Starting phenix.real_space_refine on Thu Jun 26 23:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifl_35420/06_2025/8ifl_35420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifl_35420/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifl_35420/06_2025/8ifl_35420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifl_35420/06_2025/8ifl_35420.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifl_35420/06_2025/8ifl_35420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifl_35420/06_2025/8ifl_35420.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.56, per 1000 atoms: 0.57 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: 7.99 Conformation dependent library (CDL) restraints added in 3.4 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6380 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 40 sheets defined 36.8% alpha, 23.4% beta 62 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 10.98 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: 13.40 Time building geometry restraints manager: 9.18 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 76.130 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), 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 TRP 0.079 0.002 TRP J 319 HIS 0.013 0.002 HIS O 360 PHE 0.041 0.002 PHE K 75 TYR 0.021 0.001 TYR F 190 ARG 0.006 0.000 ARG J 19 Details of bonding type rmsd hydrogen bonds : bond 0.13930 ( 1248) hydrogen bonds : angle 6.82877 ( 3670) covalent geometry : bond 0.00828 (32056) covalent geometry : angle 0.84069 (44015) *********************** 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 : 3.323 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: 0.7761 (mttp) REVERT: A 323 ILE cc_start: 0.7756 (pt) cc_final: 0.7239 (pt) REVERT: B 225 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7917 (ttp80) REVERT: B 233 ASP cc_start: 0.6986 (m-30) cc_final: 0.6302 (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: 0.6480 (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: 0.6339 (p90) REVERT: J 260 GLU cc_start: 0.6575 (tm-30) cc_final: 0.5700 (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: 0.6240 (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: 0.6281 (mmm) REVERT: O 24 ARG cc_start: 0.7328 (mpp80) cc_final: 0.6893 (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: 0.4828 time to fit residues: 588.8648 Evaluate side-chains 538 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 534 time to evaluate : 3.423 ------------------------------------------------------------------------------- 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 293 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 272 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 165 optimal weight: 0.2980 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 F 340 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 207 HIS K 371 ASN 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 ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 GLN ** O 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 484 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.193579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152740 restraints weight = 53825.085| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.30 r_work: 0.3917 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32056 Z= 0.153 Angle : 0.648 12.338 44015 Z= 0.336 Chirality : 0.044 0.279 4828 Planarity : 0.005 0.069 4975 Dihedral : 16.262 93.562 5696 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.14 % Allowed : 28.69 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3303 helix: 0.87 (0.15), residues: 1126 sheet: -0.61 (0.21), residues: 570 loop : -1.29 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 319 HIS 0.013 0.001 HIS J 340 PHE 0.037 0.002 PHE A 343 TYR 0.023 0.001 TYR J 318 ARG 0.005 0.001 ARG O 407 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 1248) hydrogen bonds : angle 5.25900 ( 3670) covalent geometry : bond 0.00346 (32056) covalent geometry : angle 0.64826 (44015) *********************** 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 708 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 584 time to evaluate : 3.557 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: 0.7440 (t0) cc_final: 0.7112 (t0) REVERT: A 92 MET cc_start: 0.6018 (tpp) cc_final: 0.5654 (mmt) REVERT: A 100 ASP cc_start: 0.8528 (t70) cc_final: 0.7925 (t0) REVERT: A 262 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: A 271 LYS cc_start: 0.8266 (tppt) cc_final: 0.7616 (mttp) REVERT: A 323 ILE cc_start: 0.7837 (pt) cc_final: 0.7389 (pt) REVERT: B 225 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.7951 (ttp80) REVERT: B 233 ASP cc_start: 0.7288 (m-30) cc_final: 0.6408 (t0) REVERT: B 354 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8330 (Cg_exo) REVERT: B 358 PHE cc_start: 0.7897 (t80) cc_final: 0.7612 (t80) REVERT: B 397 TYR cc_start: 0.7732 (m-80) cc_final: 0.7504 (m-10) REVERT: F 80 VAL cc_start: 0.8898 (p) cc_final: 0.8694 (m) REVERT: F 114 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8390 (mtp85) REVERT: F 165 ILE cc_start: 0.6535 (pt) cc_final: 0.6230 (pt) REVERT: F 242 SER cc_start: 0.8965 (t) cc_final: 0.8622 (p) REVERT: F 276 ARG cc_start: 0.7296 (tpt170) cc_final: 0.6752 (mmm160) REVERT: F 414 MET cc_start: 0.7149 (tpp) cc_final: 0.6837 (tpp) REVERT: G 231 TRP cc_start: 0.7389 (p-90) cc_final: 0.7077 (p-90) REVERT: G 449 GLU cc_start: 0.6539 (pm20) cc_final: 0.5628 (pp20) REVERT: G 458 ASP cc_start: 0.6787 (m-30) cc_final: 0.6332 (m-30) REVERT: J 33 TRP cc_start: 0.8305 (t60) cc_final: 0.7810 (t60) REVERT: J 69 ASN cc_start: 0.7508 (m-40) cc_final: 0.7268 (m-40) REVERT: J 133 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: J 160 HIS cc_start: 0.5895 (p-80) cc_final: 0.5372 (p-80) REVERT: J 170 THR cc_start: 0.7794 (m) cc_final: 0.7460 (p) REVERT: J 181 PHE cc_start: 0.4558 (p90) cc_final: 0.2425 (p90) REVERT: J 243 THR cc_start: 0.5179 (OUTLIER) cc_final: 0.3693 (t) REVERT: J 260 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6331 (mm-30) REVERT: J 323 ILE cc_start: 0.6394 (pp) cc_final: 0.5967 (pp) REVERT: J 377 LEU cc_start: 0.1579 (OUTLIER) cc_final: 0.1371 (tp) REVERT: K 79 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: K 324 GLU cc_start: 0.4109 (mp0) cc_final: 0.3891 (mp0) REVERT: N 126 LYS cc_start: 0.8092 (pttt) cc_final: 0.7875 (pttt) REVERT: N 169 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6354 (tt0) REVERT: N 345 MET cc_start: 0.4798 (mmm) cc_final: 0.4271 (ptt) REVERT: N 406 LYS cc_start: 0.6156 (mmtt) cc_final: 0.5862 (mmtm) REVERT: N 414 MET cc_start: 0.6214 (mmt) cc_final: 0.5838 (mmm) REVERT: O 6 TYR cc_start: 0.7034 (t80) cc_final: 0.6737 (t80) REVERT: O 24 ARG cc_start: 0.7157 (mpp80) cc_final: 0.6555 (mtt180) REVERT: O 85 LYS cc_start: 0.8436 (tppt) cc_final: 0.7982 (mtpp) REVERT: O 94 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7223 (mmmt) REVERT: O 95 GLU cc_start: 0.7903 (pp20) cc_final: 0.7614 (pp20) REVERT: O 210 LEU cc_start: 0.8480 (tt) cc_final: 0.7754 (mt) REVERT: O 390 LYS cc_start: 0.5342 (pptt) cc_final: 0.4861 (mmmt) REVERT: O 406 MET cc_start: 0.7294 (ppp) cc_final: 0.6766 (ppp) REVERT: O 434 SER cc_start: 0.7306 (p) cc_final: 0.7078 (t) REVERT: O 497 LYS cc_start: 0.8846 (tptt) cc_final: 0.8626 (tptp) outliers start: 124 outliers final: 64 residues processed: 664 average time/residue: 0.4660 time to fit residues: 490.3956 Evaluate side-chains 577 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 508 time to evaluate : 3.188 ------------------------------------------------------------------------------- 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 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 B residue 423 LEU 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 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 353 SER Chi-restraints excluded: chain F residue 393 LEU 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 1 MET 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 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 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 44 VAL Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 233 ASP 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 333 optimal weight: 0.9980 chunk 232 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 0.3980 chunk 308 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** F 156 GLN G 329 HIS ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS ** K 380 ASN ** 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** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 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 = 0.4533 r_free = 0.4533 target = 0.190807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.147327 restraints weight = 54382.884| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.97 r_work: 0.3911 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32056 Z= 0.153 Angle : 0.623 12.507 44015 Z= 0.321 Chirality : 0.043 0.246 4828 Planarity : 0.005 0.056 4975 Dihedral : 16.224 94.479 5692 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.60 % Allowed : 28.52 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3303 helix: 0.93 (0.15), residues: 1126 sheet: -0.75 (0.21), residues: 588 loop : -1.31 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 20 HIS 0.013 0.001 HIS J 340 PHE 0.023 0.002 PHE A 343 TYR 0.018 0.001 TYR F 330 ARG 0.005 0.000 ARG J 114 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1248) hydrogen bonds : angle 5.00772 ( 3670) covalent geometry : bond 0.00348 (32056) covalent geometry : angle 0.62333 (44015) *********************** 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 678 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 540 time to evaluate : 3.095 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: 0.7570 (t0) cc_final: 0.7225 (t0) REVERT: A 50 GLU cc_start: 0.7380 (tt0) cc_final: 0.7155 (tt0) REVERT: A 92 MET cc_start: 0.6042 (tpp) cc_final: 0.5609 (mmt) REVERT: A 100 ASP cc_start: 0.8556 (t70) cc_final: 0.8039 (t0) REVERT: A 179 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.5767 (tp) REVERT: A 262 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: A 271 LYS cc_start: 0.8281 (tppt) cc_final: 0.7655 (mttp) REVERT: B 225 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8022 (ttp80) REVERT: B 233 ASP cc_start: 0.7444 (m-30) cc_final: 0.6590 (t0) REVERT: B 321 TYR cc_start: 0.7370 (m-80) cc_final: 0.6930 (m-80) REVERT: B 358 PHE cc_start: 0.7918 (t80) cc_final: 0.7651 (t80) REVERT: B 397 TYR cc_start: 0.8085 (m-80) cc_final: 0.7820 (m-10) REVERT: F 114 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8366 (mtp85) REVERT: F 165 ILE cc_start: 0.6598 (pt) cc_final: 0.6314 (pt) REVERT: F 242 SER cc_start: 0.8922 (t) cc_final: 0.8585 (p) REVERT: F 276 ARG cc_start: 0.7217 (tpt170) cc_final: 0.6603 (mmm160) REVERT: F 295 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7804 (pt) REVERT: F 314 GLN cc_start: 0.4930 (OUTLIER) cc_final: 0.4306 (pp30) REVERT: F 330 TYR cc_start: 0.5219 (t80) cc_final: 0.4992 (t80) REVERT: F 414 MET cc_start: 0.7329 (tpp) cc_final: 0.7062 (tpp) REVERT: G 64 ILE cc_start: 0.8654 (tp) cc_final: 0.8363 (mt) REVERT: G 231 TRP cc_start: 0.7373 (p-90) cc_final: 0.7092 (p-90) REVERT: G 356 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6870 (tm-30) REVERT: G 449 GLU cc_start: 0.6437 (pm20) cc_final: 0.5550 (pp20) REVERT: G 458 ASP cc_start: 0.6758 (m-30) cc_final: 0.6335 (m-30) REVERT: J 33 TRP cc_start: 0.8289 (t60) cc_final: 0.7759 (t60) REVERT: J 46 TRP cc_start: 0.5895 (OUTLIER) cc_final: 0.4437 (m-90) REVERT: J 69 ASN cc_start: 0.7570 (m-40) cc_final: 0.7368 (m-40) REVERT: J 111 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7988 (tm-30) REVERT: J 133 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: J 137 LYS cc_start: 0.6820 (pptt) cc_final: 0.6020 (ptpt) REVERT: J 160 HIS cc_start: 0.6058 (p-80) cc_final: 0.4553 (p-80) REVERT: J 161 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.5336 (p0) REVERT: J 170 THR cc_start: 0.7860 (m) cc_final: 0.7618 (p) REVERT: J 181 PHE cc_start: 0.4659 (p90) cc_final: 0.3152 (p90) REVERT: J 243 THR cc_start: 0.5330 (OUTLIER) cc_final: 0.3980 (t) REVERT: J 260 GLU cc_start: 0.6655 (tm-30) cc_final: 0.6272 (mm-30) REVERT: J 271 LYS cc_start: 0.7306 (tptp) cc_final: 0.6456 (mmmm) REVERT: J 323 ILE cc_start: 0.6462 (pp) cc_final: 0.6128 (pp) REVERT: K 217 HIS cc_start: 0.4891 (OUTLIER) cc_final: 0.3996 (p90) REVERT: K 252 LEU cc_start: 0.7087 (tp) cc_final: 0.6836 (tp) REVERT: K 256 ILE cc_start: 0.8339 (mt) cc_final: 0.8058 (mm) REVERT: K 324 GLU cc_start: 0.4272 (mp0) cc_final: 0.3968 (mp0) REVERT: K 328 TYR cc_start: 0.6672 (m-80) cc_final: 0.5815 (m-80) REVERT: K 387 THR cc_start: 0.4274 (m) cc_final: 0.3779 (p) REVERT: K 467 TYR cc_start: 0.8197 (m-80) cc_final: 0.7740 (m-80) REVERT: N 28 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8085 (mm) REVERT: N 162 LYS cc_start: 0.7662 (mttp) cc_final: 0.7291 (mttp) REVERT: N 169 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6400 (tt0) REVERT: N 283 ARG cc_start: 0.4260 (tpp-160) cc_final: 0.2839 (ttt180) REVERT: N 345 MET cc_start: 0.5171 (mmm) cc_final: 0.4617 (ptt) REVERT: N 414 MET cc_start: 0.5752 (mmt) cc_final: 0.5314 (mmm) REVERT: O 24 ARG cc_start: 0.7154 (mpp80) cc_final: 0.6595 (mtt180) REVERT: O 68 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.6904 (t0) REVERT: O 85 LYS cc_start: 0.8544 (tppt) cc_final: 0.8031 (mtpp) REVERT: O 95 GLU cc_start: 0.7967 (pp20) cc_final: 0.7696 (pp20) REVERT: O 210 LEU cc_start: 0.8330 (tt) cc_final: 0.7640 (mt) REVERT: O 231 TRP cc_start: 0.5889 (p-90) cc_final: 0.5646 (p-90) REVERT: O 390 LYS cc_start: 0.5331 (pptt) cc_final: 0.4978 (mmmt) REVERT: O 434 SER cc_start: 0.7528 (p) cc_final: 0.7215 (t) REVERT: O 497 LYS cc_start: 0.8904 (tptt) cc_final: 0.8569 (tptp) outliers start: 138 outliers final: 84 residues processed: 632 average time/residue: 0.4309 time to fit residues: 432.3758 Evaluate side-chains 595 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 500 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 498 THR 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 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 314 GLN Chi-restraints excluded: chain F residue 345 MET 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 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 375 GLU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 463 THR Chi-restraints excluded: chain G residue 470 CYS 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 336 MET Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 39 ILE 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 28 LEU 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 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 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 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 85 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 342 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 221 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 331 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** F 147 HIS G 349 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 HIS N 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.187489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143722 restraints weight = 54561.178| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.95 r_work: 0.3864 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2838 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= 0.194 Angle : 0.649 13.483 44015 Z= 0.335 Chirality : 0.044 0.220 4828 Planarity : 0.005 0.064 4975 Dihedral : 16.246 95.240 5689 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.50 % Allowed : 28.02 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3303 helix: 0.84 (0.15), residues: 1126 sheet: -0.91 (0.21), residues: 607 loop : -1.34 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP O 370 HIS 0.013 0.001 HIS J 340 PHE 0.037 0.002 PHE B 238 TYR 0.018 0.002 TYR B 65 ARG 0.006 0.001 ARG J 114 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 1248) hydrogen bonds : angle 4.95968 ( 3670) covalent geometry : bond 0.00449 (32056) covalent geometry : angle 0.64947 (44015) *********************** 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 703 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 538 time to evaluate : 3.075 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: 0.7589 (t0) cc_final: 0.7250 (t0) REVERT: A 92 MET cc_start: 0.6042 (tpp) cc_final: 0.5587 (mmt) REVERT: A 100 ASP cc_start: 0.8554 (t70) cc_final: 0.8073 (t0) REVERT: A 149 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8587 (mtmm) REVERT: A 179 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.5857 (tp) REVERT: A 262 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: A 271 LYS cc_start: 0.8418 (tppt) cc_final: 0.7696 (mttp) REVERT: B 72 ARG cc_start: 0.7955 (ptp-110) cc_final: 0.7671 (mtt90) REVERT: B 217 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7040 (p-80) REVERT: B 225 ARG cc_start: 0.8534 (ttp-170) cc_final: 0.8072 (ttp80) REVERT: B 233 ASP cc_start: 0.7550 (m-30) cc_final: 0.6707 (t0) REVERT: B 321 TYR cc_start: 0.7542 (m-80) cc_final: 0.7147 (m-80) REVERT: B 354 PRO cc_start: 0.8670 (Cg_endo) cc_final: 0.8439 (Cg_exo) REVERT: B 358 PHE cc_start: 0.8045 (t80) cc_final: 0.7777 (t80) REVERT: B 397 TYR cc_start: 0.8091 (m-80) cc_final: 0.7889 (m-80) REVERT: F 160 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6682 (p-80) REVERT: F 242 SER cc_start: 0.9017 (t) cc_final: 0.8693 (p) REVERT: F 260 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7923 (tm-30) REVERT: F 276 ARG cc_start: 0.7289 (tpt170) cc_final: 0.6684 (mmm160) REVERT: F 295 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7872 (pt) REVERT: F 302 LYS cc_start: 0.8568 (tptp) cc_final: 0.8299 (tttt) REVERT: F 314 GLN cc_start: 0.5220 (OUTLIER) cc_final: 0.4503 (pp30) REVERT: F 414 MET cc_start: 0.7436 (tpp) cc_final: 0.7229 (mmm) REVERT: G 137 ASP cc_start: 0.7730 (m-30) cc_final: 0.7411 (m-30) REVERT: G 221 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8737 (t) REVERT: G 285 TYR cc_start: 0.8550 (m-80) cc_final: 0.8191 (m-80) REVERT: G 349 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5639 (mt0) REVERT: G 449 GLU cc_start: 0.6321 (pm20) cc_final: 0.5380 (pp20) REVERT: G 458 ASP cc_start: 0.6930 (m-30) cc_final: 0.6413 (m-30) REVERT: J 33 TRP cc_start: 0.8428 (t60) cc_final: 0.7969 (t60) REVERT: J 46 TRP cc_start: 0.6104 (OUTLIER) cc_final: 0.4585 (m-90) REVERT: J 69 ASN cc_start: 0.7603 (m-40) cc_final: 0.7348 (m-40) REVERT: J 133 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: J 137 LYS cc_start: 0.6845 (pptt) cc_final: 0.6163 (ptpt) REVERT: J 161 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.5204 (p0) REVERT: J 181 PHE cc_start: 0.4772 (p90) cc_final: 0.3644 (p90) REVERT: J 243 THR cc_start: 0.5076 (OUTLIER) cc_final: 0.3584 (t) REVERT: J 260 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6301 (mm-30) REVERT: J 354 LYS cc_start: 0.4057 (OUTLIER) cc_final: 0.3708 (tptt) REVERT: K 217 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4316 (p90) REVERT: K 256 ILE cc_start: 0.8283 (mt) cc_final: 0.8048 (mm) REVERT: K 286 LYS cc_start: 0.8513 (mmpt) cc_final: 0.8114 (mmmt) REVERT: K 324 GLU cc_start: 0.4556 (mp0) cc_final: 0.4199 (mp0) REVERT: N 28 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8133 (mm) REVERT: N 122 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8313 (mmtt) REVERT: N 126 LYS cc_start: 0.7913 (pttt) cc_final: 0.7552 (pttp) REVERT: N 162 LYS cc_start: 0.7865 (mttp) cc_final: 0.7647 (mttp) REVERT: N 191 ASP cc_start: 0.6556 (m-30) cc_final: 0.6330 (p0) REVERT: N 215 CYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5771 (t) REVERT: N 283 ARG cc_start: 0.4205 (tpp-160) cc_final: 0.2529 (mtp85) REVERT: N 345 MET cc_start: 0.5619 (mmm) cc_final: 0.5076 (ptt) REVERT: N 406 LYS cc_start: 0.6504 (mmtm) cc_final: 0.6117 (mmtm) REVERT: N 414 MET cc_start: 0.5779 (mmt) cc_final: 0.5372 (mmm) REVERT: O 6 TYR cc_start: 0.7179 (t80) cc_final: 0.6810 (t80) REVERT: O 24 ARG cc_start: 0.7289 (mpp80) cc_final: 0.6713 (mtt180) REVERT: O 85 LYS cc_start: 0.8631 (tppt) cc_final: 0.7957 (mtpp) REVERT: O 210 LEU cc_start: 0.8371 (tt) cc_final: 0.7667 (mt) REVERT: O 390 LYS cc_start: 0.5777 (pptt) cc_final: 0.5479 (mmtt) REVERT: O 434 SER cc_start: 0.7643 (p) cc_final: 0.7238 (t) REVERT: O 497 LYS cc_start: 0.8978 (tptt) cc_final: 0.8639 (tptp) outliers start: 165 outliers final: 102 residues processed: 654 average time/residue: 0.4429 time to fit residues: 461.6352 Evaluate side-chains 617 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 498 time to evaluate : 3.309 ------------------------------------------------------------------------------- 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 60 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 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 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 405 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 75 LEU 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 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 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 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 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 179 ILE 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 354 LYS Chi-restraints excluded: chain J residue 370 ASN 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 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 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 28 LEU Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 147 HIS Chi-restraints excluded: chain N residue 210 TYR Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 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 217 HIS Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 237 optimal weight: 0.9990 chunk 116 optimal weight: 0.0070 chunk 279 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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** J 267 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.191357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.147949 restraints weight = 53932.795| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.96 r_work: 0.3921 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32056 Z= 0.125 Angle : 0.600 12.558 44015 Z= 0.309 Chirality : 0.043 0.283 4828 Planarity : 0.004 0.046 4975 Dihedral : 16.148 94.283 5689 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.34 % Allowed : 29.19 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3303 helix: 1.06 (0.15), residues: 1126 sheet: -0.72 (0.21), residues: 593 loop : -1.33 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 231 HIS 0.024 0.001 HIS N 147 PHE 0.026 0.002 PHE F 17 TYR 0.026 0.001 TYR N 293 ARG 0.011 0.001 ARG N 189 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1248) hydrogen bonds : angle 4.76615 ( 3670) covalent geometry : bond 0.00281 (32056) covalent geometry : angle 0.59997 (44015) *********************** 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 670 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 540 time to evaluate : 3.282 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 71 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.6983 (ttm110) REVERT: A 92 MET cc_start: 0.6020 (tpp) cc_final: 0.5549 (mmt) REVERT: A 100 ASP cc_start: 0.8560 (t70) cc_final: 0.8047 (t0) REVERT: A 179 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.5925 (tp) REVERT: A 262 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: A 271 LYS cc_start: 0.8302 (tppt) cc_final: 0.7617 (mttp) REVERT: B 217 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6986 (p-80) REVERT: B 225 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.8032 (ttp80) REVERT: B 233 ASP cc_start: 0.7414 (m-30) cc_final: 0.6559 (t0) REVERT: B 321 TYR cc_start: 0.7504 (m-80) cc_final: 0.7147 (m-80) REVERT: B 358 PHE cc_start: 0.7891 (t80) cc_final: 0.7641 (t80) REVERT: B 397 TYR cc_start: 0.7969 (m-80) cc_final: 0.7675 (m-80) REVERT: B 504 LYS cc_start: 0.7455 (ptmt) cc_final: 0.7169 (pttt) REVERT: F 160 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.6598 (p-80) REVERT: F 242 SER cc_start: 0.9033 (t) cc_final: 0.8723 (p) REVERT: F 276 ARG cc_start: 0.7335 (tpt170) cc_final: 0.6732 (mmm160) REVERT: F 295 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (pt) REVERT: F 314 GLN cc_start: 0.5001 (OUTLIER) cc_final: 0.4562 (pp30) REVERT: F 329 LEU cc_start: 0.7940 (mt) cc_final: 0.7506 (mt) REVERT: F 414 MET cc_start: 0.7381 (tpp) cc_final: 0.6978 (mmt) REVERT: G 3 GLU cc_start: 0.7166 (tp30) cc_final: 0.6754 (tt0) REVERT: G 64 ILE cc_start: 0.8478 (tp) cc_final: 0.8249 (tt) REVERT: G 221 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8696 (t) REVERT: G 349 GLN cc_start: 0.5960 (mt0) cc_final: 0.5340 (tp40) REVERT: G 356 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6772 (tm-30) REVERT: G 449 GLU cc_start: 0.6454 (pm20) cc_final: 0.5452 (pp20) REVERT: J 33 TRP cc_start: 0.8309 (t60) cc_final: 0.7915 (t60) REVERT: J 137 LYS cc_start: 0.6725 (pptt) cc_final: 0.6100 (ptpt) REVERT: J 161 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.5172 (p0) REVERT: J 169 GLU cc_start: 0.5025 (tp30) cc_final: 0.4792 (tp30) REVERT: J 181 PHE cc_start: 0.4744 (p90) cc_final: 0.3866 (p90) REVERT: J 243 THR cc_start: 0.5164 (OUTLIER) cc_final: 0.3883 (t) REVERT: J 323 ILE cc_start: 0.6454 (pp) cc_final: 0.6227 (pp) REVERT: J 354 LYS cc_start: 0.4132 (OUTLIER) cc_final: 0.3688 (tptt) REVERT: K 57 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6078 (tp) REVERT: K 217 HIS cc_start: 0.4876 (OUTLIER) cc_final: 0.3735 (p90) REVERT: K 286 LYS cc_start: 0.8401 (mmpt) cc_final: 0.8041 (mmmt) REVERT: K 324 GLU cc_start: 0.4806 (mp0) cc_final: 0.4428 (mp0) REVERT: K 328 TYR cc_start: 0.7118 (m-80) cc_final: 0.6514 (m-80) REVERT: K 467 TYR cc_start: 0.8177 (m-80) cc_final: 0.7890 (m-80) REVERT: N 3 ASN cc_start: 0.5051 (OUTLIER) cc_final: 0.4774 (p0) REVERT: N 14 ASP cc_start: 0.7515 (m-30) cc_final: 0.7287 (m-30) REVERT: N 126 LYS cc_start: 0.7925 (pttt) cc_final: 0.7671 (pttp) REVERT: N 215 CYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5673 (t) REVERT: N 283 ARG cc_start: 0.4435 (tpp-160) cc_final: 0.3366 (mtp180) REVERT: N 345 MET cc_start: 0.5557 (mmm) cc_final: 0.4902 (ptp) REVERT: N 393 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7781 (tp) REVERT: N 406 LYS cc_start: 0.6277 (mmtm) cc_final: 0.5799 (mmtm) REVERT: N 414 MET cc_start: 0.5671 (mmt) cc_final: 0.5155 (mmm) REVERT: O 6 TYR cc_start: 0.6985 (t80) cc_final: 0.6703 (t80) REVERT: O 24 ARG cc_start: 0.7016 (mpp80) cc_final: 0.6573 (mtt180) REVERT: O 68 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7110 (t0) REVERT: O 85 LYS cc_start: 0.8602 (tppt) cc_final: 0.7924 (mtpp) REVERT: O 94 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7447 (mtpp) REVERT: O 210 LEU cc_start: 0.8309 (tt) cc_final: 0.7664 (mt) REVERT: O 217 HIS cc_start: 0.4024 (OUTLIER) cc_final: 0.2810 (p-80) REVERT: O 231 TRP cc_start: 0.5842 (p-90) cc_final: 0.5399 (p-90) REVERT: O 232 ARG cc_start: 0.8511 (mmt180) cc_final: 0.8083 (mmt90) REVERT: O 347 LYS cc_start: 0.8483 (tmtt) cc_final: 0.8021 (tppt) REVERT: O 390 LYS cc_start: 0.5791 (pptt) cc_final: 0.5397 (mmmt) REVERT: O 497 LYS cc_start: 0.8968 (tptt) cc_final: 0.8629 (tptp) outliers start: 130 outliers final: 84 residues processed: 627 average time/residue: 0.4337 time to fit residues: 430.6291 Evaluate side-chains 594 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 493 time to evaluate : 3.383 ------------------------------------------------------------------------------- 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 282 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 356 ILE 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 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 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 62 ILE 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 345 MET 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 66 ASN Chi-restraints excluded: chain G residue 74 MET 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 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain J residue 16 ASP 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 354 LYS Chi-restraints excluded: chain J residue 370 ASN 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 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 K residue 423 LEU 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 220 GLU Chi-restraints excluded: chain N residue 340 HIS 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 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 207 HIS Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 217 HIS 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 406 MET Chi-restraints excluded: chain O residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 297 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 343 optimal weight: 0.0060 chunk 152 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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** B 207 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN ** K 380 ASN ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.189498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145928 restraints weight = 54232.273| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.96 r_work: 0.3896 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32056 Z= 0.150 Angle : 0.618 14.185 44015 Z= 0.319 Chirality : 0.043 0.282 4828 Planarity : 0.004 0.065 4975 Dihedral : 16.126 94.329 5689 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.64 % Allowed : 29.59 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3303 helix: 1.05 (0.15), residues: 1126 sheet: -0.67 (0.21), residues: 591 loop : -1.38 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 231 HIS 0.007 0.001 HIS J 340 PHE 0.029 0.002 PHE K 206 TYR 0.020 0.001 TYR N 285 ARG 0.007 0.000 ARG J 114 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1248) hydrogen bonds : angle 4.74000 ( 3670) covalent geometry : bond 0.00344 (32056) covalent geometry : angle 0.61834 (44015) *********************** 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 638 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 499 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6884 (ttm110) REVERT: A 92 MET cc_start: 0.5758 (tpp) cc_final: 0.5229 (mmt) REVERT: A 100 ASP cc_start: 0.8516 (t70) cc_final: 0.8003 (t0) REVERT: A 179 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.5940 (tp) REVERT: A 262 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: A 271 LYS cc_start: 0.8359 (tppt) cc_final: 0.7596 (mttp) REVERT: B 217 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.6909 (p-80) REVERT: B 225 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8029 (ttp80) REVERT: B 233 ASP cc_start: 0.7454 (m-30) cc_final: 0.6646 (t0) REVERT: B 321 TYR cc_start: 0.7640 (m-80) cc_final: 0.7232 (m-80) REVERT: B 358 PHE cc_start: 0.8018 (t80) cc_final: 0.7738 (t80) REVERT: F 160 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6796 (p-80) REVERT: F 242 SER cc_start: 0.9033 (t) cc_final: 0.8739 (p) REVERT: F 276 ARG cc_start: 0.7395 (tpt170) cc_final: 0.6710 (mmm160) REVERT: F 294 TRP cc_start: 0.5021 (p-90) cc_final: 0.4631 (p-90) REVERT: F 295 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7863 (pt) REVERT: F 314 GLN cc_start: 0.5053 (OUTLIER) cc_final: 0.4613 (pp30) REVERT: G 64 ILE cc_start: 0.8679 (tp) cc_final: 0.8348 (mt) REVERT: G 137 ASP cc_start: 0.7807 (m-30) cc_final: 0.7473 (m-30) REVERT: G 221 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8704 (t) REVERT: G 344 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: G 356 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6791 (tm-30) REVERT: G 449 GLU cc_start: 0.6326 (pm20) cc_final: 0.5529 (pp20) REVERT: J 33 TRP cc_start: 0.8370 (t60) cc_final: 0.7951 (t60) REVERT: J 46 TRP cc_start: 0.6199 (OUTLIER) cc_final: 0.4758 (m-10) REVERT: J 69 ASN cc_start: 0.7732 (m-40) cc_final: 0.7480 (m110) REVERT: J 137 LYS cc_start: 0.6802 (pptt) cc_final: 0.6165 (ptpt) REVERT: J 161 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.5166 (p0) REVERT: J 181 PHE cc_start: 0.4803 (p90) cc_final: 0.4160 (p90) REVERT: J 213 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: J 243 THR cc_start: 0.5166 (OUTLIER) cc_final: 0.3966 (t) REVERT: J 354 LYS cc_start: 0.3979 (OUTLIER) cc_final: 0.3702 (tptt) REVERT: K 57 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6086 (tp) REVERT: K 217 HIS cc_start: 0.5071 (OUTLIER) cc_final: 0.3979 (p90) REVERT: K 286 LYS cc_start: 0.8443 (mmpt) cc_final: 0.7506 (mmpt) REVERT: K 324 GLU cc_start: 0.4812 (mp0) cc_final: 0.4409 (mp0) REVERT: K 328 TYR cc_start: 0.7165 (m-80) cc_final: 0.6497 (m-80) REVERT: N 14 ASP cc_start: 0.7530 (m-30) cc_final: 0.7312 (m-30) REVERT: N 215 CYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5851 (t) REVERT: N 283 ARG cc_start: 0.4132 (tpp-160) cc_final: 0.2754 (ttt180) REVERT: N 345 MET cc_start: 0.5471 (mmm) cc_final: 0.4953 (ptp) REVERT: N 406 LYS cc_start: 0.6354 (mmtm) cc_final: 0.5939 (mmtm) REVERT: N 414 MET cc_start: 0.5794 (mmt) cc_final: 0.5268 (mmm) REVERT: O 6 TYR cc_start: 0.6989 (t80) cc_final: 0.6675 (t80) REVERT: O 24 ARG cc_start: 0.7101 (mpp80) cc_final: 0.6663 (mtt180) REVERT: O 68 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7799 (t0) REVERT: O 85 LYS cc_start: 0.8590 (tppt) cc_final: 0.7900 (mtpp) REVERT: O 95 GLU cc_start: 0.7950 (pp20) cc_final: 0.7679 (pp20) REVERT: O 210 LEU cc_start: 0.8330 (tt) cc_final: 0.7675 (mt) REVERT: O 217 HIS cc_start: 0.4484 (OUTLIER) cc_final: 0.3329 (p-80) REVERT: O 225 ARG cc_start: 0.5825 (mtm180) cc_final: 0.5587 (mtm180) REVERT: O 232 ARG cc_start: 0.8438 (mmt180) cc_final: 0.7882 (mmt180) REVERT: O 390 LYS cc_start: 0.5863 (pptt) cc_final: 0.5518 (mmmt) REVERT: O 497 LYS cc_start: 0.8994 (tptt) cc_final: 0.8649 (tptp) outliers start: 139 outliers final: 93 residues processed: 597 average time/residue: 0.5382 time to fit residues: 506.9623 Evaluate side-chains 576 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 465 time to evaluate : 6.221 ------------------------------------------------------------------------------- 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 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 208 ASP Chi-restraints excluded: chain B residue 217 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 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL 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 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 345 MET 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 344 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 147 HIS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 161 ASP Chi-restraints excluded: chain J residue 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 392 TYR Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 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 383 LEU Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 423 LEU Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 107 ASP 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 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 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 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 207 HIS Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 217 HIS Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Chi-restraints excluded: chain O residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 170 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 279 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** 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 109 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.189811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146343 restraints weight = 54188.400| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.94 r_work: 0.3902 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32056 Z= 0.144 Angle : 0.622 13.625 44015 Z= 0.320 Chirality : 0.043 0.287 4828 Planarity : 0.004 0.087 4975 Dihedral : 16.101 94.165 5689 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.50 % Allowed : 30.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3303 helix: 1.04 (0.15), residues: 1128 sheet: -0.81 (0.21), residues: 599 loop : -1.34 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 219 HIS 0.008 0.001 HIS J 9 PHE 0.024 0.002 PHE B 238 TYR 0.019 0.001 TYR O 285 ARG 0.011 0.000 ARG O 362 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 1248) hydrogen bonds : angle 4.72808 ( 3670) covalent geometry : bond 0.00329 (32056) covalent geometry : angle 0.62177 (44015) *********************** 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 634 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 499 time to evaluate : 3.939 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: 0.7700 (t0) cc_final: 0.7333 (t0) REVERT: A 71 ARG cc_start: 0.7271 (tpp-160) cc_final: 0.6952 (ttm110) REVERT: A 92 MET cc_start: 0.5704 (tpp) cc_final: 0.5270 (mmt) REVERT: A 100 ASP cc_start: 0.8508 (t70) cc_final: 0.8024 (t0) REVERT: A 179 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.5863 (tp) REVERT: A 262 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: A 271 LYS cc_start: 0.8412 (tppt) cc_final: 0.7653 (mttp) REVERT: A 389 ASN cc_start: 0.7506 (p0) cc_final: 0.7193 (t0) REVERT: B 217 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.7029 (p-80) REVERT: B 225 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.8036 (ttp80) REVERT: B 233 ASP cc_start: 0.7429 (m-30) cc_final: 0.6595 (t0) REVERT: B 321 TYR cc_start: 0.7605 (m-80) cc_final: 0.7214 (m-80) REVERT: B 358 PHE cc_start: 0.8016 (t80) cc_final: 0.7745 (t80) REVERT: F 160 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6715 (p-80) REVERT: F 242 SER cc_start: 0.9076 (t) cc_final: 0.8870 (p) REVERT: F 276 ARG cc_start: 0.7515 (tpt170) cc_final: 0.6758 (mmm160) REVERT: F 294 TRP cc_start: 0.5040 (p-90) cc_final: 0.4686 (p-90) REVERT: F 295 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7929 (pt) REVERT: F 314 GLN cc_start: 0.5081 (OUTLIER) cc_final: 0.4654 (pp30) REVERT: G 64 ILE cc_start: 0.8612 (tp) cc_final: 0.8306 (mt) REVERT: G 221 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8731 (t) REVERT: G 349 GLN cc_start: 0.5993 (mt0) cc_final: 0.5095 (tp40) REVERT: G 356 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6791 (tm-30) REVERT: G 449 GLU cc_start: 0.6396 (pm20) cc_final: 0.5585 (pp20) REVERT: J 33 TRP cc_start: 0.8362 (t60) cc_final: 0.7954 (t60) REVERT: J 46 TRP cc_start: 0.6204 (OUTLIER) cc_final: 0.4764 (m-10) REVERT: J 69 ASN cc_start: 0.7723 (m-40) cc_final: 0.7484 (m110) REVERT: J 137 LYS cc_start: 0.6837 (pptt) cc_final: 0.6201 (ptpt) REVERT: J 160 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.4843 (p-80) REVERT: J 161 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.5076 (p0) REVERT: J 181 PHE cc_start: 0.4924 (p90) cc_final: 0.4588 (p90) REVERT: J 213 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: J 243 THR cc_start: 0.5162 (OUTLIER) cc_final: 0.4074 (t) REVERT: J 260 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5922 (mm-30) REVERT: J 354 LYS cc_start: 0.3976 (OUTLIER) cc_final: 0.3701 (tptt) REVERT: K 57 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5951 (tp) REVERT: K 217 HIS cc_start: 0.5020 (OUTLIER) cc_final: 0.3952 (p90) REVERT: K 286 LYS cc_start: 0.8451 (mmpt) cc_final: 0.7495 (mmpt) REVERT: K 324 GLU cc_start: 0.4976 (mp0) cc_final: 0.4548 (mp0) REVERT: K 328 TYR cc_start: 0.7221 (m-80) cc_final: 0.6617 (m-80) REVERT: N 14 ASP cc_start: 0.7511 (m-30) cc_final: 0.7289 (m-30) REVERT: N 122 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8571 (mmtt) REVERT: N 126 LYS cc_start: 0.8046 (pttp) cc_final: 0.7844 (pttm) REVERT: N 215 CYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6154 (t) REVERT: N 283 ARG cc_start: 0.4271 (tpp-160) cc_final: 0.3078 (mtp180) REVERT: N 345 MET cc_start: 0.5605 (mmm) cc_final: 0.5091 (ptp) REVERT: N 414 MET cc_start: 0.5768 (mmt) cc_final: 0.5243 (mmm) REVERT: O 6 TYR cc_start: 0.7058 (t80) cc_final: 0.6813 (t80) REVERT: O 24 ARG cc_start: 0.7060 (mpp80) cc_final: 0.6657 (mtt180) REVERT: O 68 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7766 (t0) REVERT: O 85 LYS cc_start: 0.8538 (tppt) cc_final: 0.7988 (mtpp) REVERT: O 210 LEU cc_start: 0.8334 (tt) cc_final: 0.7692 (mt) REVERT: O 217 HIS cc_start: 0.4564 (OUTLIER) cc_final: 0.3449 (p-80) REVERT: O 231 TRP cc_start: 0.5761 (p-90) cc_final: 0.5295 (p-90) REVERT: O 347 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8276 (tmmt) REVERT: O 359 ILE cc_start: 0.8003 (mp) cc_final: 0.7586 (pt) REVERT: O 390 LYS cc_start: 0.6197 (pptt) cc_final: 0.5885 (mmmt) REVERT: O 497 LYS cc_start: 0.8965 (tptt) cc_final: 0.8659 (tptp) outliers start: 135 outliers final: 98 residues processed: 596 average time/residue: 0.4332 time to fit residues: 408.6970 Evaluate side-chains 589 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 473 time to evaluate : 3.149 ------------------------------------------------------------------------------- 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 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 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 423 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 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 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 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 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 16 ASP 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 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 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 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 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 431 SER 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 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 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 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 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 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 463 THR Chi-restraints excluded: chain O residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 218 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 316 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** F 109 ASN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 484 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** ** K 380 ASN ** 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 109 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.190807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.147436 restraints weight = 54304.509| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.97 r_work: 0.3915 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32056 Z= 0.134 Angle : 0.620 13.671 44015 Z= 0.319 Chirality : 0.043 0.236 4828 Planarity : 0.005 0.089 4975 Dihedral : 16.068 93.906 5689 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.67 % Allowed : 30.52 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3303 helix: 1.09 (0.15), residues: 1128 sheet: -0.77 (0.21), residues: 599 loop : -1.34 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP O 231 HIS 0.007 0.001 HIS J 9 PHE 0.025 0.001 PHE F 273 TYR 0.013 0.001 TYR N 285 ARG 0.020 0.001 ARG O 362 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 1248) hydrogen bonds : angle 4.67117 ( 3670) covalent geometry : bond 0.00303 (32056) covalent geometry : angle 0.61965 (44015) *********************** 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 638 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 498 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7693 (t0) cc_final: 0.7280 (t0) REVERT: A 71 ARG cc_start: 0.7240 (tpp-160) cc_final: 0.6948 (ttm110) REVERT: A 92 MET cc_start: 0.5693 (tpp) cc_final: 0.5255 (mmt) REVERT: A 100 ASP cc_start: 0.8472 (t70) cc_final: 0.7988 (t0) REVERT: A 179 ILE cc_start: 0.6624 (OUTLIER) cc_final: 0.5840 (tp) REVERT: A 262 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: A 271 LYS cc_start: 0.8416 (tppt) cc_final: 0.7658 (mttp) REVERT: A 389 ASN cc_start: 0.7581 (p0) cc_final: 0.7234 (t0) REVERT: B 74 MET cc_start: 0.5462 (tpp) cc_final: 0.4830 (ttm) REVERT: B 132 ASP cc_start: 0.7757 (m-30) cc_final: 0.7552 (m-30) REVERT: B 225 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8028 (ttp80) REVERT: B 233 ASP cc_start: 0.7387 (m-30) cc_final: 0.6576 (t0) REVERT: B 321 TYR cc_start: 0.7586 (m-80) cc_final: 0.7259 (m-80) REVERT: B 358 PHE cc_start: 0.7983 (t80) cc_final: 0.7718 (t80) REVERT: F 160 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.6656 (p-80) REVERT: F 276 ARG cc_start: 0.7492 (tpt170) cc_final: 0.6730 (mmm160) REVERT: F 294 TRP cc_start: 0.4979 (p-90) cc_final: 0.4751 (p-90) REVERT: F 295 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7917 (pt) REVERT: F 314 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4817 (pp30) REVERT: G 221 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8721 (t) REVERT: G 243 ARG cc_start: 0.6432 (mtp180) cc_final: 0.5964 (mtp180) REVERT: G 349 GLN cc_start: 0.5938 (mt0) cc_final: 0.5093 (tp40) REVERT: G 449 GLU cc_start: 0.6425 (pm20) cc_final: 0.5609 (pp20) REVERT: J 33 TRP cc_start: 0.8332 (t60) cc_final: 0.7939 (t60) REVERT: J 69 ASN cc_start: 0.7532 (m-40) cc_final: 0.7310 (m110) REVERT: J 137 LYS cc_start: 0.6855 (pptt) cc_final: 0.6231 (ptpt) REVERT: J 160 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.4854 (p-80) REVERT: J 161 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.5007 (p0) REVERT: J 213 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: J 243 THR cc_start: 0.5137 (OUTLIER) cc_final: 0.4100 (t) REVERT: J 260 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6003 (mm-30) REVERT: J 271 LYS cc_start: 0.7050 (tptp) cc_final: 0.5746 (mmmt) REVERT: J 291 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6436 (t80) REVERT: J 354 LYS cc_start: 0.3952 (OUTLIER) cc_final: 0.3682 (tptt) REVERT: K 57 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5738 (tp) REVERT: K 215 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7627 (mt) REVERT: K 217 HIS cc_start: 0.4989 (OUTLIER) cc_final: 0.3882 (p90) REVERT: K 324 GLU cc_start: 0.4776 (mp0) cc_final: 0.4316 (mp0) REVERT: K 328 TYR cc_start: 0.7081 (m-80) cc_final: 0.6540 (m-80) REVERT: N 14 ASP cc_start: 0.7488 (m-30) cc_final: 0.7274 (m-30) REVERT: N 122 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8550 (mmtt) REVERT: N 215 CYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6237 (t) REVERT: N 283 ARG cc_start: 0.4331 (tpp-160) cc_final: 0.3016 (mtp180) REVERT: N 345 MET cc_start: 0.5611 (mmm) cc_final: 0.5059 (ptp) REVERT: N 414 MET cc_start: 0.5718 (mmt) cc_final: 0.5198 (mmm) REVERT: O 24 ARG cc_start: 0.7046 (mpp80) cc_final: 0.6708 (mtt180) REVERT: O 68 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7641 (t0) REVERT: O 85 LYS cc_start: 0.8401 (tppt) cc_final: 0.7836 (mtpp) REVERT: O 210 LEU cc_start: 0.8346 (tt) cc_final: 0.7737 (mt) REVERT: O 217 HIS cc_start: 0.4409 (OUTLIER) cc_final: 0.3278 (p-80) REVERT: O 347 LYS cc_start: 0.8484 (tmtt) cc_final: 0.8017 (tppt) REVERT: O 359 ILE cc_start: 0.8007 (mp) cc_final: 0.7595 (pt) REVERT: O 390 LYS cc_start: 0.6301 (pptt) cc_final: 0.5954 (mmmt) REVERT: O 497 LYS cc_start: 0.8965 (tptt) cc_final: 0.8658 (tptp) outliers start: 140 outliers final: 101 residues processed: 595 average time/residue: 0.4411 time to fit residues: 417.7442 Evaluate side-chains 594 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 475 time to evaluate : 3.142 ------------------------------------------------------------------------------- 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 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 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 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 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 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 316 ASN Chi-restraints excluded: chain F residue 345 MET 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 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 344 GLU 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 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 291 PHE 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 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 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 305 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 N residue 8 SER 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 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 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 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 283 LEU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 367 ASP Chi-restraints excluded: chain O residue 389 THR Chi-restraints excluded: chain O residue 405 ILE Chi-restraints excluded: chain O residue 406 MET Chi-restraints excluded: chain O residue 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 138 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 273 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 245 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** 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 188 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.192469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149292 restraints weight = 54211.388| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.97 r_work: 0.3939 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32056 Z= 0.124 Angle : 0.617 14.361 44015 Z= 0.318 Chirality : 0.043 0.413 4828 Planarity : 0.004 0.045 4975 Dihedral : 16.006 93.565 5689 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.04 % Allowed : 31.42 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3303 helix: 1.13 (0.15), residues: 1128 sheet: -0.76 (0.21), residues: 603 loop : -1.33 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP O 231 HIS 0.006 0.001 HIS J 9 PHE 0.037 0.001 PHE F 17 TYR 0.018 0.001 TYR F 233 ARG 0.010 0.001 ARG J 114 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 1248) hydrogen bonds : angle 4.63303 ( 3670) covalent geometry : bond 0.00279 (32056) covalent geometry : angle 0.61683 (44015) *********************** 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 633 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 512 time to evaluate : 3.571 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: 0.7598 (t0) cc_final: 0.7096 (t0) REVERT: A 71 ARG cc_start: 0.7042 (tpp-160) cc_final: 0.6797 (ttm110) REVERT: A 92 MET cc_start: 0.5735 (tpp) cc_final: 0.5240 (mmt) REVERT: A 100 ASP cc_start: 0.8530 (t70) cc_final: 0.8002 (t0) REVERT: A 122 LYS cc_start: 0.7870 (ptpt) cc_final: 0.7666 (mttm) REVERT: A 179 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.5959 (tp) REVERT: A 262 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: A 271 LYS cc_start: 0.8318 (tppt) cc_final: 0.7551 (mttp) REVERT: A 389 ASN cc_start: 0.7744 (p0) cc_final: 0.7299 (t0) REVERT: B 74 MET cc_start: 0.5517 (tpp) cc_final: 0.4866 (ttm) REVERT: B 132 ASP cc_start: 0.7579 (m-30) cc_final: 0.7319 (m-30) REVERT: B 225 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8118 (ttp-170) REVERT: B 233 ASP cc_start: 0.7312 (m-30) cc_final: 0.6510 (t0) REVERT: B 321 TYR cc_start: 0.7663 (m-80) cc_final: 0.7350 (m-80) REVERT: B 358 PHE cc_start: 0.7952 (t80) cc_final: 0.7685 (t80) REVERT: F 160 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6732 (p-80) REVERT: F 215 CYS cc_start: 0.6096 (t) cc_final: 0.5743 (p) REVERT: F 276 ARG cc_start: 0.7472 (tpt170) cc_final: 0.6721 (mmm160) REVERT: F 295 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7954 (pt) REVERT: F 314 GLN cc_start: 0.5167 (OUTLIER) cc_final: 0.4922 (pp30) REVERT: G 226 GLU cc_start: 0.6310 (mt-10) cc_final: 0.6070 (mt-10) REVERT: G 243 ARG cc_start: 0.6370 (mtp180) cc_final: 0.5898 (mtp180) REVERT: G 349 GLN cc_start: 0.5926 (mt0) cc_final: 0.5068 (tp40) REVERT: G 449 GLU cc_start: 0.6377 (pm20) cc_final: 0.5587 (pp20) REVERT: J 33 TRP cc_start: 0.8240 (t60) cc_final: 0.7873 (t60) REVERT: J 69 ASN cc_start: 0.7533 (m-40) cc_final: 0.7319 (m110) REVERT: J 137 LYS cc_start: 0.6798 (pptt) cc_final: 0.6215 (ptpt) REVERT: J 160 HIS cc_start: 0.6220 (OUTLIER) cc_final: 0.4758 (p-80) REVERT: J 161 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.4793 (p0) REVERT: J 189 ARG cc_start: 0.5987 (ttt-90) cc_final: 0.5517 (ttt-90) REVERT: J 213 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: J 260 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6133 (mm-30) REVERT: J 271 LYS cc_start: 0.7030 (tptp) cc_final: 0.5734 (mmmt) REVERT: J 354 LYS cc_start: 0.4162 (OUTLIER) cc_final: 0.3811 (tptt) REVERT: K 57 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5693 (tp) REVERT: K 79 GLU cc_start: 0.7467 (mp0) cc_final: 0.6914 (mp0) REVERT: K 86 TRP cc_start: 0.7365 (t60) cc_final: 0.7148 (t60) REVERT: K 215 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7549 (mt) REVERT: K 217 HIS cc_start: 0.4850 (OUTLIER) cc_final: 0.3838 (p90) REVERT: K 271 LEU cc_start: 0.5395 (pt) cc_final: 0.5038 (tp) REVERT: K 286 LYS cc_start: 0.8363 (mmpt) cc_final: 0.7990 (mmmt) REVERT: K 324 GLU cc_start: 0.4777 (mp0) cc_final: 0.4325 (mp0) REVERT: K 328 TYR cc_start: 0.6990 (m-80) cc_final: 0.6590 (m-80) REVERT: K 467 TYR cc_start: 0.8167 (m-80) cc_final: 0.7760 (m-80) REVERT: N 278 LYS cc_start: 0.2434 (mmmt) cc_final: 0.1996 (tptt) REVERT: N 283 ARG cc_start: 0.4280 (tpp-160) cc_final: 0.3339 (mtp180) REVERT: N 345 MET cc_start: 0.5471 (mmm) cc_final: 0.4775 (ptp) REVERT: N 393 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7484 (tp) REVERT: N 414 MET cc_start: 0.5719 (mmt) cc_final: 0.5447 (mmm) REVERT: O 24 ARG cc_start: 0.7020 (mpp80) cc_final: 0.6687 (mtt180) REVERT: O 68 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7632 (t0) REVERT: O 85 LYS cc_start: 0.8411 (tppt) cc_final: 0.7825 (mtpp) REVERT: O 210 LEU cc_start: 0.8292 (tt) cc_final: 0.7738 (mt) REVERT: O 217 HIS cc_start: 0.4504 (OUTLIER) cc_final: 0.3424 (p-80) REVERT: O 225 ARG cc_start: 0.5551 (mtm180) cc_final: 0.5324 (mtm180) REVERT: O 233 ASP cc_start: 0.6890 (p0) cc_final: 0.6172 (t0) REVERT: O 347 LYS cc_start: 0.8472 (tmtt) cc_final: 0.8005 (tppt) REVERT: O 390 LYS cc_start: 0.6382 (pptt) cc_final: 0.5995 (mmmt) REVERT: O 497 LYS cc_start: 0.8943 (tptt) cc_final: 0.8637 (tptp) outliers start: 121 outliers final: 89 residues processed: 590 average time/residue: 0.4311 time to fit residues: 405.0332 Evaluate side-chains 582 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 478 time to evaluate : 3.017 ------------------------------------------------------------------------------- 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 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 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 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 423 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 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 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 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 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 370 ASN 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 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 305 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 N residue 3 ASN Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 210 TYR 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 393 LEU Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain O residue 72 ARG 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 367 ASP Chi-restraints excluded: chain O residue 389 THR 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 106 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 336 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 165 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 GLN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 446 ASN N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 HIS ** N 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.192177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.148864 restraints weight = 54500.799| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.98 r_work: 0.3936 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32056 Z= 0.134 Angle : 0.639 14.263 44015 Z= 0.328 Chirality : 0.044 0.321 4828 Planarity : 0.004 0.068 4975 Dihedral : 15.994 93.168 5689 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.80 % Allowed : 31.85 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3303 helix: 1.10 (0.15), residues: 1128 sheet: -0.76 (0.21), residues: 603 loop : -1.33 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP F 20 HIS 0.006 0.001 HIS K 217 PHE 0.033 0.002 PHE F 17 TYR 0.012 0.001 TYR O 6 ARG 0.017 0.001 ARG O 362 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1248) hydrogen bonds : angle 4.66628 ( 3670) covalent geometry : bond 0.00305 (32056) covalent geometry : angle 0.63887 (44015) ********************** 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 615 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 501 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7680 (t0) cc_final: 0.7103 (t0) REVERT: A 71 ARG cc_start: 0.7024 (tpp-160) cc_final: 0.6776 (ttm110) REVERT: A 92 MET cc_start: 0.5753 (tpp) cc_final: 0.5188 (mmt) REVERT: A 100 ASP cc_start: 0.8540 (t70) cc_final: 0.8011 (t0) REVERT: A 179 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.5870 (tp) REVERT: A 262 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: A 389 ASN cc_start: 0.7714 (p0) cc_final: 0.7332 (t0) REVERT: B 74 MET cc_start: 0.5700 (tpp) cc_final: 0.5183 (ttm) REVERT: B 132 ASP cc_start: 0.7639 (m-30) cc_final: 0.7378 (m-30) REVERT: B 233 ASP cc_start: 0.7313 (m-30) cc_final: 0.6488 (t0) REVERT: B 358 PHE cc_start: 0.7980 (t80) cc_final: 0.7702 (t80) REVERT: F 160 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.6737 (p-80) REVERT: F 215 CYS cc_start: 0.6164 (t) cc_final: 0.5762 (p) REVERT: F 276 ARG cc_start: 0.7484 (tpt170) cc_final: 0.6769 (mmm160) REVERT: F 295 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7858 (pt) REVERT: F 314 GLN cc_start: 0.5172 (OUTLIER) cc_final: 0.4813 (pp30) REVERT: G 226 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6022 (mt-10) REVERT: G 243 ARG cc_start: 0.6400 (mtp180) cc_final: 0.5935 (mtp180) REVERT: G 349 GLN cc_start: 0.5956 (mt0) cc_final: 0.5070 (tp40) REVERT: G 356 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6426 (tm-30) REVERT: G 449 GLU cc_start: 0.6326 (pm20) cc_final: 0.5557 (pp20) REVERT: J 33 TRP cc_start: 0.8184 (t60) cc_final: 0.7733 (t60) REVERT: J 69 ASN cc_start: 0.7570 (m-40) cc_final: 0.7364 (m110) REVERT: J 137 LYS cc_start: 0.6931 (pptt) cc_final: 0.6351 (ptpt) REVERT: J 160 HIS cc_start: 0.6205 (OUTLIER) cc_final: 0.4755 (p-80) REVERT: J 161 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.4790 (p0) REVERT: J 189 ARG cc_start: 0.5879 (ttt-90) cc_final: 0.5393 (ttt-90) REVERT: J 213 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: J 260 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6150 (mm-30) REVERT: J 271 LYS cc_start: 0.6934 (tptp) cc_final: 0.5615 (mmmt) REVERT: J 291 PHE cc_start: 0.6046 (t80) cc_final: 0.5828 (t80) REVERT: J 354 LYS cc_start: 0.4162 (OUTLIER) cc_final: 0.3838 (tptt) REVERT: K 57 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5727 (tp) REVERT: K 86 TRP cc_start: 0.7461 (t60) cc_final: 0.7223 (t60) REVERT: K 215 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7588 (mt) REVERT: K 217 HIS cc_start: 0.4852 (OUTLIER) cc_final: 0.3841 (p90) REVERT: K 271 LEU cc_start: 0.5588 (pt) cc_final: 0.5358 (tt) REVERT: K 286 LYS cc_start: 0.8390 (mmpt) cc_final: 0.8060 (mmmt) REVERT: K 324 GLU cc_start: 0.4775 (mp0) cc_final: 0.4320 (mp0) REVERT: K 328 TYR cc_start: 0.7088 (m-80) cc_final: 0.6714 (m-80) REVERT: K 467 TYR cc_start: 0.8171 (m-80) cc_final: 0.7798 (m-80) REVERT: N 215 CYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6293 (t) REVERT: N 278 LYS cc_start: 0.2717 (mmmt) cc_final: 0.2167 (tptt) REVERT: N 283 ARG cc_start: 0.4333 (tpp-160) cc_final: 0.3105 (ttt180) REVERT: N 345 MET cc_start: 0.5444 (mmm) cc_final: 0.4767 (ptp) REVERT: N 393 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7487 (tp) REVERT: N 414 MET cc_start: 0.5710 (mmt) cc_final: 0.5447 (mmm) REVERT: O 24 ARG cc_start: 0.7020 (mpp80) cc_final: 0.6670 (mtt180) REVERT: O 68 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7658 (t0) REVERT: O 85 LYS cc_start: 0.8384 (tppt) cc_final: 0.7794 (mtpp) REVERT: O 210 LEU cc_start: 0.8268 (tt) cc_final: 0.7730 (mt) REVERT: O 217 HIS cc_start: 0.4518 (OUTLIER) cc_final: 0.3432 (p-80) REVERT: O 225 ARG cc_start: 0.5343 (mtm180) cc_final: 0.5130 (mtm180) REVERT: O 347 LYS cc_start: 0.8465 (tmtt) cc_final: 0.7986 (tppt) REVERT: O 358 PHE cc_start: 0.7714 (t80) cc_final: 0.7495 (t80) REVERT: O 390 LYS cc_start: 0.6296 (pptt) cc_final: 0.6056 (mmmt) REVERT: O 409 ASN cc_start: 0.7281 (m-40) cc_final: 0.7060 (m-40) REVERT: O 497 LYS cc_start: 0.8984 (tptt) cc_final: 0.8647 (tptp) outliers start: 114 outliers final: 86 residues processed: 577 average time/residue: 0.4847 time to fit residues: 449.1005 Evaluate side-chains 579 residues out of total 2998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 477 time to evaluate : 3.073 ------------------------------------------------------------------------------- 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 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 B residue 60 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 75 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 311 VAL Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 345 MET 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 217 HIS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain J residue 16 ASP 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 370 ASN 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 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 305 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 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 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 68 ASN Chi-restraints excluded: chain O residue 72 ARG 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 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 389 THR Chi-restraints excluded: chain O residue 443 ILE 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 33 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 305 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** G 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 HIS ** N 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.191481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.148100 restraints weight = 54278.856| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.98 r_work: 0.3926 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32056 Z= 0.141 Angle : 0.642 14.182 44015 Z= 0.329 Chirality : 0.044 0.266 4828 Planarity : 0.004 0.048 4975 Dihedral : 15.987 93.778 5689 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.67 % Allowed : 32.15 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3303 helix: 1.04 (0.15), residues: 1128 sheet: -0.79 (0.21), residues: 603 loop : -1.35 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP F 20 HIS 0.008 0.001 HIS F 320 PHE 0.038 0.002 PHE F 273 TYR 0.019 0.001 TYR F 233 ARG 0.011 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 1248) hydrogen bonds : angle 4.65427 ( 3670) covalent geometry : bond 0.00325 (32056) covalent geometry : angle 0.64160 (44015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21046.18 seconds wall clock time: 363 minutes 0.49 seconds (21780.49 seconds total)