Starting phenix.real_space_refine on Thu Mar 14 13:24:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/03_2024/8g05_29645_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 61 5.16 5 C 5701 2.51 5 N 1525 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 14": "OE1" <-> "OE2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "R ARG 387": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8944 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2256 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'YI9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.06, per 1000 atoms: 0.57 Number of scatterers: 8944 At special positions: 0 Unit cell: (109.14, 128.4, 113.42, 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 61 16.00 O 1657 8.00 N 1525 7.00 C 5701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.02 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 13 sheets defined 30.0% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'R' and resid 15 through 33 removed outlier: 4.300A pdb=" N GLY R 18 " --> pdb=" O SER R 15 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 19 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG R 20 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER R 25 " --> pdb=" O VAL R 22 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL R 28 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL R 30 " --> pdb=" O GLY R 27 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA R 31 " --> pdb=" O VAL R 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR R 33 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.729A pdb=" N THR R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU R 42 " --> pdb=" O ASN R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 65 Processing helix chain 'R' and resid 67 through 71 Processing helix chain 'R' and resid 80 through 83 No H-bonds generated for 'chain 'R' and resid 80 through 83' Processing helix chain 'R' and resid 90 through 119 removed outlier: 3.821A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 98 " --> pdb=" O ARG R 94 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 131 No H-bonds generated for 'chain 'R' and resid 128 through 131' Processing helix chain 'R' and resid 136 through 148 removed outlier: 3.798A pdb=" N THR R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 188 Processing helix chain 'R' and resid 197 through 209 removed outlier: 3.771A pdb=" N HIS R 202 " --> pdb=" O TYR R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 329 removed outlier: 3.787A pdb=" N ARG R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE R 325 " --> pdb=" O CYS R 321 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS R 327 " --> pdb=" O ALA R 323 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE R 328 " --> pdb=" O VAL R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 341 removed outlier: 4.014A pdb=" N ILE R 340 " --> pdb=" O LEU R 336 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 357 Processing helix chain 'R' and resid 361 through 363 No H-bonds generated for 'chain 'R' and resid 361 through 363' Processing helix chain 'R' and resid 366 through 369 No H-bonds generated for 'chain 'R' and resid 366 through 369' Processing helix chain 'R' and resid 375 through 386 Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.085A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.972A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.638A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'R' and resid 159 through 162 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.700A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.826A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.881A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.537A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.814A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.896A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.560A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.152A pdb=" N GLY E 16 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG E 18 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR E 84 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU E 20 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N CYS E 22 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA E 24 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR E 78 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 6.002A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.518A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 155 through 160 327 hydrogen bonds defined for protein. 903 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: 2.78 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1442 1.31 - 1.43: 2517 1.43 - 1.56: 5085 1.56 - 1.69: 1 1.69 - 1.81: 86 Bond restraints: 9131 Sorted by residual: bond pdb=" C15 YI9 R 401 " pdb=" N14 YI9 R 401 " ideal model delta sigma weight residual 1.489 1.323 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C15 YI9 R 401 " pdb=" N17 YI9 R 401 " ideal model delta sigma weight residual 1.486 1.330 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C12 YI9 R 401 " pdb=" N14 YI9 R 401 " ideal model delta sigma weight residual 1.453 1.315 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C10 YI9 R 401 " pdb=" N17 YI9 R 401 " ideal model delta sigma weight residual 1.450 1.322 0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 YI9 R 401 " pdb=" C12 YI9 R 401 " ideal model delta sigma weight residual 1.492 1.365 0.127 2.00e-02 2.50e+03 4.00e+01 ... (remaining 9126 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.81: 213 106.81 - 114.75: 5395 114.75 - 122.69: 5750 122.69 - 130.63: 969 130.63 - 138.57: 48 Bond angle restraints: 12375 Sorted by residual: angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.82 128.48 -5.66 1.42e+00 4.96e-01 1.59e+01 angle pdb=" CA ARG E 218 " pdb=" CB ARG E 218 " pdb=" CG ARG E 218 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N VAL R 146 " pdb=" CA VAL R 146 " pdb=" C VAL R 146 " ideal model delta sigma weight residual 112.29 109.25 3.04 9.40e-01 1.13e+00 1.05e+01 angle pdb=" CA LEU B 70 " pdb=" CB LEU B 70 " pdb=" CG LEU B 70 " ideal model delta sigma weight residual 116.30 127.58 -11.28 3.50e+00 8.16e-02 1.04e+01 ... (remaining 12370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4915 17.83 - 35.67: 451 35.67 - 53.50: 72 53.50 - 71.33: 12 71.33 - 89.17: 13 Dihedral angle restraints: 5463 sinusoidal: 2162 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 166 " pdb=" CB CYS R 166 " ideal model delta sinusoidal sigma weight residual -86.00 -150.17 64.17 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CA LYS R 135 " pdb=" C LYS R 135 " pdb=" N GLY R 136 " pdb=" CA GLY R 136 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA THR E 172 " pdb=" C THR E 172 " pdb=" N TYR E 173 " pdb=" CA TYR E 173 " ideal model delta harmonic sigma weight residual 180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.991: 1409 0.991 - 1.981: 0 1.981 - 2.972: 0 2.972 - 3.962: 0 3.962 - 4.953: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 -2.40 4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 232 " pdb=" CA ILE B 232 " pdb=" CG1 ILE B 232 " pdb=" CG2 ILE B 232 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1407 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 YI9 R 401 " -0.082 2.00e-02 2.50e+03 3.84e-02 3.32e+01 pdb=" C10 YI9 R 401 " 0.034 2.00e-02 2.50e+03 pdb=" C11 YI9 R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C12 YI9 R 401 " 0.004 2.00e-02 2.50e+03 pdb=" C15 YI9 R 401 " -0.012 2.00e-02 2.50e+03 pdb=" N09 YI9 R 401 " 0.057 2.00e-02 2.50e+03 pdb=" N14 YI9 R 401 " -0.011 2.00e-02 2.50e+03 pdb=" N17 YI9 R 401 " 0.012 2.00e-02 2.50e+03 pdb=" O16 YI9 R 401 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 153 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO R 154 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 154 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 154 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 366 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO R 367 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 367 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 367 " -0.035 5.00e-02 4.00e+02 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2174 2.79 - 3.31: 7699 3.31 - 3.84: 15144 3.84 - 4.37: 18330 4.37 - 4.90: 31501 Nonbonded interactions: 74848 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.257 2.440 nonbonded pdb=" O VAL R 106 " pdb=" OG1 THR R 110 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.305 2.440 nonbonded pdb=" OG SER R 105 " pdb=" OH TYR R 186 " model vdw 2.312 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.316 2.440 ... (remaining 74843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 1.920 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.110 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.007 0.166 9131 Z= 0.449 Angle : 0.896 17.165 12375 Z= 0.489 Chirality : 0.143 4.953 1410 Planarity : 0.007 0.065 1559 Dihedral : 14.329 89.168 3325 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.62 % Allowed : 7.33 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.21), residues: 1124 helix: -3.16 (0.19), residues: 359 sheet: -0.93 (0.29), residues: 284 loop : -1.91 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.023 0.002 PHE B 199 TYR 0.019 0.002 TYR B 59 ARG 0.014 0.001 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 1.024 Fit side-chains REVERT: R 186 TYR cc_start: 0.6991 (m-80) cc_final: 0.6775 (m-80) REVERT: R 316 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7323 (tttm) REVERT: A 204 GLN cc_start: 0.7891 (mt0) cc_final: 0.7583 (mm-40) REVERT: B 16 ASN cc_start: 0.7828 (m110) cc_final: 0.7602 (m110) REVERT: B 46 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6647 (mmt180) REVERT: B 188 MET cc_start: 0.8124 (mmm) cc_final: 0.7846 (mmp) REVERT: B 214 ARG cc_start: 0.6800 (mmp-170) cc_final: 0.5932 (mmm-85) REVERT: G 38 MET cc_start: 0.7873 (ttp) cc_final: 0.7515 (ttp) outliers start: 6 outliers final: 2 residues processed: 201 average time/residue: 1.1400 time to fit residues: 244.9029 Evaluate side-chains 151 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 38 ASN R 74 GLN R 83 HIS R 85 HIS R 357 ASN R 362 ASN R 379 GLN A 22 ASN A 241 ASN A 256 ASN A 306 GLN B 88 ASN B 91 HIS B 156 GLN B 259 GLN E 231 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9131 Z= 0.203 Angle : 0.567 8.004 12375 Z= 0.296 Chirality : 0.042 0.164 1410 Planarity : 0.004 0.045 1559 Dihedral : 6.812 59.848 1313 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.62 % Allowed : 14.57 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.23), residues: 1124 helix: -1.64 (0.25), residues: 361 sheet: -0.61 (0.30), residues: 275 loop : -1.38 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS R 85 PHE 0.014 0.001 PHE A 334 TYR 0.010 0.001 TYR E 94 ARG 0.005 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 0.970 Fit side-chains REVERT: R 94 ARG cc_start: 0.5718 (mtt180) cc_final: 0.5409 (tpp80) REVERT: R 316 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7287 (tttm) REVERT: R 344 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7194 (mtm110) REVERT: R 376 GLN cc_start: 0.7939 (mp10) cc_final: 0.7714 (mp10) REVERT: A 204 GLN cc_start: 0.7635 (mt0) cc_final: 0.7272 (mm-40) REVERT: A 298 GLU cc_start: 0.7550 (tp30) cc_final: 0.7200 (tm-30) REVERT: B 10 GLU cc_start: 0.8370 (tp30) cc_final: 0.7867 (tp30) REVERT: B 16 ASN cc_start: 0.7833 (m110) cc_final: 0.7508 (m110) REVERT: B 42 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6810 (tpp-160) REVERT: B 46 ARG cc_start: 0.6919 (mtp-110) cc_final: 0.6605 (mmt180) REVERT: B 105 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6236 (t80) REVERT: B 188 MET cc_start: 0.7999 (mmm) cc_final: 0.7767 (mmp) REVERT: B 214 ARG cc_start: 0.6526 (mmp-170) cc_final: 0.5866 (mmm160) REVERT: G 38 MET cc_start: 0.7750 (ttp) cc_final: 0.7463 (ttp) outliers start: 35 outliers final: 15 residues processed: 186 average time/residue: 1.0950 time to fit residues: 218.0719 Evaluate side-chains 165 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.0030 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 85 HIS R 357 ASN R 379 GLN A 241 ASN A 256 ASN A 311 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9131 Z= 0.197 Angle : 0.559 8.251 12375 Z= 0.288 Chirality : 0.042 0.147 1410 Planarity : 0.004 0.040 1559 Dihedral : 6.284 54.767 1311 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.96 % Allowed : 15.29 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1124 helix: -0.99 (0.27), residues: 367 sheet: -0.37 (0.31), residues: 275 loop : -1.15 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS R 85 PHE 0.013 0.001 PHE A 334 TYR 0.008 0.001 TYR G 40 ARG 0.004 0.000 ARG R 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 162 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5749 (mtt180) cc_final: 0.5412 (tpp80) REVERT: R 316 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7262 (tttm) REVERT: R 344 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7051 (mtm110) REVERT: R 376 GLN cc_start: 0.7991 (mp10) cc_final: 0.7610 (mp10) REVERT: A 297 GLU cc_start: 0.7689 (mp0) cc_final: 0.7464 (mp0) REVERT: A 298 GLU cc_start: 0.7696 (tp30) cc_final: 0.7304 (tm-30) REVERT: B 42 ARG cc_start: 0.7078 (tpt170) cc_final: 0.6805 (tpp-160) REVERT: B 46 ARG cc_start: 0.6868 (mtp-110) cc_final: 0.6578 (mmt180) REVERT: B 105 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6351 (t80) REVERT: B 175 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: B 188 MET cc_start: 0.7979 (mmm) cc_final: 0.7759 (mmp) REVERT: B 198 LEU cc_start: 0.8091 (mt) cc_final: 0.7846 (mt) REVERT: B 214 ARG cc_start: 0.6471 (mmp-170) cc_final: 0.5880 (mmm160) REVERT: B 338 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8078 (mm) REVERT: G 38 MET cc_start: 0.7685 (ttp) cc_final: 0.7454 (ttp) outliers start: 48 outliers final: 27 residues processed: 190 average time/residue: 1.0388 time to fit residues: 212.1227 Evaluate side-chains 179 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.0370 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 2.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 311 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9131 Z= 0.337 Angle : 0.629 9.812 12375 Z= 0.325 Chirality : 0.045 0.151 1410 Planarity : 0.004 0.037 1559 Dihedral : 6.430 54.959 1311 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.48 % Allowed : 16.74 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1124 helix: -0.76 (0.28), residues: 361 sheet: -0.26 (0.31), residues: 272 loop : -1.08 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS R 85 PHE 0.015 0.002 PHE B 199 TYR 0.013 0.002 TYR B 105 ARG 0.004 0.000 ARG R 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 156 time to evaluate : 0.950 Fit side-chains REVERT: R 344 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7074 (mtm110) REVERT: R 376 GLN cc_start: 0.8134 (mp10) cc_final: 0.7704 (mp10) REVERT: A 204 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6996 (mm-40) REVERT: A 297 GLU cc_start: 0.7688 (mp0) cc_final: 0.7465 (mp0) REVERT: A 298 GLU cc_start: 0.7900 (tp30) cc_final: 0.7418 (tm-30) REVERT: B 42 ARG cc_start: 0.7270 (tpt170) cc_final: 0.7019 (tpp-160) REVERT: B 44 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6963 (mm-40) REVERT: B 105 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6504 (t80) REVERT: B 175 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7626 (mt0) REVERT: B 214 ARG cc_start: 0.6431 (mmp-170) cc_final: 0.5805 (mmm160) REVERT: B 338 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8080 (mm) REVERT: E 67 ARG cc_start: 0.6608 (mtm110) cc_final: 0.6297 (mtm-85) REVERT: E 218 ARG cc_start: 0.6991 (mmp-170) cc_final: 0.6519 (mtm-85) REVERT: E 220 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: E 238 THR cc_start: 0.8287 (p) cc_final: 0.8061 (p) REVERT: G 38 MET cc_start: 0.7730 (ttp) cc_final: 0.7507 (ttp) outliers start: 53 outliers final: 33 residues processed: 187 average time/residue: 1.1162 time to fit residues: 223.8292 Evaluate side-chains 191 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 231 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 311 ASN B 16 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9131 Z= 0.162 Angle : 0.544 7.466 12375 Z= 0.279 Chirality : 0.041 0.151 1410 Planarity : 0.003 0.038 1559 Dihedral : 5.951 58.931 1311 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.03 % Allowed : 18.90 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1124 helix: -0.43 (0.28), residues: 367 sheet: -0.25 (0.30), residues: 277 loop : -0.95 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 85 PHE 0.011 0.001 PHE A 334 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG R 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5762 (mtt180) cc_final: 0.5414 (tpp80) REVERT: R 316 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7295 (tttm) REVERT: R 344 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7085 (mtm110) REVERT: R 376 GLN cc_start: 0.8066 (mp10) cc_final: 0.7586 (mm-40) REVERT: A 204 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6821 (mm-40) REVERT: A 252 SER cc_start: 0.8847 (m) cc_final: 0.8322 (p) REVERT: A 297 GLU cc_start: 0.7632 (mp0) cc_final: 0.7428 (mp0) REVERT: B 46 ARG cc_start: 0.6947 (mtp-110) cc_final: 0.6653 (mmt180) REVERT: B 105 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6269 (t80) REVERT: B 198 LEU cc_start: 0.8036 (mt) cc_final: 0.7795 (mt) REVERT: B 214 ARG cc_start: 0.6409 (mmp-170) cc_final: 0.5685 (mmm-85) REVERT: B 338 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8079 (mm) REVERT: G 38 MET cc_start: 0.7690 (ttp) cc_final: 0.7418 (ttp) outliers start: 39 outliers final: 26 residues processed: 189 average time/residue: 1.1074 time to fit residues: 224.4388 Evaluate side-chains 179 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 40.0000 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 311 ASN E 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9131 Z= 0.416 Angle : 0.678 10.312 12375 Z= 0.349 Chirality : 0.047 0.185 1410 Planarity : 0.004 0.036 1559 Dihedral : 6.119 47.955 1310 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.37 % Allowed : 18.90 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1124 helix: -0.64 (0.27), residues: 367 sheet: -0.20 (0.30), residues: 282 loop : -1.07 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS R 85 PHE 0.019 0.002 PHE R 92 TYR 0.021 0.002 TYR B 59 ARG 0.005 0.001 ARG R 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 146 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 344 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7022 (mtm110) REVERT: R 376 GLN cc_start: 0.8204 (mp10) cc_final: 0.7734 (mm-40) REVERT: A 204 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6946 (mm-40) REVERT: A 297 GLU cc_start: 0.7749 (mp0) cc_final: 0.7478 (mp0) REVERT: A 298 GLU cc_start: 0.7749 (tp30) cc_final: 0.7252 (tm-30) REVERT: B 42 ARG cc_start: 0.7340 (tpt170) cc_final: 0.7046 (tpp-160) REVERT: B 44 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7059 (mm-40) REVERT: B 105 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.6590 (t80) REVERT: B 175 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: B 214 ARG cc_start: 0.6502 (mmp-170) cc_final: 0.5830 (mmm160) REVERT: B 338 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8096 (mm) REVERT: E 67 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5958 (mtp180) REVERT: E 218 ARG cc_start: 0.7019 (mmp-170) cc_final: 0.6582 (mtm-85) REVERT: G 38 MET cc_start: 0.7691 (ttp) cc_final: 0.7476 (ttp) outliers start: 52 outliers final: 34 residues processed: 180 average time/residue: 1.0524 time to fit residues: 203.0377 Evaluate side-chains 182 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 364 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 231 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0770 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 38 ASN R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9131 Z= 0.141 Angle : 0.546 7.576 12375 Z= 0.280 Chirality : 0.041 0.139 1410 Planarity : 0.003 0.036 1559 Dihedral : 5.434 51.863 1310 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.41 % Allowed : 20.66 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1124 helix: -0.21 (0.28), residues: 367 sheet: -0.13 (0.31), residues: 276 loop : -0.86 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 85 PHE 0.010 0.001 PHE A 334 TYR 0.010 0.001 TYR E 175 ARG 0.004 0.000 ARG R 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5710 (mtt180) cc_final: 0.5348 (tpp80) REVERT: R 316 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7261 (tttm) REVERT: R 344 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7046 (mtm110) REVERT: R 364 CYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7788 (t) REVERT: R 376 GLN cc_start: 0.8094 (mp10) cc_final: 0.7689 (mt0) REVERT: A 204 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6703 (mm-40) REVERT: A 252 SER cc_start: 0.8846 (m) cc_final: 0.8333 (p) REVERT: A 298 GLU cc_start: 0.7690 (tp30) cc_final: 0.7292 (tm-30) REVERT: A 302 TYR cc_start: 0.7786 (t80) cc_final: 0.7523 (t80) REVERT: A 306 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7553 (mm110) REVERT: B 42 ARG cc_start: 0.7128 (tpt170) cc_final: 0.6781 (mmp-170) REVERT: B 46 ARG cc_start: 0.6978 (mtp-110) cc_final: 0.6662 (mmt180) REVERT: B 198 LEU cc_start: 0.7968 (mt) cc_final: 0.7723 (mt) REVERT: B 214 ARG cc_start: 0.6451 (mmp-170) cc_final: 0.5825 (mmm160) REVERT: B 303 ASP cc_start: 0.7452 (m-30) cc_final: 0.7227 (m-30) REVERT: E 218 ARG cc_start: 0.7030 (mmp-170) cc_final: 0.6521 (mmm160) REVERT: G 38 MET cc_start: 0.7700 (ttp) cc_final: 0.7427 (ttp) outliers start: 33 outliers final: 18 residues processed: 178 average time/residue: 1.1002 time to fit residues: 210.2861 Evaluate side-chains 175 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 364 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 311 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9131 Z= 0.199 Angle : 0.564 7.416 12375 Z= 0.292 Chirality : 0.042 0.138 1410 Planarity : 0.003 0.036 1559 Dihedral : 5.401 49.868 1310 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.82 % Allowed : 20.35 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1124 helix: -0.09 (0.28), residues: 365 sheet: -0.07 (0.31), residues: 277 loop : -0.81 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 85 PHE 0.020 0.001 PHE R 92 TYR 0.009 0.001 TYR B 105 ARG 0.004 0.000 ARG R 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5721 (mtt180) cc_final: 0.5363 (tpp80) REVERT: R 316 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7252 (tttm) REVERT: R 344 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7090 (mtm110) REVERT: R 376 GLN cc_start: 0.8100 (mp10) cc_final: 0.7701 (mm-40) REVERT: A 204 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6840 (mm-40) REVERT: A 252 SER cc_start: 0.8817 (m) cc_final: 0.8332 (p) REVERT: A 298 GLU cc_start: 0.7756 (tp30) cc_final: 0.7325 (tm-30) REVERT: B 46 ARG cc_start: 0.7058 (mtp-110) cc_final: 0.6732 (mmt180) REVERT: B 105 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.6297 (t80) REVERT: B 198 LEU cc_start: 0.8015 (mt) cc_final: 0.7771 (mt) REVERT: B 214 ARG cc_start: 0.6411 (mmp-170) cc_final: 0.5684 (mmm-85) REVERT: B 303 ASP cc_start: 0.7450 (m-30) cc_final: 0.7242 (m-30) REVERT: B 338 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8040 (mm) REVERT: G 27 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7741 (mtt180) REVERT: G 38 MET cc_start: 0.7701 (ttp) cc_final: 0.7429 (ttp) outliers start: 37 outliers final: 25 residues processed: 183 average time/residue: 1.1403 time to fit residues: 225.3759 Evaluate side-chains 181 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 364 CYS Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9131 Z= 0.218 Angle : 0.587 8.362 12375 Z= 0.300 Chirality : 0.043 0.139 1410 Planarity : 0.003 0.035 1559 Dihedral : 5.416 48.967 1310 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.24 % Allowed : 20.45 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1124 helix: 0.09 (0.29), residues: 357 sheet: -0.01 (0.31), residues: 275 loop : -0.80 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 85 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR B 124 ARG 0.004 0.000 ARG R 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5709 (mtt180) cc_final: 0.5357 (tpp80) REVERT: R 109 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7230 (mt) REVERT: R 316 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7256 (tttm) REVERT: R 376 GLN cc_start: 0.8083 (mp10) cc_final: 0.7642 (mm-40) REVERT: A 204 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: A 252 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8290 (p) REVERT: A 298 GLU cc_start: 0.7762 (tp30) cc_final: 0.7358 (tm-30) REVERT: A 302 TYR cc_start: 0.7796 (t80) cc_final: 0.7526 (t80) REVERT: A 306 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7587 (mm110) REVERT: B 46 ARG cc_start: 0.7076 (mtp-110) cc_final: 0.6744 (mmt180) REVERT: B 105 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6321 (t80) REVERT: B 198 LEU cc_start: 0.8023 (mt) cc_final: 0.7796 (mt) REVERT: B 214 ARG cc_start: 0.6414 (mmp-170) cc_final: 0.5702 (mmm-85) REVERT: B 338 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8060 (mm) REVERT: E 67 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5995 (mtp180) REVERT: E 218 ARG cc_start: 0.6956 (mmp-170) cc_final: 0.6599 (mtm-85) REVERT: G 38 MET cc_start: 0.7712 (ttp) cc_final: 0.7442 (ttp) outliers start: 41 outliers final: 26 residues processed: 184 average time/residue: 1.0679 time to fit residues: 211.0239 Evaluate side-chains 186 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 73 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9131 Z= 0.220 Angle : 0.592 8.514 12375 Z= 0.303 Chirality : 0.043 0.139 1410 Planarity : 0.003 0.035 1559 Dihedral : 5.399 48.765 1310 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.51 % Allowed : 21.49 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1124 helix: 0.09 (0.29), residues: 360 sheet: -0.04 (0.31), residues: 277 loop : -0.79 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 85 PHE 0.023 0.001 PHE R 92 TYR 0.011 0.001 TYR A 230 ARG 0.005 0.000 ARG R 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5670 (mtt180) cc_final: 0.5353 (tpp80) REVERT: R 109 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7279 (mt) REVERT: R 316 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7258 (tttm) REVERT: R 344 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7219 (mtm110) REVERT: R 376 GLN cc_start: 0.8181 (mp10) cc_final: 0.7669 (mm-40) REVERT: A 204 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6847 (mm-40) REVERT: A 252 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 298 GLU cc_start: 0.7743 (tp30) cc_final: 0.7352 (tm-30) REVERT: A 302 TYR cc_start: 0.7830 (t80) cc_final: 0.7538 (t80) REVERT: A 306 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7592 (mm110) REVERT: B 46 ARG cc_start: 0.7072 (mtp-110) cc_final: 0.6743 (mmt180) REVERT: B 105 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6342 (t80) REVERT: B 198 LEU cc_start: 0.8026 (mt) cc_final: 0.7797 (mt) REVERT: B 214 ARG cc_start: 0.6419 (mmp-170) cc_final: 0.5713 (mmm-85) REVERT: B 338 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8059 (mm) REVERT: E 67 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5988 (mtp180) REVERT: E 218 ARG cc_start: 0.6994 (mmp-170) cc_final: 0.6659 (mtm-85) REVERT: G 38 MET cc_start: 0.7709 (ttp) cc_final: 0.7436 (ttp) outliers start: 34 outliers final: 24 residues processed: 175 average time/residue: 1.0940 time to fit residues: 205.3659 Evaluate side-chains 179 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN A 241 ASN A 256 ASN B 16 ASN B 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126099 restraints weight = 10510.395| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.11 r_work: 0.3288 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9131 Z= 0.181 Angle : 0.582 8.014 12375 Z= 0.296 Chirality : 0.042 0.137 1410 Planarity : 0.003 0.035 1559 Dihedral : 5.284 49.721 1310 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.31 % Allowed : 21.80 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1124 helix: 0.01 (0.28), residues: 373 sheet: 0.10 (0.31), residues: 273 loop : -0.81 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 85 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR A 230 ARG 0.005 0.000 ARG R 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.17 seconds wall clock time: 69 minutes 47.97 seconds (4187.97 seconds total)