pm20) cc_final: 0.5693 (pm20) REVERT: K 217 HIS cc_start: 0.4899 (OUTLIER) cc_final: 0.3852 (p90) REVERT: K 324 GLU cc_start: 0.4853 (mp0) cc_final: 0.4378 (mp0) REVERT: K 328 TYR cc_start: 0.6994 (m-80) cc_final: 0.6605 (m-80) REVERT: N 19 ARG cc_start: 0.7311 (ptp90) cc_final: 0.7031 (ptp90) REVERT: N 158 PHE cc_start: 0.8141 (m-80) cc_final: 0.7903 (m-80) REVERT: N 162 LYS cc_start: 0.8065 (mttp) cc_final: 0.7810 (mtmm) REVERT: N 215 CYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6115 (t) REVERT: N 295 ILE cc_start: 0.7391 (tp) cc_final: 0.6927 (pt) REVERT: N 345 MET cc_start: 0.5460 (mmm) cc_final: 0.4941 (ptt) REVERT: N 393 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7205 (tp) REVERT: N 407 PRO cc_start: 0.6639 (Cg_endo) cc_final: 0.6313 (Cg_exo) REVERT: N 414 MET cc_start: 0.5590 (mmt) cc_final: 0.4961 (mmt) REVERT: O 24 ARG cc_start: 0.7117 (mpp80) cc_final: 0.6776 (mtt180) REVERT: O 85 LYS cc_start: 0.8426 (tppt) cc_final: 0.7815 (mtpp) REVERT: O 210 LEU cc_start: 0.8371 (tt) cc_final: 0.7728 (mt) REVERT: O 217 HIS cc_start: 0.4994 (OUTLIER) cc_final: 0.3782 (p-80) REVERT: O 225 ARG cc_start: 0.5329 (mtm180) cc_final: 0.5057 (mtm180) REVERT: O 390 LYS cc_start: 0.6195 (pptt) cc_final: 0.5864 (mmmt) REVERT: O 497 LYS cc_start: 0.8983 (tptt) cc_final: 0.8668 (tptp) outliers start: 119 outliers final: 95 residues processed: 582 average time/residue: 0.1926 time to fit residues: 179.0410 Evaluate side-chains 593 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 481 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 103 LEU 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 291 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 57 LEU 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 217 HIS 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 498 THR Chi-restraints excluded: chain F residue 15 ASP 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 296 GLU 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 66 ASN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 317 VAL 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 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 213 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 354 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 420 SER 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 120 LEU 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 283 LEU Chi-restraints excluded: chain K residue 383 LEU 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 478 VAL Chi-restraints excluded: chain N residue 103 LEU 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 354 LYS Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 114 THR 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 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 248 ILE Chi-restraints excluded: chain O residue 303 MET Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 384 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 297 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 310 optimal weight: 0.3980 chunk 57 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS F 109 ASN ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** 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 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 = 0.4527 r_free = 0.4527 target = 0.190182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147089 restraints weight = 54830.460| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.98 r_work: 0.3875 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32056 Z= 0.166 Angle : 0.669 13.935 44015 Z= 0.343 Chirality : 0.045 0.296 4828 Planarity : 0.005 0.059 4975 Dihedral : 16.040 92.547 5687 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.14 % Allowed : 31.45 % Favored : 64.41 % 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 aren not related in a simple way. whole: -0.82 (0.14), residues: 3303 helix: 0.90 (0.15), residues: 1128 sheet: -0.97 (0.22), residues: 604 loop : -1.43 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 135 TYR 0.019 0.001 TYR F 233 PHE 0.041 0.002 PHE F 273 TRP 0.043 0.002 TRP K 370 HIS 0.006 0.001 HIS J 340 Details of bonding type rmsd covalent geometry : bond 0.00386 (32056) covalent geometry : angle 0.66864 (44015) hydrogen bonds : bond 0.03760 ( 1248) hydrogen bonds : angle 4.78769 ( 3670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9626.81 seconds wall clock time: 165 minutes 22.14 seconds (9922.14 seconds total)