Starting phenix.real_space_refine on Wed Jan 14 22:33:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y22_33583/01_2026/7y22_33583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y22_33583/01_2026/7y22_33583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y22_33583/01_2026/7y22_33583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y22_33583/01_2026/7y22_33583.map" model { file = "/net/cci-nas-00/data/ceres_data/7y22_33583/01_2026/7y22_33583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y22_33583/01_2026/7y22_33583.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 12624 2.51 5 N 3393 2.21 5 O 3772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19881 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3121 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 4 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3121 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 4 Chain: "M" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1687 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 9, 'TRANS': 205} Chain: "X" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1650 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "Y" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6195 Classifications: {'peptide': 794} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 761} Chain: "e" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1369 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "f" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1369 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "g" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1369 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Time building chain proxies: 4.10, per 1000 atoms: 0.21 Number of scatterers: 19881 At special positions: 0 Unit cell: (111.15, 152.1, 294.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3772 8.00 N 3393 7.00 C 12624 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: 1.59 Conformation dependent library (CDL) restraints added in 781.6 milliseconds 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 30 sheets defined 31.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 41 removed outlier: 4.824A pdb=" N GLU A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 40 " --> pdb=" O HIS A 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 79 Processing helix chain 'A' and resid 107 through 125 removed outlier: 4.533A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 271 through 298 removed outlier: 4.035A pdb=" N TYR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 341 through 360 removed outlier: 3.711A pdb=" N ASP A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.769A pdb=" N VAL A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.600A pdb=" N ASN A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'B' and resid 16 through 41 removed outlier: 3.917A pdb=" N LYS B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 40 " --> pdb=" O HIS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 79 Processing helix chain 'B' and resid 108 through 125 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.531A pdb=" N THR B 192 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 193 " --> pdb=" O LEU B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 193' Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 271 through 274 Processing helix chain 'B' and resid 275 through 298 removed outlier: 3.517A pdb=" N ASP B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 341 through 360 removed outlier: 3.986A pdb=" N ASP B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.688A pdb=" N ASN B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.549A pdb=" N LEU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'M' and resid 6 through 12 removed outlier: 3.732A pdb=" N MET M 11 " --> pdb=" O THR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 30 removed outlier: 3.583A pdb=" N ALA M 25 " --> pdb=" O THR M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 65 removed outlier: 3.840A pdb=" N GLU M 49 " --> pdb=" O ASP M 45 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN M 60 " --> pdb=" O ASP M 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN M 65 " --> pdb=" O ARG M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 74 Processing helix chain 'M' and resid 151 through 171 removed outlier: 3.530A pdb=" N LEU M 155 " --> pdb=" O PRO M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 198 removed outlier: 4.711A pdb=" N GLU M 194 " --> pdb=" O GLY M 190 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 195 " --> pdb=" O MET M 191 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER M 196 " --> pdb=" O GLN M 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS M 197 " --> pdb=" O VAL M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Processing helix chain 'X' and resid 21 through 31 removed outlier: 3.632A pdb=" N ALA X 25 " --> pdb=" O THR X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 63 removed outlier: 3.734A pdb=" N ASP X 50 " --> pdb=" O LEU X 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN X 60 " --> pdb=" O ASP X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 131 Processing helix chain 'X' and resid 151 through 170 removed outlier: 3.631A pdb=" N LEU X 155 " --> pdb=" O PRO X 151 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 198 removed outlier: 3.565A pdb=" N VAL X 193 " --> pdb=" O THR X 189 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU X 194 " --> pdb=" O GLY X 190 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU X 195 " --> pdb=" O MET X 191 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER X 196 " --> pdb=" O GLN X 192 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 216 Processing helix chain 'Y' and resid 55 through 59 removed outlier: 3.515A pdb=" N LEU Y 58 " --> pdb=" O ASP Y 55 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE Y 59 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 55 through 59' Processing helix chain 'Y' and resid 104 through 108 removed outlier: 3.820A pdb=" N SER Y 107 " --> pdb=" O GLY Y 104 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR Y 108 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 108' Processing helix chain 'Y' and resid 113 through 118 Processing helix chain 'Y' and resid 182 through 189 removed outlier: 3.831A pdb=" N VAL Y 186 " --> pdb=" O ALA Y 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU Y 187 " --> pdb=" O SER Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 205 Processing helix chain 'Y' and resid 206 through 210 removed outlier: 3.720A pdb=" N SER Y 209 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 274 through 278 removed outlier: 3.532A pdb=" N ARG Y 278 " --> pdb=" O PRO Y 275 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 32 No H-bonds generated for 'chain 'e' and resid 30 through 32' Processing helix chain 'e' and resid 92 through 113 removed outlier: 4.221A pdb=" N LEU e 96 " --> pdb=" O ASP e 92 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR e 107 " --> pdb=" O LEU e 103 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU e 109 " --> pdb=" O GLU e 105 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU e 110 " --> pdb=" O ILE e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 174 removed outlier: 3.771A pdb=" N LEU e 150 " --> pdb=" O ASN e 146 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 32 No H-bonds generated for 'chain 'f' and resid 30 through 32' Processing helix chain 'f' and resid 92 through 112 removed outlier: 3.942A pdb=" N THR f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 146 through 173 removed outlier: 3.579A pdb=" N ARG f 170 " --> pdb=" O ILE f 166 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN f 171 " --> pdb=" O TRP f 167 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN f 173 " --> pdb=" O ASP f 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 32 No H-bonds generated for 'chain 'g' and resid 30 through 32' Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.597A pdb=" N PHE g 100 " --> pdb=" O LEU g 96 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR g 107 " --> pdb=" O LEU g 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU g 110 " --> pdb=" O ILE g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 146 through 174 removed outlier: 3.688A pdb=" N LEU g 150 " --> pdb=" O ASN g 146 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN g 171 " --> pdb=" O TRP g 167 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN g 173 " --> pdb=" O ASP g 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 164 removed outlier: 3.641A pdb=" N CYS A 145 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 removed outlier: 7.822A pdb=" N MET A 180 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A 224 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP A 230 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N SER A 245 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 232 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS A 243 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN A 234 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 173 removed outlier: 7.207A pdb=" N MET B 180 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 224 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TRP B 230 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER B 245 " --> pdb=" O TRP B 230 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 232 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS B 243 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN B 234 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 99 removed outlier: 4.228A pdb=" N GLN M 96 " --> pdb=" O MET M 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 111 through 112 Processing sheet with id=AA7, first strand: chain 'X' and resid 74 through 75 removed outlier: 3.716A pdb=" N LEU X 141 " --> pdb=" O GLU X 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 111 through 112 Processing sheet with id=AA9, first strand: chain 'Y' and resid 3 through 9 removed outlier: 6.228A pdb=" N ILE Y 781 " --> pdb=" O LEU Y 7 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG Y 9 " --> pdb=" O ARG Y 779 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ARG Y 779 " --> pdb=" O ARG Y 9 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU Y 778 " --> pdb=" O ASP Y 709 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP Y 709 " --> pdb=" O LEU Y 778 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER Y 786 " --> pdb=" O ILE Y 701 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE Y 701 " --> pdb=" O SER Y 786 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL Y 700 " --> pdb=" O ALA Y 759 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA Y 759 " --> pdb=" O VAL Y 700 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLY Y 702 " --> pdb=" O LEU Y 757 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU Y 757 " --> pdb=" O GLY Y 702 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 29 through 31 Processing sheet with id=AB2, first strand: chain 'Y' and resid 35 through 36 Processing sheet with id=AB3, first strand: chain 'Y' and resid 47 through 54 removed outlier: 5.381A pdb=" N HIS Y 49 " --> pdb=" O ALA Y 579 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA Y 579 " --> pdb=" O HIS Y 49 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA Y 51 " --> pdb=" O LEU Y 577 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL Y 575 " --> pdb=" O LEU Y 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE Y 568 " --> pdb=" O GLY Y 557 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY Y 557 " --> pdb=" O ILE Y 568 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS Y 570 " --> pdb=" O ILE Y 555 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE Y 555 " --> pdb=" O LYS Y 570 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 64 through 70 removed outlier: 3.506A pdb=" N ASN Y 64 " --> pdb=" O THR Y 81 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Y 75 " --> pdb=" O ARG Y 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 98 through 100 removed outlier: 6.421A pdb=" N THR Y 98 " --> pdb=" O PHE Y 326 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE Y 328 " --> pdb=" O THR Y 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR Y 100 " --> pdb=" O ILE Y 328 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE Y 323 " --> pdb=" O ILE Y 319 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE Y 319 " --> pdb=" O ILE Y 323 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN Y 325 " --> pdb=" O THR Y 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 212 through 216 Processing sheet with id=AB7, first strand: chain 'Y' and resid 162 through 166 removed outlier: 3.783A pdb=" N ILE Y 165 " --> pdb=" O ALA Y 173 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ALA Y 173 " --> pdb=" O ILE Y 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 249 through 250 removed outlier: 3.511A pdb=" N TYR Y 264 " --> pdb=" O ALA Y 283 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP Y 280 " --> pdb=" O THR Y 296 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR Y 292 " --> pdb=" O GLU Y 284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 356 through 360 removed outlier: 3.879A pdb=" N CYS Y 372 " --> pdb=" O VAL Y 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 411 through 415 Processing sheet with id=AC2, first strand: chain 'Y' and resid 458 through 459 removed outlier: 3.594A pdb=" N TYR Y 480 " --> pdb=" O LYS Y 489 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 505 through 511 removed outlier: 4.794A pdb=" N HIS Y 507 " --> pdb=" O LEU Y 520 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER Y 521 " --> pdb=" O ARG Y 527 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG Y 527 " --> pdb=" O SER Y 521 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN Y 542 " --> pdb=" O LEU Y 534 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN Y 536 " --> pdb=" O LYS Y 540 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS Y 540 " --> pdb=" O GLN Y 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 642 through 643 removed outlier: 4.600A pdb=" N ALA Y 629 " --> pdb=" O PHE Y 643 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU Y 628 " --> pdb=" O GLY Y 672 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY Y 672 " --> pdb=" O GLU Y 628 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA Y 668 " --> pdb=" O THR Y 632 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN Y 673 " --> pdb=" O ARG Y 597 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARG Y 597 " --> pdb=" O GLN Y 673 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU Y 654 " --> pdb=" O SER Y 614 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 6 through 10 removed outlier: 4.589A pdb=" N VAL e 69 " --> pdb=" O TRP e 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 16 through 18 Processing sheet with id=AC7, first strand: chain 'e' and resid 132 through 133 removed outlier: 3.955A pdb=" N VAL e 133 " --> pdb=" O LEU f 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'f' and resid 6 through 10 removed outlier: 3.513A pdb=" N GLN f 68 " --> pdb=" O GLY f 10 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL f 69 " --> pdb=" O TRP f 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 16 through 18 Processing sheet with id=AD1, first strand: chain 'f' and resid 132 through 133 removed outlier: 3.866A pdb=" N VAL f 133 " --> pdb=" O LEU g 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'g' and resid 6 through 8 removed outlier: 4.829A pdb=" N VAL g 69 " --> pdb=" O TRP g 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'g' and resid 16 through 17 removed outlier: 3.551A pdb=" N THR g 59 " --> pdb=" O SER g 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER g 51 " --> pdb=" O THR g 59 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6548 1.34 - 1.46: 4380 1.46 - 1.58: 9234 1.58 - 1.70: 0 1.70 - 1.82: 169 Bond restraints: 20331 Sorted by residual: bond pdb=" CA ALA X 32 " pdb=" CB ALA X 32 " ideal model delta sigma weight residual 1.539 1.516 0.022 1.20e-02 6.94e+03 3.46e+00 bond pdb=" N VAL X 168 " pdb=" CA VAL X 168 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.25e-02 6.40e+03 3.03e+00 bond pdb=" C MET X 144 " pdb=" N LEU X 145 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.47e-02 4.63e+03 2.94e+00 bond pdb=" C PHE g 85 " pdb=" N GLU g 86 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.35e-02 5.49e+03 2.54e+00 bond pdb=" N GLN X 174 " pdb=" CA GLN X 174 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.21e-02 6.83e+03 1.90e+00 ... (remaining 20326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 27067 2.09 - 4.18: 448 4.18 - 6.27: 71 6.27 - 8.36: 15 8.36 - 10.45: 5 Bond angle restraints: 27606 Sorted by residual: angle pdb=" N ILE X 167 " pdb=" CA ILE X 167 " pdb=" C ILE X 167 " ideal model delta sigma weight residual 109.30 99.58 9.72 1.25e+00 6.40e-01 6.04e+01 angle pdb=" N PHE X 166 " pdb=" CA PHE X 166 " pdb=" C PHE X 166 " ideal model delta sigma weight residual 111.28 104.19 7.09 1.09e+00 8.42e-01 4.23e+01 angle pdb=" N VAL X 168 " pdb=" CA VAL X 168 " pdb=" CB VAL X 168 " ideal model delta sigma weight residual 111.23 120.94 -9.71 1.65e+00 3.67e-01 3.46e+01 angle pdb=" C ILE X 167 " pdb=" N VAL X 168 " pdb=" CA VAL X 168 " ideal model delta sigma weight residual 121.97 132.42 -10.45 1.80e+00 3.09e-01 3.37e+01 angle pdb=" C SER X 18 " pdb=" CA SER X 18 " pdb=" CB SER X 18 " ideal model delta sigma weight residual 116.63 110.10 6.53 1.16e+00 7.43e-01 3.17e+01 ... (remaining 27601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10862 17.96 - 35.92: 973 35.92 - 53.88: 135 53.88 - 71.84: 33 71.84 - 89.80: 24 Dihedral angle restraints: 12027 sinusoidal: 4753 harmonic: 7274 Sorted by residual: dihedral pdb=" N VAL X 168 " pdb=" C VAL X 168 " pdb=" CA VAL X 168 " pdb=" CB VAL X 168 " ideal model delta harmonic sigma weight residual 123.40 136.47 -13.07 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" CA ASP Y 486 " pdb=" C ASP Y 486 " pdb=" N THR Y 487 " pdb=" CA THR Y 487 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TRP A 259 " pdb=" C TRP A 259 " pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 12024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2666 0.065 - 0.130: 350 0.130 - 0.196: 20 0.196 - 0.261: 1 0.261 - 0.326: 4 Chirality restraints: 3041 Sorted by residual: chirality pdb=" CB VAL X 168 " pdb=" CA VAL X 168 " pdb=" CG1 VAL X 168 " pdb=" CG2 VAL X 168 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA VAL X 168 " pdb=" N VAL X 168 " pdb=" C VAL X 168 " pdb=" CB VAL X 168 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA ASP e 79 " pdb=" N ASP e 79 " pdb=" C ASP e 79 " pdb=" CB ASP e 79 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3038 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET f 136 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO f 137 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO f 137 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO f 137 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 156 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO A 157 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO X 133 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C PRO X 133 " 0.048 2.00e-02 2.50e+03 pdb=" O PRO X 133 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP X 134 " -0.016 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 428 2.68 - 3.24: 20207 3.24 - 3.79: 30053 3.79 - 4.35: 38858 4.35 - 4.90: 62968 Nonbonded interactions: 152514 Sorted by model distance: nonbonded pdb=" O ASN X 17 " pdb=" OG SER X 18 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP B 459 " pdb=" N ALA B 460 " model vdw 2.195 3.120 nonbonded pdb=" OD1 ASP g 140 " pdb=" N GLY g 141 " model vdw 2.206 3.120 nonbonded pdb=" O LEU X 204 " pdb=" N HIS X 206 " model vdw 2.219 3.120 nonbonded pdb=" OG SER X 124 " pdb=" OD1 ASP X 126 " model vdw 2.219 3.040 ... (remaining 152509 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' selection = chain 'B' } ncs_group { reference = (chain 'M' and resid 9 through 218) selection = chain 'X' } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' } 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 group one per residue 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: 97.520 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.750 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20331 Z= 0.139 Angle : 0.666 10.450 27606 Z= 0.362 Chirality : 0.044 0.326 3041 Planarity : 0.004 0.084 3579 Dihedral : 14.081 89.795 7353 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.42 % Favored : 93.14 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2491 helix: 1.67 (0.21), residues: 655 sheet: 0.04 (0.24), residues: 525 loop : -1.31 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 758 TYR 0.020 0.002 TYR A 301 PHE 0.017 0.001 PHE X 72 TRP 0.033 0.002 TRP g 167 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00277 (20331) covalent geometry : angle 0.66640 (27606) hydrogen bonds : bond 0.22467 ( 805) hydrogen bonds : angle 7.09404 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 612 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TRP cc_start: 0.9191 (t-100) cc_final: 0.8828 (t-100) REVERT: A 26 LYS cc_start: 0.9459 (tptp) cc_final: 0.9228 (tptt) REVERT: A 28 ASN cc_start: 0.8527 (m-40) cc_final: 0.7511 (t0) REVERT: A 32 ASP cc_start: 0.8046 (m-30) cc_final: 0.7319 (m-30) REVERT: A 33 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8122 (ttm110) REVERT: A 37 TYR cc_start: 0.8549 (m-10) cc_final: 0.7995 (m-10) REVERT: A 57 ASN cc_start: 0.7517 (m110) cc_final: 0.7236 (m110) REVERT: A 65 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8773 (tm-30) REVERT: A 112 PHE cc_start: 0.8938 (m-80) cc_final: 0.8543 (m-80) REVERT: A 127 GLN cc_start: 0.8487 (mp10) cc_final: 0.8247 (mp10) REVERT: A 172 GLN cc_start: 0.8733 (tt0) cc_final: 0.7448 (pt0) REVERT: A 185 LEU cc_start: 0.9198 (mp) cc_final: 0.8909 (mp) REVERT: A 304 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7725 (ttm110) REVERT: A 349 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 396 SER cc_start: 0.9245 (t) cc_final: 0.8971 (p) REVERT: A 410 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 453 TRP cc_start: 0.8244 (m-10) cc_final: 0.7203 (m100) REVERT: A 482 MET cc_start: 0.7342 (mmt) cc_final: 0.6625 (ttt) REVERT: B 79 PHE cc_start: 0.8630 (m-80) cc_final: 0.8418 (m-80) REVERT: B 112 PHE cc_start: 0.9478 (m-10) cc_final: 0.9270 (m-10) REVERT: B 191 ARG cc_start: 0.9420 (ptp90) cc_final: 0.8059 (ttt180) REVERT: B 230 TRP cc_start: 0.9269 (m100) cc_final: 0.8595 (m100) REVERT: B 263 TYR cc_start: 0.8292 (t80) cc_final: 0.7830 (t80) REVERT: B 274 ASP cc_start: 0.7524 (t0) cc_final: 0.6729 (t0) REVERT: B 287 GLU cc_start: 0.8893 (tt0) cc_final: 0.7791 (tt0) REVERT: B 438 ASP cc_start: 0.8517 (t70) cc_final: 0.8272 (t0) REVERT: B 467 MET cc_start: 0.8853 (mtm) cc_final: 0.8584 (mtm) REVERT: M 17 ASN cc_start: 0.8952 (t0) cc_final: 0.8546 (t0) REVERT: M 50 ASP cc_start: 0.8682 (m-30) cc_final: 0.8406 (m-30) REVERT: M 52 ASP cc_start: 0.9094 (t70) cc_final: 0.8827 (t0) REVERT: M 77 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7742 (mtp85) REVERT: M 83 ASP cc_start: 0.8305 (p0) cc_final: 0.7899 (p0) REVERT: M 116 ARG cc_start: 0.8937 (ptp90) cc_final: 0.7047 (ptt180) REVERT: M 176 LYS cc_start: 0.9519 (mttt) cc_final: 0.9199 (mtpt) REVERT: M 195 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8561 (tm-30) REVERT: M 202 ASN cc_start: 0.8738 (p0) cc_final: 0.7417 (t0) REVERT: X 40 ASN cc_start: 0.9106 (t0) cc_final: 0.8725 (t0) REVERT: X 47 ASP cc_start: 0.8455 (t70) cc_final: 0.8222 (t70) REVERT: X 144 MET cc_start: 0.8460 (tmm) cc_final: 0.7964 (tmm) REVERT: X 170 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8031 (mttt) REVERT: X 176 LYS cc_start: 0.9265 (mttm) cc_final: 0.8516 (mmtt) REVERT: Y 36 ASP cc_start: 0.8588 (t70) cc_final: 0.7892 (p0) REVERT: Y 374 MET cc_start: 0.8412 (mmp) cc_final: 0.8169 (mmp) REVERT: Y 395 ASP cc_start: 0.8220 (m-30) cc_final: 0.7765 (m-30) REVERT: Y 696 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7720 (tm-30) REVERT: Y 697 ASP cc_start: 0.8062 (m-30) cc_final: 0.7437 (m-30) REVERT: e 24 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8610 (mmmt) REVERT: e 37 GLU cc_start: 0.6081 (tm-30) cc_final: 0.4353 (tm-30) REVERT: e 85 PHE cc_start: 0.8389 (m-80) cc_final: 0.7427 (m-80) REVERT: e 86 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7576 (mm-30) REVERT: e 93 MET cc_start: 0.7323 (ttp) cc_final: 0.7103 (ttp) REVERT: f 90 MET cc_start: 0.7679 (mmt) cc_final: 0.7379 (tpp) REVERT: g 79 ASP cc_start: 0.8398 (p0) cc_final: 0.8172 (p0) REVERT: g 105 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8555 (tm-30) REVERT: g 132 ILE cc_start: 0.8970 (mm) cc_final: 0.8741 (mm) REVERT: g 155 SER cc_start: 0.9286 (p) cc_final: 0.8914 (p) REVERT: g 158 ASP cc_start: 0.9064 (m-30) cc_final: 0.8849 (m-30) REVERT: g 169 ASP cc_start: 0.9065 (m-30) cc_final: 0.8728 (m-30) outliers start: 2 outliers final: 0 residues processed: 614 average time/residue: 0.1375 time to fit residues: 131.7513 Evaluate side-chains 499 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 170 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 186 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 331 HIS A 409 GLN B 127 GLN B 138 HIS B 316 ASN B 448 ASN M 73 ASN M 153 ASN M 198 GLN ** X 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 96 GLN ** X 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 GLN ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 156 HIS ** e 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 130 ASN ** f 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.086371 restraints weight = 65544.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088543 restraints weight = 35829.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090025 restraints weight = 23563.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091032 restraints weight = 17377.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091753 restraints weight = 13887.582| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20331 Z= 0.226 Angle : 0.684 10.025 27606 Z= 0.359 Chirality : 0.046 0.328 3041 Planarity : 0.005 0.058 3579 Dihedral : 4.772 43.695 2720 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.66 % Favored : 92.89 % Rotamer: Outliers : 2.30 % Allowed : 14.39 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2491 helix: 1.94 (0.20), residues: 655 sheet: 0.08 (0.24), residues: 513 loop : -1.32 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 71 TYR 0.029 0.002 TYR Y 560 PHE 0.028 0.002 PHE B 128 TRP 0.063 0.002 TRP g 167 HIS 0.004 0.001 HIS g 156 Details of bonding type rmsd covalent geometry : bond 0.00504 (20331) covalent geometry : angle 0.68442 (27606) hydrogen bonds : bond 0.04663 ( 805) hydrogen bonds : angle 5.16324 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 524 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8631 (m-40) cc_final: 0.7528 (t0) REVERT: A 32 ASP cc_start: 0.8104 (m-30) cc_final: 0.7414 (m-30) REVERT: A 33 ARG cc_start: 0.8922 (mmm-85) cc_final: 0.8286 (ttm110) REVERT: A 57 ASN cc_start: 0.7572 (m110) cc_final: 0.7115 (m110) REVERT: A 112 PHE cc_start: 0.8875 (m-80) cc_final: 0.8270 (m-80) REVERT: A 164 ILE cc_start: 0.8687 (pt) cc_final: 0.8385 (pt) REVERT: A 244 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9096 (p) REVERT: A 304 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7562 (ttp80) REVERT: A 349 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 396 SER cc_start: 0.9288 (t) cc_final: 0.9031 (p) REVERT: A 409 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.6738 (pp30) REVERT: A 410 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 459 ASP cc_start: 0.8996 (p0) cc_final: 0.8530 (p0) REVERT: A 477 ASP cc_start: 0.7076 (t0) cc_final: 0.6846 (t0) REVERT: A 482 MET cc_start: 0.7462 (mmt) cc_final: 0.6793 (ttt) REVERT: B 15 LYS cc_start: 0.8539 (ttmt) cc_final: 0.7251 (ttmm) REVERT: B 112 PHE cc_start: 0.9435 (m-10) cc_final: 0.9200 (m-10) REVERT: B 174 ASP cc_start: 0.8260 (p0) cc_final: 0.8005 (p0) REVERT: B 180 MET cc_start: 0.8609 (mmm) cc_final: 0.7966 (mmm) REVERT: B 191 ARG cc_start: 0.9377 (ptp90) cc_final: 0.8045 (ttt180) REVERT: B 230 TRP cc_start: 0.9382 (m100) cc_final: 0.8675 (m100) REVERT: B 233 GLN cc_start: 0.8700 (tt0) cc_final: 0.8482 (mt0) REVERT: B 238 ASP cc_start: 0.7619 (t0) cc_final: 0.7369 (t0) REVERT: B 274 ASP cc_start: 0.7521 (t0) cc_final: 0.6774 (t0) REVERT: B 287 GLU cc_start: 0.9038 (tt0) cc_final: 0.7973 (tt0) REVERT: B 304 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7697 (mtm110) REVERT: B 321 GLU cc_start: 0.6340 (mp0) cc_final: 0.5952 (mp0) REVERT: B 438 ASP cc_start: 0.8467 (t70) cc_final: 0.8195 (t0) REVERT: M 17 ASN cc_start: 0.8944 (t0) cc_final: 0.8371 (t0) REVERT: M 50 ASP cc_start: 0.8625 (m-30) cc_final: 0.8315 (m-30) REVERT: M 77 ARG cc_start: 0.8205 (mtp-110) cc_final: 0.7710 (mtp-110) REVERT: M 121 THR cc_start: 0.9372 (t) cc_final: 0.9074 (m) REVERT: M 176 LYS cc_start: 0.9278 (mttt) cc_final: 0.9014 (mtpt) REVERT: M 195 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8645 (tm-30) REVERT: M 197 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8181 (tptt) REVERT: X 29 CYS cc_start: 0.9002 (t) cc_final: 0.8743 (t) REVERT: X 33 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8366 (mm) REVERT: X 40 ASN cc_start: 0.9122 (t0) cc_final: 0.8640 (t0) REVERT: X 46 LEU cc_start: 0.9141 (pt) cc_final: 0.8933 (pp) REVERT: X 122 LEU cc_start: 0.9048 (tp) cc_final: 0.8825 (tt) REVERT: X 150 MET cc_start: 0.8430 (mmt) cc_final: 0.8061 (mtt) REVERT: X 183 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7625 (ttm) REVERT: X 194 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8844 (tm-30) REVERT: X 195 GLU cc_start: 0.8363 (tp30) cc_final: 0.7970 (tp30) REVERT: Y 508 MET cc_start: 0.8167 (mtp) cc_final: 0.7922 (mtp) REVERT: Y 674 MET cc_start: 0.8477 (tpp) cc_final: 0.7655 (tpt) REVERT: Y 678 GLU cc_start: 0.8464 (tt0) cc_final: 0.8127 (tp30) REVERT: Y 696 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7944 (tm-30) REVERT: Y 697 ASP cc_start: 0.7720 (m-30) cc_final: 0.7154 (m-30) REVERT: Y 758 ARG cc_start: 0.8412 (mmp80) cc_final: 0.6306 (tpt170) REVERT: e 37 GLU cc_start: 0.6449 (tm-30) cc_final: 0.5657 (tm-30) REVERT: e 85 PHE cc_start: 0.8575 (m-80) cc_final: 0.7543 (m-80) REVERT: e 86 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7839 (mm-30) REVERT: e 93 MET cc_start: 0.7273 (ttp) cc_final: 0.6935 (ttp) outliers start: 49 outliers final: 32 residues processed: 541 average time/residue: 0.1376 time to fit residues: 116.3852 Evaluate side-chains 537 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 501 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 183 MET Chi-restraints excluded: chain Y residue 156 TYR Chi-restraints excluded: chain Y residue 512 THR Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain Y residue 749 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain f residue 157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 96 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 218 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 448 ASN B 331 HIS M 73 ASN ** X 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 206 HIS ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 134 ASN ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.087084 restraints weight = 65207.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089291 restraints weight = 35239.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090786 restraints weight = 23044.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.091809 restraints weight = 16914.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092518 restraints weight = 13469.813| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20331 Z= 0.162 Angle : 0.625 9.770 27606 Z= 0.325 Chirality : 0.044 0.295 3041 Planarity : 0.004 0.060 3579 Dihedral : 4.654 47.927 2720 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.30 % Favored : 93.26 % Rotamer: Outliers : 3.09 % Allowed : 17.53 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2491 helix: 2.05 (0.19), residues: 658 sheet: 0.14 (0.24), residues: 508 loop : -1.36 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 74 TYR 0.030 0.002 TYR B 446 PHE 0.024 0.001 PHE B 128 TRP 0.069 0.002 TRP g 167 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00361 (20331) covalent geometry : angle 0.62542 (27606) hydrogen bonds : bond 0.04194 ( 805) hydrogen bonds : angle 4.82219 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 532 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TRP cc_start: 0.9312 (t-100) cc_final: 0.8970 (t-100) REVERT: A 28 ASN cc_start: 0.8610 (m-40) cc_final: 0.7548 (t0) REVERT: A 32 ASP cc_start: 0.8052 (m-30) cc_final: 0.7322 (m-30) REVERT: A 33 ARG cc_start: 0.8926 (mmm-85) cc_final: 0.8334 (ttm110) REVERT: A 65 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 231 LYS cc_start: 0.9209 (mmpt) cc_final: 0.8866 (mmmt) REVERT: A 244 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9108 (p) REVERT: A 260 LYS cc_start: 0.5998 (tttt) cc_final: 0.5618 (tttp) REVERT: A 304 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7653 (ttm110) REVERT: A 349 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 396 SER cc_start: 0.9281 (t) cc_final: 0.9024 (p) REVERT: A 410 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 455 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 459 ASP cc_start: 0.8869 (p0) cc_final: 0.8657 (p0) REVERT: A 477 ASP cc_start: 0.7055 (t0) cc_final: 0.6769 (t0) REVERT: A 482 MET cc_start: 0.7430 (mmt) cc_final: 0.6717 (ttt) REVERT: B 21 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 112 PHE cc_start: 0.9407 (m-10) cc_final: 0.9121 (m-10) REVERT: B 116 GLU cc_start: 0.8978 (tt0) cc_final: 0.8765 (tt0) REVERT: B 174 ASP cc_start: 0.8352 (p0) cc_final: 0.8067 (p0) REVERT: B 180 MET cc_start: 0.8692 (mmm) cc_final: 0.8145 (mmm) REVERT: B 191 ARG cc_start: 0.9402 (ptp90) cc_final: 0.8113 (ttt180) REVERT: B 227 ASP cc_start: 0.7198 (t0) cc_final: 0.6992 (t0) REVERT: B 230 TRP cc_start: 0.9452 (m100) cc_final: 0.8749 (m100) REVERT: B 304 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7675 (mtm110) REVERT: B 321 GLU cc_start: 0.6458 (mp0) cc_final: 0.6116 (mp0) REVERT: B 438 ASP cc_start: 0.8483 (t70) cc_final: 0.8207 (t0) REVERT: B 445 ASN cc_start: 0.9050 (t0) cc_final: 0.8577 (t0) REVERT: B 459 ASP cc_start: 0.8934 (t70) cc_final: 0.8628 (p0) REVERT: M 17 ASN cc_start: 0.9135 (t0) cc_final: 0.8578 (t0) REVERT: M 50 ASP cc_start: 0.8679 (m-30) cc_final: 0.8359 (m-30) REVERT: M 83 ASP cc_start: 0.8447 (p0) cc_final: 0.8056 (p0) REVERT: M 152 LEU cc_start: 0.8846 (mm) cc_final: 0.8545 (mp) REVERT: M 176 LYS cc_start: 0.9241 (mttt) cc_final: 0.8978 (mtpt) REVERT: M 195 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8651 (tm-30) REVERT: M 197 LYS cc_start: 0.9305 (tmtt) cc_final: 0.8210 (tppt) REVERT: X 29 CYS cc_start: 0.8954 (t) cc_final: 0.8679 (t) REVERT: X 33 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (mm) REVERT: X 40 ASN cc_start: 0.9087 (t0) cc_final: 0.8739 (t0) REVERT: X 61 ARG cc_start: 0.9271 (tmm-80) cc_final: 0.9023 (tmm-80) REVERT: X 170 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8340 (tppp) REVERT: X 179 MET cc_start: 0.8422 (tmm) cc_final: 0.8014 (tmm) REVERT: X 183 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7717 (ttm) REVERT: X 195 GLU cc_start: 0.8420 (tp30) cc_final: 0.8036 (tp30) REVERT: X 203 MET cc_start: 0.8787 (mmm) cc_final: 0.8229 (mtt) REVERT: Y 395 ASP cc_start: 0.8136 (m-30) cc_final: 0.7666 (m-30) REVERT: Y 674 MET cc_start: 0.8626 (tpp) cc_final: 0.7656 (tpt) REVERT: Y 678 GLU cc_start: 0.8516 (tt0) cc_final: 0.8176 (tp30) REVERT: Y 696 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8139 (tm-30) REVERT: Y 758 ARG cc_start: 0.8408 (mmp80) cc_final: 0.6365 (tpt170) REVERT: f 127 MET cc_start: 0.7211 (pmm) cc_final: 0.6787 (pmm) REVERT: g 164 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6537 (t70) REVERT: g 167 TRP cc_start: 0.8303 (t60) cc_final: 0.8099 (t60) outliers start: 66 outliers final: 41 residues processed: 562 average time/residue: 0.1393 time to fit residues: 121.2579 Evaluate side-chains 551 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 505 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 183 MET Chi-restraints excluded: chain X residue 204 LEU Chi-restraints excluded: chain Y residue 156 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 359 MET Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain Y residue 715 THR Chi-restraints excluded: chain Y residue 749 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 164 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 217 optimal weight: 1.9990 chunk 235 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 448 ASN M 60 GLN M 73 ASN ** X 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 206 HIS X 212 ASN ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** 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 = 0.3365 r_free = 0.3365 target = 0.101793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.086470 restraints weight = 64965.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088641 restraints weight = 35162.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090050 restraints weight = 23049.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091084 restraints weight = 17088.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091752 restraints weight = 13609.409| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20331 Z= 0.178 Angle : 0.633 10.821 27606 Z= 0.328 Chirality : 0.044 0.316 3041 Planarity : 0.004 0.065 3579 Dihedral : 4.632 48.980 2720 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.15 % Favored : 92.45 % Rotamer: Outliers : 4.08 % Allowed : 17.86 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2491 helix: 1.91 (0.20), residues: 673 sheet: 0.05 (0.24), residues: 513 loop : -1.40 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 74 TYR 0.025 0.002 TYR B 169 PHE 0.022 0.001 PHE B 128 TRP 0.048 0.001 TRP g 167 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00399 (20331) covalent geometry : angle 0.63305 (27606) hydrogen bonds : bond 0.04042 ( 805) hydrogen bonds : angle 4.71002 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 513 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8643 (m-40) cc_final: 0.7565 (t0) REVERT: A 32 ASP cc_start: 0.7997 (m-30) cc_final: 0.7285 (m-30) REVERT: A 33 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8320 (ttm110) REVERT: A 65 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 178 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8741 (tp-100) REVERT: A 225 GLU cc_start: 0.9068 (pm20) cc_final: 0.8691 (pm20) REVERT: A 231 LYS cc_start: 0.9207 (mmpt) cc_final: 0.8745 (mmmt) REVERT: A 260 LYS cc_start: 0.5914 (tttt) cc_final: 0.5414 (tttp) REVERT: A 304 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7602 (ttm110) REVERT: A 349 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 396 SER cc_start: 0.9273 (t) cc_final: 0.9035 (p) REVERT: A 405 ILE cc_start: 0.9547 (mm) cc_final: 0.9320 (mm) REVERT: A 409 GLN cc_start: 0.8299 (pp30) cc_final: 0.7405 (pp30) REVERT: A 410 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7317 (mm-30) REVERT: A 455 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 456 TRP cc_start: 0.8942 (p-90) cc_final: 0.8670 (p-90) REVERT: A 459 ASP cc_start: 0.8825 (p0) cc_final: 0.8532 (p0) REVERT: A 477 ASP cc_start: 0.7129 (t0) cc_final: 0.6817 (t0) REVERT: A 482 MET cc_start: 0.7583 (mmt) cc_final: 0.6867 (ttt) REVERT: B 15 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7451 (tppp) REVERT: B 18 GLU cc_start: 0.8500 (pm20) cc_final: 0.8156 (pm20) REVERT: B 21 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 112 PHE cc_start: 0.9415 (m-10) cc_final: 0.9128 (m-10) REVERT: B 116 GLU cc_start: 0.8916 (tt0) cc_final: 0.8672 (tt0) REVERT: B 127 GLN cc_start: 0.8500 (mp10) cc_final: 0.8293 (mp10) REVERT: B 174 ASP cc_start: 0.8406 (p0) cc_final: 0.8137 (p0) REVERT: B 180 MET cc_start: 0.8574 (mmm) cc_final: 0.7994 (mmm) REVERT: B 191 ARG cc_start: 0.9423 (ptp90) cc_final: 0.8104 (ttt180) REVERT: B 227 ASP cc_start: 0.7302 (t0) cc_final: 0.7027 (t0) REVERT: B 230 TRP cc_start: 0.9472 (m100) cc_final: 0.8765 (m100) REVERT: B 233 GLN cc_start: 0.8647 (mt0) cc_final: 0.8050 (mm110) REVERT: B 239 LEU cc_start: 0.8878 (tt) cc_final: 0.8603 (pp) REVERT: B 274 ASP cc_start: 0.8055 (t0) cc_final: 0.7049 (t0) REVERT: B 304 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7647 (mtp85) REVERT: B 321 GLU cc_start: 0.5703 (mp0) cc_final: 0.5153 (mp0) REVERT: B 438 ASP cc_start: 0.8594 (t70) cc_final: 0.8349 (t0) REVERT: B 445 ASN cc_start: 0.9120 (t0) cc_final: 0.8662 (t0) REVERT: B 446 TYR cc_start: 0.7771 (m-10) cc_final: 0.7552 (m-10) REVERT: B 459 ASP cc_start: 0.9000 (t70) cc_final: 0.8738 (t0) REVERT: M 17 ASN cc_start: 0.9148 (t0) cc_final: 0.8597 (t0) REVERT: M 49 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: M 50 ASP cc_start: 0.8583 (m-30) cc_final: 0.8308 (m-30) REVERT: M 83 ASP cc_start: 0.8530 (p0) cc_final: 0.7975 (p0) REVERT: M 176 LYS cc_start: 0.9216 (mttt) cc_final: 0.8962 (mtpt) REVERT: M 177 LEU cc_start: 0.9427 (tp) cc_final: 0.9184 (tp) REVERT: M 181 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: M 195 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8652 (tm-30) REVERT: M 197 LYS cc_start: 0.9343 (tmtt) cc_final: 0.8291 (tptt) REVERT: X 29 CYS cc_start: 0.8896 (t) cc_final: 0.8585 (t) REVERT: X 40 ASN cc_start: 0.9110 (t0) cc_final: 0.8623 (t0) REVERT: X 170 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8344 (tppp) REVERT: X 179 MET cc_start: 0.8504 (tmm) cc_final: 0.8049 (tmm) REVERT: X 183 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8076 (ttm) REVERT: X 195 GLU cc_start: 0.8532 (tp30) cc_final: 0.8085 (tp30) REVERT: X 203 MET cc_start: 0.8639 (mmm) cc_final: 0.8171 (mtt) REVERT: Y 626 MET cc_start: 0.8528 (tpp) cc_final: 0.8325 (tpp) REVERT: Y 674 MET cc_start: 0.8611 (tpp) cc_final: 0.7619 (tpt) REVERT: Y 678 GLU cc_start: 0.8521 (tt0) cc_final: 0.8167 (tp30) REVERT: Y 758 ARG cc_start: 0.8454 (mmp80) cc_final: 0.6461 (tpt170) REVERT: f 105 GLU cc_start: 0.8826 (pt0) cc_final: 0.8613 (pt0) REVERT: f 108 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: g 164 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6429 (t70) REVERT: g 167 TRP cc_start: 0.8342 (t60) cc_final: 0.8090 (t60) outliers start: 87 outliers final: 54 residues processed: 553 average time/residue: 0.1415 time to fit residues: 121.1802 Evaluate side-chains 559 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 499 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 183 MET Chi-restraints excluded: chain X residue 204 LEU Chi-restraints excluded: chain Y residue 156 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 359 MET Chi-restraints excluded: chain Y residue 512 THR Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain Y residue 715 THR Chi-restraints excluded: chain Y residue 749 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain g residue 164 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 209 optimal weight: 0.5980 chunk 163 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 225 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 386 GLN A 409 GLN A 448 ASN B 168 HIS B 448 ASN M 73 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.086362 restraints weight = 64623.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088552 restraints weight = 34645.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089955 restraints weight = 22521.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091011 restraints weight = 16575.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.091668 restraints weight = 13170.484| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20331 Z= 0.177 Angle : 0.644 10.636 27606 Z= 0.331 Chirality : 0.044 0.314 3041 Planarity : 0.004 0.068 3579 Dihedral : 4.657 51.591 2720 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.07 % Favored : 92.53 % Rotamer: Outliers : 4.31 % Allowed : 18.80 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2491 helix: 1.85 (0.19), residues: 689 sheet: 0.10 (0.24), residues: 513 loop : -1.45 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 71 TYR 0.022 0.002 TYR B 169 PHE 0.022 0.001 PHE B 128 TRP 0.041 0.001 TRP g 167 HIS 0.004 0.001 HIS M 149 Details of bonding type rmsd covalent geometry : bond 0.00399 (20331) covalent geometry : angle 0.64363 (27606) hydrogen bonds : bond 0.03949 ( 805) hydrogen bonds : angle 4.63950 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 515 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8637 (m-40) cc_final: 0.7531 (t0) REVERT: A 32 ASP cc_start: 0.8136 (m-30) cc_final: 0.7367 (m-30) REVERT: A 33 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8316 (ttm110) REVERT: A 57 ASN cc_start: 0.7578 (m110) cc_final: 0.7248 (m110) REVERT: A 65 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 112 PHE cc_start: 0.8957 (m-10) cc_final: 0.8702 (m-10) REVERT: A 231 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8719 (mmmt) REVERT: A 260 LYS cc_start: 0.6018 (tttt) cc_final: 0.5457 (tttp) REVERT: A 304 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7647 (ttm110) REVERT: A 360 MET cc_start: 0.8775 (ppp) cc_final: 0.8373 (ppp) REVERT: A 396 SER cc_start: 0.9291 (t) cc_final: 0.9055 (p) REVERT: A 409 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7297 (pp30) REVERT: A 410 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 446 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 455 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 456 TRP cc_start: 0.8940 (p-90) cc_final: 0.8564 (p-90) REVERT: A 459 ASP cc_start: 0.8919 (p0) cc_final: 0.8652 (p0) REVERT: A 482 MET cc_start: 0.7631 (mmt) cc_final: 0.6913 (ttt) REVERT: B 21 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 74 LEU cc_start: 0.9462 (tp) cc_final: 0.9237 (tp) REVERT: B 79 PHE cc_start: 0.8651 (m-80) cc_final: 0.8299 (m-10) REVERT: B 112 PHE cc_start: 0.9415 (m-10) cc_final: 0.9135 (m-10) REVERT: B 116 GLU cc_start: 0.8864 (tt0) cc_final: 0.8592 (tt0) REVERT: B 127 GLN cc_start: 0.8618 (mp10) cc_final: 0.8307 (mp10) REVERT: B 148 TYR cc_start: 0.9194 (t80) cc_final: 0.8797 (t80) REVERT: B 168 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (m-70) REVERT: B 174 ASP cc_start: 0.8430 (p0) cc_final: 0.8124 (p0) REVERT: B 180 MET cc_start: 0.8521 (mmm) cc_final: 0.7979 (mmm) REVERT: B 191 ARG cc_start: 0.9401 (ptp90) cc_final: 0.8123 (ttt180) REVERT: B 227 ASP cc_start: 0.7297 (t0) cc_final: 0.7029 (t0) REVERT: B 230 TRP cc_start: 0.9500 (m100) cc_final: 0.8789 (m100) REVERT: B 233 GLN cc_start: 0.8634 (mt0) cc_final: 0.8034 (mm110) REVERT: B 239 LEU cc_start: 0.8833 (tt) cc_final: 0.8536 (pp) REVERT: B 274 ASP cc_start: 0.8259 (t0) cc_final: 0.7760 (t0) REVERT: B 287 GLU cc_start: 0.8972 (tt0) cc_final: 0.8056 (tt0) REVERT: B 304 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7745 (mtm110) REVERT: B 321 GLU cc_start: 0.5574 (mp0) cc_final: 0.4784 (mp0) REVERT: B 438 ASP cc_start: 0.8603 (t70) cc_final: 0.8338 (t0) REVERT: B 445 ASN cc_start: 0.9123 (t0) cc_final: 0.8612 (t0) REVERT: B 459 ASP cc_start: 0.9001 (t70) cc_final: 0.8749 (t0) REVERT: B 469 TRP cc_start: 0.9283 (t60) cc_final: 0.9074 (t60) REVERT: M 17 ASN cc_start: 0.9186 (t0) cc_final: 0.8730 (t0) REVERT: M 49 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: M 50 ASP cc_start: 0.8604 (m-30) cc_final: 0.8306 (m-30) REVERT: M 83 ASP cc_start: 0.8560 (p0) cc_final: 0.8202 (p0) REVERT: M 176 LYS cc_start: 0.9223 (mttt) cc_final: 0.8991 (mtpt) REVERT: M 177 LEU cc_start: 0.9439 (tp) cc_final: 0.9191 (tp) REVERT: M 181 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8505 (mtm) REVERT: M 195 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8665 (tm-30) REVERT: M 197 LYS cc_start: 0.9303 (tmtt) cc_final: 0.8253 (tptt) REVERT: X 29 CYS cc_start: 0.8871 (t) cc_final: 0.8570 (t) REVERT: X 40 ASN cc_start: 0.9099 (t0) cc_final: 0.8675 (t0) REVERT: X 150 MET cc_start: 0.7730 (mtt) cc_final: 0.7503 (mtt) REVERT: X 170 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8364 (tppp) REVERT: X 179 MET cc_start: 0.8563 (tmm) cc_final: 0.8105 (tmm) REVERT: X 183 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8044 (ttm) REVERT: X 195 GLU cc_start: 0.8554 (tp30) cc_final: 0.8029 (tp30) REVERT: X 203 MET cc_start: 0.8592 (mmm) cc_final: 0.8200 (mtt) REVERT: Y 674 MET cc_start: 0.8655 (tpp) cc_final: 0.7815 (tpt) REVERT: Y 678 GLU cc_start: 0.8501 (tt0) cc_final: 0.8060 (tp30) REVERT: Y 758 ARG cc_start: 0.8464 (mmp80) cc_final: 0.6316 (tpt170) REVERT: e 24 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8919 (mmtt) REVERT: e 134 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7586 (t0) REVERT: f 105 GLU cc_start: 0.8758 (pt0) cc_final: 0.8463 (pt0) REVERT: f 108 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: f 109 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7372 (mt-10) REVERT: g 80 TYR cc_start: 0.9004 (m-10) cc_final: 0.8562 (m-10) outliers start: 92 outliers final: 65 residues processed: 562 average time/residue: 0.1386 time to fit residues: 121.4572 Evaluate side-chains 567 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 493 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 125 PHE Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 183 MET Chi-restraints excluded: chain X residue 204 LEU Chi-restraints excluded: chain Y residue 68 TYR Chi-restraints excluded: chain Y residue 156 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 354 LEU Chi-restraints excluded: chain Y residue 359 MET Chi-restraints excluded: chain Y residue 512 THR Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 595 MET Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain Y residue 715 THR Chi-restraints excluded: chain Y residue 749 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 134 ASN Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain f residue 159 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 119 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 201 optimal weight: 0.0670 chunk 92 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 220 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 GLN X 212 ASN ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** 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 = 0.3336 r_free = 0.3336 target = 0.100706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085491 restraints weight = 64671.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087607 restraints weight = 35287.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089048 restraints weight = 23246.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089954 restraints weight = 17173.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090684 restraints weight = 13875.189| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20331 Z= 0.169 Angle : 0.647 10.725 27606 Z= 0.331 Chirality : 0.044 0.316 3041 Planarity : 0.004 0.065 3579 Dihedral : 4.628 51.978 2720 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.07 % Favored : 92.53 % Rotamer: Outliers : 4.36 % Allowed : 20.25 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2491 helix: 1.91 (0.20), residues: 683 sheet: 0.39 (0.25), residues: 489 loop : -1.59 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 211 TYR 0.027 0.002 TYR B 169 PHE 0.022 0.001 PHE B 128 TRP 0.073 0.002 TRP g 167 HIS 0.014 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00380 (20331) covalent geometry : angle 0.64705 (27606) hydrogen bonds : bond 0.03898 ( 805) hydrogen bonds : angle 4.62349 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 513 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8639 (m-40) cc_final: 0.7557 (t0) REVERT: A 32 ASP cc_start: 0.8091 (m-30) cc_final: 0.7375 (m-30) REVERT: A 33 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8388 (ttm110) REVERT: A 57 ASN cc_start: 0.7505 (m110) cc_final: 0.7106 (m110) REVERT: A 65 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 112 PHE cc_start: 0.8980 (m-10) cc_final: 0.8691 (m-10) REVERT: A 231 LYS cc_start: 0.9170 (mmpt) cc_final: 0.8773 (mmmt) REVERT: A 243 LYS cc_start: 0.9197 (tmmt) cc_final: 0.8717 (tmmt) REVERT: A 260 LYS cc_start: 0.5870 (tttt) cc_final: 0.5147 (tttp) REVERT: A 304 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7647 (ttm110) REVERT: A 349 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 350 LYS cc_start: 0.9235 (tptt) cc_final: 0.8925 (mmmt) REVERT: A 396 SER cc_start: 0.9293 (t) cc_final: 0.9067 (p) REVERT: A 409 GLN cc_start: 0.8389 (pp30) cc_final: 0.7198 (pp30) REVERT: A 410 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 446 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7604 (t80) REVERT: A 456 TRP cc_start: 0.8941 (p-90) cc_final: 0.8735 (p-90) REVERT: A 459 ASP cc_start: 0.8908 (p0) cc_final: 0.8381 (t0) REVERT: A 462 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: A 482 MET cc_start: 0.7612 (mmt) cc_final: 0.6898 (ttt) REVERT: B 21 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 79 PHE cc_start: 0.8652 (m-80) cc_final: 0.8291 (m-10) REVERT: B 108 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 112 PHE cc_start: 0.9405 (m-10) cc_final: 0.9022 (m-80) REVERT: B 148 TYR cc_start: 0.9189 (t80) cc_final: 0.8788 (t80) REVERT: B 174 ASP cc_start: 0.8468 (p0) cc_final: 0.8199 (p0) REVERT: B 180 MET cc_start: 0.8481 (mmm) cc_final: 0.7951 (mmm) REVERT: B 191 ARG cc_start: 0.9386 (ptp90) cc_final: 0.8135 (ttt180) REVERT: B 227 ASP cc_start: 0.7403 (t0) cc_final: 0.7153 (t0) REVERT: B 230 TRP cc_start: 0.9504 (m100) cc_final: 0.8811 (m100) REVERT: B 233 GLN cc_start: 0.8633 (mt0) cc_final: 0.8036 (mm110) REVERT: B 274 ASP cc_start: 0.8157 (t0) cc_final: 0.7710 (t0) REVERT: B 287 GLU cc_start: 0.8959 (tt0) cc_final: 0.8013 (tt0) REVERT: B 304 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7706 (mtm110) REVERT: B 438 ASP cc_start: 0.8609 (t70) cc_final: 0.8342 (t0) REVERT: B 445 ASN cc_start: 0.9107 (t0) cc_final: 0.8599 (t0) REVERT: B 459 ASP cc_start: 0.9024 (t70) cc_final: 0.8754 (t0) REVERT: B 469 TRP cc_start: 0.9283 (t60) cc_final: 0.9077 (t60) REVERT: M 17 ASN cc_start: 0.9233 (t0) cc_final: 0.8772 (t0) REVERT: M 50 ASP cc_start: 0.8597 (m-30) cc_final: 0.8253 (m-30) REVERT: M 70 TRP cc_start: 0.9209 (m100) cc_final: 0.8829 (m100) REVERT: M 83 ASP cc_start: 0.8563 (p0) cc_final: 0.8194 (p0) REVERT: M 176 LYS cc_start: 0.9214 (mttt) cc_final: 0.8976 (mtpt) REVERT: M 177 LEU cc_start: 0.9454 (tp) cc_final: 0.9214 (tp) REVERT: M 181 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: M 195 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8683 (tm-30) REVERT: M 197 LYS cc_start: 0.9282 (tmtt) cc_final: 0.8228 (tptt) REVERT: X 29 CYS cc_start: 0.8857 (t) cc_final: 0.8555 (t) REVERT: X 40 ASN cc_start: 0.9153 (t0) cc_final: 0.8708 (t0) REVERT: X 150 MET cc_start: 0.7810 (mtt) cc_final: 0.7364 (mtt) REVERT: X 170 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (tppp) REVERT: X 179 MET cc_start: 0.8574 (tmm) cc_final: 0.8095 (tmm) REVERT: X 183 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8055 (ttm) REVERT: X 191 MET cc_start: 0.8903 (tmm) cc_final: 0.8601 (tmm) REVERT: X 195 GLU cc_start: 0.8582 (tp30) cc_final: 0.8180 (tp30) REVERT: X 203 MET cc_start: 0.8519 (mmm) cc_final: 0.8167 (mtt) REVERT: Y 678 GLU cc_start: 0.8410 (tt0) cc_final: 0.8068 (tp30) REVERT: Y 758 ARG cc_start: 0.8429 (mmp80) cc_final: 0.6270 (tpt170) REVERT: f 105 GLU cc_start: 0.8716 (pt0) cc_final: 0.8327 (pt0) REVERT: f 108 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: f 164 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7154 (t70) REVERT: g 24 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8572 (mmtt) REVERT: g 80 TYR cc_start: 0.8999 (m-10) cc_final: 0.8671 (m-10) REVERT: g 167 TRP cc_start: 0.8416 (t60) cc_final: 0.8075 (t60) outliers start: 93 outliers final: 67 residues processed: 560 average time/residue: 0.1382 time to fit residues: 119.5527 Evaluate side-chains 570 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 495 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 125 PHE Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 136 PHE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 183 MET Chi-restraints excluded: chain Y residue 68 TYR Chi-restraints excluded: chain Y residue 156 TYR Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 354 LEU Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 595 MET Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain Y residue 715 THR Chi-restraints excluded: chain Y residue 749 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 164 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 167 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 167 HIS ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** f 171 GLN ** 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 = 0.3309 r_free = 0.3309 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084049 restraints weight = 65605.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.086128 restraints weight = 35858.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087468 restraints weight = 23770.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088469 restraints weight = 17770.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089097 restraints weight = 14250.823| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20331 Z= 0.231 Angle : 0.701 11.272 27606 Z= 0.357 Chirality : 0.045 0.325 3041 Planarity : 0.004 0.064 3579 Dihedral : 4.853 52.028 2720 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.67 % Favored : 91.93 % Rotamer: Outliers : 4.55 % Allowed : 20.86 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2491 helix: 1.71 (0.20), residues: 699 sheet: -0.01 (0.24), residues: 513 loop : -1.57 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 211 TYR 0.031 0.002 TYR A 169 PHE 0.020 0.002 PHE B 128 TRP 0.062 0.002 TRP g 167 HIS 0.006 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00519 (20331) covalent geometry : angle 0.70112 (27606) hydrogen bonds : bond 0.04233 ( 805) hydrogen bonds : angle 4.74502 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 506 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8749 (m-40) cc_final: 0.7674 (t0) REVERT: A 32 ASP cc_start: 0.8201 (m-30) cc_final: 0.7335 (m-30) REVERT: A 33 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8398 (ttm110) REVERT: A 57 ASN cc_start: 0.7448 (m110) cc_final: 0.7059 (m110) REVERT: A 65 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 231 LYS cc_start: 0.9171 (mmpt) cc_final: 0.8706 (mmmt) REVERT: A 243 LYS cc_start: 0.9215 (tmmt) cc_final: 0.8726 (tmmt) REVERT: A 255 MET cc_start: 0.8120 (tmm) cc_final: 0.7567 (tmm) REVERT: A 260 LYS cc_start: 0.5598 (tttt) cc_final: 0.4965 (tttp) REVERT: A 301 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6718 (t80) REVERT: A 304 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7537 (ttm110) REVERT: A 313 HIS cc_start: 0.9183 (t70) cc_final: 0.8813 (t-90) REVERT: A 396 SER cc_start: 0.9287 (t) cc_final: 0.9058 (p) REVERT: A 409 GLN cc_start: 0.8318 (pp30) cc_final: 0.7206 (pp30) REVERT: A 410 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 446 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 455 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 462 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8397 (mtmm) REVERT: A 482 MET cc_start: 0.7637 (mmt) cc_final: 0.6871 (ttt) REVERT: B 108 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8202 (mt) REVERT: B 112 PHE cc_start: 0.9430 (m-10) cc_final: 0.9056 (m-80) REVERT: B 148 TYR cc_start: 0.9180 (t80) cc_final: 0.8751 (t80) REVERT: B 180 MET cc_start: 0.8501 (mmm) cc_final: 0.8223 (mmm) REVERT: B 191 ARG cc_start: 0.9392 (ptp90) cc_final: 0.8132 (ttt180) REVERT: B 227 ASP cc_start: 0.7419 (t0) cc_final: 0.7141 (t0) REVERT: B 233 GLN cc_start: 0.8639 (mt0) cc_final: 0.8394 (mt0) REVERT: B 287 GLU cc_start: 0.8973 (tt0) cc_final: 0.8567 (tt0) REVERT: B 304 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7738 (mtm110) REVERT: B 438 ASP cc_start: 0.8651 (t70) cc_final: 0.8410 (t0) REVERT: B 445 ASN cc_start: 0.9114 (t0) cc_final: 0.8633 (t0) REVERT: B 459 ASP cc_start: 0.9074 (t70) cc_final: 0.8745 (t0) REVERT: B 469 TRP cc_start: 0.9273 (t60) cc_final: 0.9012 (t60) REVERT: M 17 ASN cc_start: 0.9297 (t0) cc_final: 0.8784 (t0) REVERT: M 50 ASP cc_start: 0.8616 (m-30) cc_final: 0.8246 (m-30) REVERT: M 68 LYS cc_start: 0.7787 (pttt) cc_final: 0.7571 (pttt) REVERT: M 70 TRP cc_start: 0.9284 (m100) cc_final: 0.8871 (m100) REVERT: M 77 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.7909 (mtp-110) REVERT: M 83 ASP cc_start: 0.8745 (p0) cc_final: 0.8265 (p0) REVERT: M 152 LEU cc_start: 0.9061 (mm) cc_final: 0.8757 (mp) REVERT: M 176 LYS cc_start: 0.9260 (mttt) cc_final: 0.9042 (mtpt) REVERT: M 195 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8684 (tm-30) REVERT: M 197 LYS cc_start: 0.9308 (tmtt) cc_final: 0.8237 (tptt) REVERT: M 200 ARG cc_start: 0.9210 (ptp-170) cc_final: 0.8960 (ptm-80) REVERT: X 29 CYS cc_start: 0.8875 (t) cc_final: 0.8587 (t) REVERT: X 40 ASN cc_start: 0.9200 (t0) cc_final: 0.8772 (t0) REVERT: X 50 ASP cc_start: 0.8893 (m-30) cc_final: 0.8648 (m-30) REVERT: X 144 MET cc_start: 0.8831 (tmm) cc_final: 0.8313 (tmm) REVERT: X 150 MET cc_start: 0.8025 (mtt) cc_final: 0.7666 (mtt) REVERT: X 170 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8347 (tppp) REVERT: X 179 MET cc_start: 0.8648 (tmm) cc_final: 0.8301 (tmm) REVERT: X 183 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8156 (ttm) REVERT: X 191 MET cc_start: 0.8924 (tmm) cc_final: 0.8611 (tmm) REVERT: X 195 GLU cc_start: 0.8644 (tp30) cc_final: 0.8130 (tp30) REVERT: X 203 MET cc_start: 0.8468 (mmm) cc_final: 0.8182 (mtt) REVERT: Y 674 MET cc_start: 0.8561 (tpp) cc_final: 0.7832 (tpt) REVERT: Y 678 GLU cc_start: 0.8393 (tt0) cc_final: 0.8077 (tp30) REVERT: Y 758 ARG cc_start: 0.8662 (mmp80) cc_final: 0.6408 (tpt170) REVERT: Y 765 GLU cc_start: 0.8005 (mp0) cc_final: 0.7624 (mp0) REVERT: e 24 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8892 (mptt) REVERT: f 80 TYR cc_start: 0.9049 (m-10) cc_final: 0.8726 (m-10) REVERT: f 108 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: f 109 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7095 (mt-10) REVERT: f 164 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7033 (t70) REVERT: g 80 TYR cc_start: 0.8903 (m-10) cc_final: 0.8477 (m-10) REVERT: g 167 TRP cc_start: 0.8460 (t60) cc_final: 0.7988 (t60) outliers start: 97 outliers final: 71 residues processed: 555 average time/residue: 0.1375 time to fit residues: 118.1965 Evaluate side-chains 577 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 498 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 125 PHE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 215 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 112 ILE Chi-restraints excluded: chain X residue 136 PHE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 183 MET Chi-restraints excluded: chain Y residue 17 GLN Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 68 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 242 ASP Chi-restraints excluded: chain Y residue 354 LEU Chi-restraints excluded: chain Y residue 359 MET Chi-restraints excluded: chain Y residue 394 THR Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 595 MET Chi-restraints excluded: chain Y residue 682 THR Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain Y residue 715 THR Chi-restraints excluded: chain Y residue 749 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 164 HIS Chi-restraints excluded: chain g residue 164 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 7 optimal weight: 0.9980 chunk 188 optimal weight: 0.0980 chunk 121 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 178 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 248 optimal weight: 0.6980 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 GLN ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.087867 restraints weight = 64610.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090088 restraints weight = 34481.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091508 restraints weight = 22296.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092558 restraints weight = 16396.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093217 restraints weight = 12969.991| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20331 Z= 0.122 Angle : 0.674 11.358 27606 Z= 0.335 Chirality : 0.044 0.307 3041 Planarity : 0.004 0.065 3579 Dihedral : 4.537 56.657 2720 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.70 % Favored : 92.89 % Rotamer: Outliers : 3.28 % Allowed : 23.02 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2491 helix: 2.05 (0.20), residues: 671 sheet: 0.79 (0.26), residues: 421 loop : -1.67 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 211 TYR 0.030 0.001 TYR A 169 PHE 0.023 0.001 PHE B 128 TRP 0.052 0.001 TRP g 167 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00271 (20331) covalent geometry : angle 0.67367 (27606) hydrogen bonds : bond 0.03491 ( 805) hydrogen bonds : angle 4.50732 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 523 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8633 (m-40) cc_final: 0.7665 (t0) REVERT: A 32 ASP cc_start: 0.8013 (m-30) cc_final: 0.7306 (m-30) REVERT: A 37 TYR cc_start: 0.8796 (m-80) cc_final: 0.8548 (m-80) REVERT: A 65 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8788 (tm-30) REVERT: A 112 PHE cc_start: 0.8955 (m-10) cc_final: 0.8720 (m-10) REVERT: A 231 LYS cc_start: 0.9170 (mmpt) cc_final: 0.8787 (mmmt) REVERT: A 243 LYS cc_start: 0.9226 (tmmt) cc_final: 0.8880 (tmmt) REVERT: A 260 LYS cc_start: 0.5364 (tttt) cc_final: 0.4611 (tttp) REVERT: A 304 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7345 (ttp80) REVERT: A 350 LYS cc_start: 0.9243 (tptt) cc_final: 0.8870 (mmmt) REVERT: A 396 SER cc_start: 0.9299 (t) cc_final: 0.9097 (p) REVERT: A 409 GLN cc_start: 0.8305 (pp30) cc_final: 0.6997 (pp30) REVERT: A 410 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 446 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 456 TRP cc_start: 0.9033 (p-90) cc_final: 0.8770 (p-90) REVERT: A 459 ASP cc_start: 0.8986 (p0) cc_final: 0.8261 (t0) REVERT: A 462 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8441 (mtmm) REVERT: A 482 MET cc_start: 0.7602 (mmt) cc_final: 0.6995 (mmt) REVERT: B 21 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 112 PHE cc_start: 0.9383 (m-10) cc_final: 0.9094 (m-10) REVERT: B 148 TYR cc_start: 0.9191 (t80) cc_final: 0.8811 (t80) REVERT: B 180 MET cc_start: 0.8429 (mmm) cc_final: 0.8182 (mmm) REVERT: B 191 ARG cc_start: 0.9330 (ptp90) cc_final: 0.8217 (ttt180) REVERT: B 227 ASP cc_start: 0.7441 (t0) cc_final: 0.7219 (t0) REVERT: B 230 TRP cc_start: 0.9487 (m100) cc_final: 0.8869 (m100) REVERT: B 233 GLN cc_start: 0.8607 (mt0) cc_final: 0.8268 (mm110) REVERT: B 274 ASP cc_start: 0.8090 (t0) cc_final: 0.7878 (t0) REVERT: B 287 GLU cc_start: 0.8917 (tt0) cc_final: 0.7837 (tt0) REVERT: B 304 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7658 (mtm110) REVERT: B 438 ASP cc_start: 0.8563 (t70) cc_final: 0.8286 (t0) REVERT: B 445 ASN cc_start: 0.9062 (t0) cc_final: 0.8607 (t0) REVERT: B 459 ASP cc_start: 0.9011 (t70) cc_final: 0.8647 (t0) REVERT: M 17 ASN cc_start: 0.9260 (t0) cc_final: 0.8787 (t0) REVERT: M 50 ASP cc_start: 0.8524 (m-30) cc_final: 0.8143 (m-30) REVERT: M 70 TRP cc_start: 0.9076 (m100) cc_final: 0.8715 (m100) REVERT: M 77 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.7948 (mtp-110) REVERT: M 176 LYS cc_start: 0.9161 (mttt) cc_final: 0.8941 (mtpt) REVERT: M 177 LEU cc_start: 0.9392 (tp) cc_final: 0.9051 (tp) REVERT: M 195 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8734 (tm-30) REVERT: M 197 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8159 (tptt) REVERT: M 200 ARG cc_start: 0.9175 (ptp-170) cc_final: 0.8642 (ptm160) REVERT: X 29 CYS cc_start: 0.8801 (t) cc_final: 0.8485 (t) REVERT: X 40 ASN cc_start: 0.9178 (t0) cc_final: 0.8710 (t0) REVERT: X 50 ASP cc_start: 0.8883 (m-30) cc_final: 0.8649 (m-30) REVERT: X 170 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8258 (tppp) REVERT: X 178 GLN cc_start: 0.8217 (pp30) cc_final: 0.7838 (pt0) REVERT: X 179 MET cc_start: 0.8677 (tmm) cc_final: 0.7654 (tmm) REVERT: X 183 MET cc_start: 0.8450 (ttm) cc_final: 0.8126 (ttp) REVERT: X 203 MET cc_start: 0.8494 (mmm) cc_final: 0.8165 (mtt) REVERT: Y 36 ASP cc_start: 0.8522 (t0) cc_final: 0.7463 (p0) REVERT: Y 395 ASP cc_start: 0.8148 (m-30) cc_final: 0.7794 (m-30) REVERT: Y 674 MET cc_start: 0.8535 (tpp) cc_final: 0.7829 (tpt) REVERT: Y 758 ARG cc_start: 0.8514 (mmp80) cc_final: 0.6286 (tpt170) REVERT: Y 788 ASN cc_start: 0.8407 (t0) cc_final: 0.8103 (p0) REVERT: e 93 MET cc_start: 0.7675 (ptm) cc_final: 0.7443 (ttt) REVERT: f 105 GLU cc_start: 0.8709 (pt0) cc_final: 0.8485 (pt0) REVERT: f 108 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: f 109 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7094 (mt-10) REVERT: g 90 MET cc_start: 0.6814 (tpp) cc_final: 0.6606 (tpp) REVERT: g 158 ASP cc_start: 0.9143 (m-30) cc_final: 0.8751 (p0) REVERT: g 164 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6171 (t70) REVERT: g 167 TRP cc_start: 0.8374 (t60) cc_final: 0.8018 (t60) outliers start: 70 outliers final: 45 residues processed: 561 average time/residue: 0.1350 time to fit residues: 117.0010 Evaluate side-chains 561 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 511 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 125 PHE Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 136 PHE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 17 GLN Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 68 TYR Chi-restraints excluded: chain Y residue 156 TYR Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 394 THR Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 595 MET Chi-restraints excluded: chain Y residue 653 ILE Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain g residue 164 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 89 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 chunk 230 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 197 optimal weight: 0.0010 chunk 7 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 448 ASN B 176 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 178 GLN X 212 ASN ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.085699 restraints weight = 64803.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087815 restraints weight = 35730.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.089259 restraints weight = 23497.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090246 restraints weight = 17332.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090917 restraints weight = 13869.836| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20331 Z= 0.167 Angle : 0.697 11.833 27606 Z= 0.350 Chirality : 0.044 0.345 3041 Planarity : 0.004 0.067 3579 Dihedral : 4.590 56.451 2720 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.19 % Favored : 92.45 % Rotamer: Outliers : 3.28 % Allowed : 23.96 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2491 helix: 1.74 (0.20), residues: 704 sheet: 0.41 (0.25), residues: 479 loop : -1.59 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 211 TYR 0.032 0.002 TYR A 169 PHE 0.027 0.001 PHE Y 755 TRP 0.048 0.002 TRP g 167 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00380 (20331) covalent geometry : angle 0.69693 (27606) hydrogen bonds : bond 0.03748 ( 805) hydrogen bonds : angle 4.53554 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 504 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8659 (m-40) cc_final: 0.7664 (t0) REVERT: A 32 ASP cc_start: 0.8072 (m-30) cc_final: 0.7353 (m-30) REVERT: A 33 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8358 (ttm110) REVERT: A 65 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 112 PHE cc_start: 0.8986 (m-10) cc_final: 0.8735 (m-10) REVERT: A 146 MET cc_start: 0.7710 (pmm) cc_final: 0.7474 (pmm) REVERT: A 231 LYS cc_start: 0.9166 (mmpt) cc_final: 0.8766 (mmmt) REVERT: A 243 LYS cc_start: 0.9220 (tmmt) cc_final: 0.8749 (tmmt) REVERT: A 244 SER cc_start: 0.9178 (p) cc_final: 0.8850 (m) REVERT: A 260 LYS cc_start: 0.5383 (tttt) cc_final: 0.4596 (tttm) REVERT: A 304 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7551 (ttm110) REVERT: A 350 LYS cc_start: 0.9323 (tptt) cc_final: 0.8965 (mmmt) REVERT: A 396 SER cc_start: 0.9313 (t) cc_final: 0.9111 (p) REVERT: A 409 GLN cc_start: 0.8321 (pp30) cc_final: 0.7054 (pp30) REVERT: A 410 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 446 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7655 (t80) REVERT: A 459 ASP cc_start: 0.8928 (p0) cc_final: 0.8326 (t0) REVERT: A 462 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8390 (mtmm) REVERT: A 482 MET cc_start: 0.7655 (mmt) cc_final: 0.7026 (mmt) REVERT: B 21 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 65 GLN cc_start: 0.8727 (pp30) cc_final: 0.8502 (pp30) REVERT: B 79 PHE cc_start: 0.8653 (m-10) cc_final: 0.8438 (m-10) REVERT: B 108 LEU cc_start: 0.8785 (mt) cc_final: 0.8130 (mp) REVERT: B 112 PHE cc_start: 0.9390 (m-10) cc_final: 0.9019 (m-80) REVERT: B 148 TYR cc_start: 0.9206 (t80) cc_final: 0.8801 (t80) REVERT: B 191 ARG cc_start: 0.9361 (ptp90) cc_final: 0.8214 (ttt180) REVERT: B 227 ASP cc_start: 0.7425 (t0) cc_final: 0.7176 (t0) REVERT: B 230 TRP cc_start: 0.9496 (m100) cc_final: 0.8730 (m100) REVERT: B 233 GLN cc_start: 0.8721 (mt0) cc_final: 0.8514 (mm-40) REVERT: B 287 GLU cc_start: 0.8938 (tt0) cc_final: 0.7972 (tt0) REVERT: B 304 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7725 (mtm110) REVERT: B 312 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8119 (tp30) REVERT: B 438 ASP cc_start: 0.8574 (t70) cc_final: 0.8297 (t0) REVERT: B 445 ASN cc_start: 0.9081 (t0) cc_final: 0.8639 (t0) REVERT: B 459 ASP cc_start: 0.9013 (t70) cc_final: 0.8615 (t0) REVERT: M 17 ASN cc_start: 0.9260 (t0) cc_final: 0.8701 (t0) REVERT: M 50 ASP cc_start: 0.8565 (m-30) cc_final: 0.8174 (m-30) REVERT: M 83 ASP cc_start: 0.8563 (p0) cc_final: 0.7959 (p0) REVERT: M 176 LYS cc_start: 0.9189 (mttt) cc_final: 0.8976 (mtpt) REVERT: M 195 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8708 (tm-30) REVERT: M 197 LYS cc_start: 0.9223 (tmtt) cc_final: 0.8194 (tptt) REVERT: M 200 ARG cc_start: 0.9195 (ptp-170) cc_final: 0.8652 (ptm160) REVERT: X 29 CYS cc_start: 0.8856 (t) cc_final: 0.8553 (t) REVERT: X 40 ASN cc_start: 0.9195 (t0) cc_final: 0.8738 (t0) REVERT: X 50 ASP cc_start: 0.8850 (m-30) cc_final: 0.8613 (m-30) REVERT: X 144 MET cc_start: 0.8679 (tmm) cc_final: 0.8251 (tmm) REVERT: X 170 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8322 (tppp) REVERT: X 178 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: X 179 MET cc_start: 0.8678 (tmm) cc_final: 0.7716 (tmm) REVERT: X 183 MET cc_start: 0.8510 (ttm) cc_final: 0.8005 (ttm) REVERT: X 195 GLU cc_start: 0.8682 (tp30) cc_final: 0.8215 (tp30) REVERT: X 203 MET cc_start: 0.8403 (mmm) cc_final: 0.8110 (mtt) REVERT: Y 595 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8597 (tpp) REVERT: Y 678 GLU cc_start: 0.8427 (tp30) cc_final: 0.8199 (tp30) REVERT: Y 758 ARG cc_start: 0.8619 (mmp80) cc_final: 0.6394 (tpt170) REVERT: Y 788 ASN cc_start: 0.8403 (t0) cc_final: 0.8035 (p0) REVERT: e 93 MET cc_start: 0.7561 (ptm) cc_final: 0.7282 (ttt) REVERT: f 105 GLU cc_start: 0.8684 (pt0) cc_final: 0.8481 (pt0) REVERT: f 108 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: f 109 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7130 (mt-10) REVERT: g 158 ASP cc_start: 0.9138 (m-30) cc_final: 0.8749 (p0) REVERT: g 164 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6122 (t70) REVERT: g 167 TRP cc_start: 0.8451 (t60) cc_final: 0.8065 (t60) outliers start: 70 outliers final: 51 residues processed: 540 average time/residue: 0.1392 time to fit residues: 116.6072 Evaluate side-chains 546 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 488 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 136 PHE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 68 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 394 THR Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 595 MET Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 121 LEU Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain g residue 164 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 243 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 179 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 157 optimal weight: 0.0020 chunk 239 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 448 ASN B 400 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 GLN ** 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 = 0.3354 r_free = 0.3354 target = 0.101549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.086337 restraints weight = 65012.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088460 restraints weight = 35798.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089917 restraints weight = 23487.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090921 restraints weight = 17275.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091603 restraints weight = 13777.999| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20331 Z= 0.147 Angle : 0.704 12.254 27606 Z= 0.351 Chirality : 0.044 0.331 3041 Planarity : 0.004 0.068 3579 Dihedral : 4.570 57.820 2720 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.03 % Favored : 92.61 % Rotamer: Outliers : 3.00 % Allowed : 24.75 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2491 helix: 1.79 (0.20), residues: 698 sheet: 0.59 (0.26), residues: 431 loop : -1.59 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 211 TYR 0.030 0.001 TYR A 169 PHE 0.026 0.001 PHE M 72 TRP 0.048 0.001 TRP g 167 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00336 (20331) covalent geometry : angle 0.70427 (27606) hydrogen bonds : bond 0.03631 ( 805) hydrogen bonds : angle 4.50675 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4982 Ramachandran restraints generated. 2491 Oldfield, 0 Emsley, 2491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 489 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8645 (m-40) cc_final: 0.7660 (t0) REVERT: A 32 ASP cc_start: 0.8062 (m-30) cc_final: 0.7355 (m-30) REVERT: A 65 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8787 (tm-30) REVERT: A 112 PHE cc_start: 0.8978 (m-10) cc_final: 0.8733 (m-10) REVERT: A 231 LYS cc_start: 0.9170 (mmpt) cc_final: 0.8677 (mmmt) REVERT: A 243 LYS cc_start: 0.9221 (tmmt) cc_final: 0.8717 (tmmt) REVERT: A 244 SER cc_start: 0.9166 (p) cc_final: 0.8847 (m) REVERT: A 255 MET cc_start: 0.8003 (tmm) cc_final: 0.7243 (tmm) REVERT: A 260 LYS cc_start: 0.5373 (tttt) cc_final: 0.4678 (tttp) REVERT: A 304 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7569 (ttm110) REVERT: A 350 LYS cc_start: 0.9331 (tptt) cc_final: 0.8985 (mmmt) REVERT: A 396 SER cc_start: 0.9314 (t) cc_final: 0.9087 (p) REVERT: A 409 GLN cc_start: 0.8297 (pp30) cc_final: 0.7020 (pp30) REVERT: A 410 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 446 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 459 ASP cc_start: 0.8909 (p0) cc_final: 0.8346 (t0) REVERT: A 462 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8448 (mtmm) REVERT: A 482 MET cc_start: 0.7669 (mmt) cc_final: 0.6981 (mmt) REVERT: B 21 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 108 LEU cc_start: 0.8760 (mt) cc_final: 0.8559 (mp) REVERT: B 112 PHE cc_start: 0.9378 (m-10) cc_final: 0.9098 (m-10) REVERT: B 148 TYR cc_start: 0.9201 (t80) cc_final: 0.8819 (t80) REVERT: B 191 ARG cc_start: 0.9346 (ptp90) cc_final: 0.8222 (ttt180) REVERT: B 227 ASP cc_start: 0.7236 (t0) cc_final: 0.6979 (t0) REVERT: B 233 GLN cc_start: 0.8707 (mt0) cc_final: 0.8427 (mm-40) REVERT: B 287 GLU cc_start: 0.8923 (tt0) cc_final: 0.7964 (tt0) REVERT: B 304 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7725 (mtm110) REVERT: B 312 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 438 ASP cc_start: 0.8495 (t70) cc_final: 0.8266 (t0) REVERT: B 445 ASN cc_start: 0.9074 (t0) cc_final: 0.8635 (t0) REVERT: B 459 ASP cc_start: 0.8983 (t70) cc_final: 0.8594 (t0) REVERT: M 17 ASN cc_start: 0.9263 (t0) cc_final: 0.8716 (t0) REVERT: M 50 ASP cc_start: 0.8549 (m-30) cc_final: 0.8157 (m-30) REVERT: M 77 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.7977 (mtp-110) REVERT: M 195 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8692 (tm-30) REVERT: M 197 LYS cc_start: 0.9210 (tmtt) cc_final: 0.8174 (tptt) REVERT: M 200 ARG cc_start: 0.9182 (ptp-170) cc_final: 0.8645 (ptm160) REVERT: X 29 CYS cc_start: 0.8814 (t) cc_final: 0.8518 (t) REVERT: X 33 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8375 (mm) REVERT: X 40 ASN cc_start: 0.9194 (t0) cc_final: 0.8726 (t0) REVERT: X 50 ASP cc_start: 0.8840 (m-30) cc_final: 0.8611 (m-30) REVERT: X 144 MET cc_start: 0.8676 (tmm) cc_final: 0.8255 (tmm) REVERT: X 170 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8287 (tppp) REVERT: X 178 GLN cc_start: 0.8164 (pp30) cc_final: 0.7815 (pt0) REVERT: X 179 MET cc_start: 0.8672 (tmm) cc_final: 0.7748 (tmm) REVERT: X 183 MET cc_start: 0.8490 (ttm) cc_final: 0.8035 (ttm) REVERT: X 203 MET cc_start: 0.8394 (mmm) cc_final: 0.8131 (mtt) REVERT: Y 395 ASP cc_start: 0.8076 (m-30) cc_final: 0.7664 (m-30) REVERT: Y 595 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8406 (tpp) REVERT: Y 674 MET cc_start: 0.8408 (tpp) cc_final: 0.7686 (tpt) REVERT: Y 758 ARG cc_start: 0.8599 (mmp80) cc_final: 0.6534 (tpt170) REVERT: Y 788 ASN cc_start: 0.8389 (t0) cc_final: 0.8128 (p0) REVERT: e 93 MET cc_start: 0.7516 (ptm) cc_final: 0.7169 (ttt) REVERT: e 127 MET cc_start: 0.7894 (pmm) cc_final: 0.7663 (pmm) REVERT: f 105 GLU cc_start: 0.8658 (pt0) cc_final: 0.8432 (pt0) REVERT: f 108 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: f 109 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7096 (mt-10) REVERT: g 158 ASP cc_start: 0.9123 (m-30) cc_final: 0.8741 (p0) REVERT: g 164 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6262 (t70) REVERT: g 167 TRP cc_start: 0.8443 (t60) cc_final: 0.8136 (t60) outliers start: 64 outliers final: 52 residues processed: 524 average time/residue: 0.1399 time to fit residues: 113.6058 Evaluate side-chains 550 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 491 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 125 PHE Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 47 ASP Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain X residue 109 ASP Chi-restraints excluded: chain X residue 136 PHE Chi-restraints excluded: chain X residue 170 LYS Chi-restraints excluded: chain Y residue 17 GLN Chi-restraints excluded: chain Y residue 33 CYS Chi-restraints excluded: chain Y residue 68 TYR Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 167 ILE Chi-restraints excluded: chain Y residue 216 MET Chi-restraints excluded: chain Y residue 394 THR Chi-restraints excluded: chain Y residue 528 VAL Chi-restraints excluded: chain Y residue 551 TYR Chi-restraints excluded: chain Y residue 595 MET Chi-restraints excluded: chain Y residue 693 VAL Chi-restraints excluded: chain Y residue 698 VAL Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 121 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 164 HIS Chi-restraints excluded: chain f residue 108 GLN Chi-restraints excluded: chain f residue 121 LEU Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain g residue 164 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 121 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 240 optimal weight: 0.0000 chunk 78 optimal weight: 0.0370 chunk 181 optimal weight: 0.3980 chunk 249 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 56 optimal weight: 0.0980 chunk 183 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 448 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 178 GLN ** Y 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 GLN ** 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 = 0.3399 r_free = 0.3399 target = 0.103858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088612 restraints weight = 64829.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090818 restraints weight = 35179.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092291 restraints weight = 22995.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093302 restraints weight = 16896.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094006 restraints weight = 13452.851| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20331 Z= 0.123 Angle : 0.699 11.769 27606 Z= 0.346 Chirality : 0.045 0.534 3041 Planarity : 0.004 0.069 3579 Dihedral : 4.412 58.549 2720 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.70 % Favored : 92.97 % Rotamer: Outliers : 2.72 % Allowed : 25.13 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2491 helix: 1.88 (0.20), residues: 695 sheet: 0.83 (0.26), residues: 426 loop : -1.60 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 211 TYR 0.029 0.001 TYR A 169 PHE 0.021 0.001 PHE B 128 TRP 0.047 0.001 TRP g 167 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00279 (20331) covalent geometry : angle 0.69859 (27606) hydrogen bonds : bond 0.03308 ( 805) hydrogen bonds : angle 4.40642 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.40 seconds wall clock time: 91 minutes 41.96 seconds (5501.96 seconds total)