Starting phenix.real_space_refine on Mon Mar 11 12:43:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcn_32425/03_2024/7wcn_32425_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcn_32425/03_2024/7wcn_32425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcn_32425/03_2024/7wcn_32425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcn_32425/03_2024/7wcn_32425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcn_32425/03_2024/7wcn_32425_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcn_32425/03_2024/7wcn_32425_updated.pdb" } resolution = 2.87 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= 0.005 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5232 2.51 5 N 1436 2.21 5 O 1526 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 203": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8252 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1947 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 451 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2275 Unusual residues: {'8WL': 1} Classifications: {'peptide': 289, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 279, None: 1} Not linked: pdbres="VAL R 300 " pdbres="8WL R 401 " Chain breaks: 1 Time building chain proxies: 4.77, per 1000 atoms: 0.58 Number of scatterers: 8252 At special positions: 0 Unit cell: (79.994, 102.971, 131.054, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 1 9.00 O 1526 8.00 N 1436 7.00 C 5232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 37.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.939A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.781A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.860A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'B' and resid 18 through 36 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.951A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 6 through 35 removed outlier: 3.795A pdb=" N LEU R 11 " --> pdb=" O PHE R 7 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 65 removed outlier: 3.558A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 108 removed outlier: 3.944A pdb=" N VAL R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 115 removed outlier: 3.686A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 137 Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 164 through 171 Processing helix chain 'R' and resid 174 through 209 removed outlier: 3.838A pdb=" N ALA R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 236 Processing helix chain 'R' and resid 239 through 249 Processing helix chain 'R' and resid 254 through 262 removed outlier: 3.786A pdb=" N LEU R 260 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 279 removed outlier: 3.722A pdb=" N ASN R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN R 275 " --> pdb=" O ASN R 271 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 284 through 299 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.420A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.817A pdb=" N ALA B 84 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 72 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 82 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP B 74 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B 80 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP B 94 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS B 100 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.628A pdb=" N ARG B 148 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 136 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 146 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 157 through 162 removed outlier: 6.749A pdb=" N SER B 171 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 160 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 169 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 168 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 181 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN B 187 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.871A pdb=" N GLY B 213 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 201 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 211 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 203 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 209 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 240 through 245 removed outlier: 6.719A pdb=" N GLY B 255 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE B 243 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 253 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 245 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA B 251 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 273 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 265 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU B 271 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.638A pdb=" N GLY B 299 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 297 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 289 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 295 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP B 309 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG B 315 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.735A pdb=" N ILE B 349 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 61 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 347 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.817A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1047 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: 2.32 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1343 1.30 - 1.43: 2221 1.43 - 1.56: 4772 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8418 Sorted by residual: bond pdb=" C12 8WL R 401 " pdb=" N11 8WL R 401 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C16 8WL R 401 " pdb=" N17 8WL R 401 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C8 8WL R 401 " pdb=" C9 8WL R 401 " ideal model delta sigma weight residual 1.544 1.453 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C34 8WL R 401 " pdb=" C8 8WL R 401 " ideal model delta sigma weight residual 1.533 1.445 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C SER B 256 " pdb=" O SER B 256 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.28e-02 6.10e+03 1.85e+01 ... (remaining 8413 not shown) Histogram of bond angle deviations from ideal: 96.43 - 103.95: 84 103.95 - 111.47: 3680 111.47 - 118.99: 3090 118.99 - 126.50: 4423 126.50 - 134.02: 118 Bond angle restraints: 11395 Sorted by residual: angle pdb=" N SER B 256 " pdb=" CA SER B 256 " pdb=" C SER B 256 " ideal model delta sigma weight residual 109.41 117.59 -8.18 1.52e+00 4.33e-01 2.90e+01 angle pdb=" O24 8WL R 401 " pdb=" S22 8WL R 401 " pdb=" O25 8WL R 401 " ideal model delta sigma weight residual 117.77 102.02 15.75 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C7 8WL R 401 " pdb=" C8 8WL R 401 " pdb=" C9 8WL R 401 " ideal model delta sigma weight residual 111.30 96.43 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" N SER B 256 " pdb=" CA SER B 256 " pdb=" CB SER B 256 " ideal model delta sigma weight residual 111.43 103.96 7.47 1.59e+00 3.96e-01 2.21e+01 angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 109.41 114.94 -5.53 1.52e+00 4.33e-01 1.32e+01 ... (remaining 11390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4508 17.57 - 35.15: 417 35.15 - 52.72: 72 52.72 - 70.30: 23 70.30 - 87.87: 10 Dihedral angle restraints: 5030 sinusoidal: 1992 harmonic: 3038 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP A 310 " pdb=" C ASP A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA MET B 273 " pdb=" C MET B 273 " pdb=" N THR B 274 " pdb=" CA THR B 274 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1133 0.070 - 0.141: 141 0.141 - 0.211: 6 0.211 - 0.281: 1 0.281 - 0.351: 1 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA SER B 85 " pdb=" N SER B 85 " pdb=" C SER B 85 " pdb=" CB SER B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA TYR B 70 " pdb=" N TYR B 70 " pdb=" C TYR B 70 " pdb=" CB TYR B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR A 325 " pdb=" CA THR A 325 " pdb=" OG1 THR A 325 " pdb=" CG2 THR A 325 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 1279 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.034 2.00e-02 2.50e+03 2.54e-02 1.30e+01 pdb=" CG TYR B 70 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO B 247 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO N 88 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.028 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1833 2.79 - 3.31: 7458 3.31 - 3.84: 13226 3.84 - 4.37: 15741 4.37 - 4.90: 27361 Nonbonded interactions: 65619 Sorted by model distance: nonbonded pdb=" OE1 GLU B 226 " pdb=" NH2 ARG B 230 " model vdw 2.257 2.520 nonbonded pdb=" OD2 ASP R 64 " pdb=" NH2 ARG R 81 " model vdw 2.327 2.520 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.333 2.520 nonbonded pdb=" OG SER B 85 " pdb=" OD1 ASP B 87 " model vdw 2.360 2.440 nonbonded pdb=" O ASP B 174 " pdb=" OG1 THR B 175 " model vdw 2.381 2.440 ... (remaining 65614 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: 0.970 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: 5.210 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.560 Find NCS groups from input model: 0.240 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.005 0.125 8418 Z= 0.329 Angle : 0.703 15.746 11395 Z= 0.357 Chirality : 0.047 0.351 1282 Planarity : 0.004 0.063 1450 Dihedral : 14.765 87.874 3062 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 1033 helix: 1.82 (0.28), residues: 390 sheet: -0.10 (0.35), residues: 208 loop : -1.04 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 282 HIS 0.012 0.001 HIS A 357 PHE 0.019 0.002 PHE B 245 TYR 0.062 0.002 TYR B 70 ARG 0.008 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.049 Fit side-chains REVERT: A 27 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6641 (mm-30) REVERT: R 145 MET cc_start: 0.6431 (ptt) cc_final: 0.6230 (ptm) outliers start: 0 outliers final: 1 residues processed: 119 average time/residue: 1.5919 time to fit residues: 199.2210 Evaluate side-chains 96 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN N 5 GLN R 46 ASN R 147 GLN R 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8418 Z= 0.182 Angle : 0.539 10.479 11395 Z= 0.282 Chirality : 0.043 0.154 1282 Planarity : 0.004 0.063 1450 Dihedral : 6.303 53.429 1172 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.35 % Allowed : 8.56 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1033 helix: 2.19 (0.28), residues: 394 sheet: 0.05 (0.36), residues: 207 loop : -1.01 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.001 PHE R 181 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.974 Fit side-chains REVERT: A 27 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6662 (mm-30) REVERT: A 60 MET cc_start: 0.4651 (mmp) cc_final: 0.4203 (mmp) REVERT: B 206 ASP cc_start: 0.7423 (p0) cc_final: 0.7162 (p0) REVERT: R 141 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6932 (mp) REVERT: R 145 MET cc_start: 0.6446 (ptt) cc_final: 0.6177 (ptm) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 1.3449 time to fit residues: 159.3984 Evaluate side-chains 108 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 197 GLN R 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8418 Z= 0.133 Angle : 0.493 8.936 11395 Z= 0.258 Chirality : 0.041 0.164 1282 Planarity : 0.004 0.060 1450 Dihedral : 5.791 47.473 1169 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.03 % Allowed : 11.26 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1033 helix: 2.45 (0.28), residues: 389 sheet: 0.23 (0.36), residues: 205 loop : -1.04 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 181 TYR 0.010 0.001 TYR A 37 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.978 Fit side-chains REVERT: A 27 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6581 (mm-30) REVERT: A 60 MET cc_start: 0.4535 (mmp) cc_final: 0.4109 (mmp) REVERT: B 206 ASP cc_start: 0.7444 (p0) cc_final: 0.7203 (p0) REVERT: R 145 MET cc_start: 0.6548 (ptt) cc_final: 0.6224 (ptm) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 1.3805 time to fit residues: 160.8260 Evaluate side-chains 104 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 0.0010 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 3 GLN N 5 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8418 Z= 0.196 Angle : 0.536 10.328 11395 Z= 0.280 Chirality : 0.043 0.158 1282 Planarity : 0.004 0.060 1450 Dihedral : 5.813 42.692 1169 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.25 % Allowed : 13.51 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1033 helix: 2.33 (0.28), residues: 391 sheet: 0.13 (0.36), residues: 207 loop : -0.98 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.014 0.001 TYR R 185 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.968 Fit side-chains REVERT: A 27 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6610 (mm-30) REVERT: B 70 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: B 206 ASP cc_start: 0.7350 (p0) cc_final: 0.7117 (p0) REVERT: B 225 ARG cc_start: 0.7039 (mmt-90) cc_final: 0.6655 (mmt-90) REVERT: R 145 MET cc_start: 0.6522 (ptt) cc_final: 0.6191 (ptm) outliers start: 20 outliers final: 10 residues processed: 118 average time/residue: 1.4024 time to fit residues: 175.0924 Evaluate side-chains 111 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 147 GLN R 197 GLN R 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8418 Z= 0.194 Angle : 0.535 10.221 11395 Z= 0.279 Chirality : 0.043 0.155 1282 Planarity : 0.004 0.059 1450 Dihedral : 5.763 39.726 1169 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.82 % Allowed : 14.19 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1033 helix: 2.33 (0.28), residues: 391 sheet: 0.18 (0.36), residues: 207 loop : -0.99 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.015 0.001 TYR R 185 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.044 Fit side-chains REVERT: A 27 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6613 (mm-30) REVERT: B 70 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: B 206 ASP cc_start: 0.7318 (p0) cc_final: 0.7057 (p0) REVERT: B 225 ARG cc_start: 0.6983 (mmt-90) cc_final: 0.6564 (mmt-90) REVERT: R 145 MET cc_start: 0.6550 (ptt) cc_final: 0.6203 (ptm) outliers start: 25 outliers final: 15 residues processed: 119 average time/residue: 1.2594 time to fit residues: 159.1388 Evaluate side-chains 119 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN R 197 GLN R 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8418 Z= 0.220 Angle : 0.556 10.646 11395 Z= 0.290 Chirality : 0.044 0.200 1282 Planarity : 0.004 0.059 1450 Dihedral : 5.814 39.123 1169 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.70 % Allowed : 14.64 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1033 helix: 2.22 (0.28), residues: 392 sheet: 0.17 (0.36), residues: 207 loop : -1.00 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.016 0.002 TYR R 185 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.058 Fit side-chains REVERT: A 27 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6617 (mm-30) REVERT: A 299 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6153 (mt-10) REVERT: B 70 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: B 206 ASP cc_start: 0.7324 (p0) cc_final: 0.7049 (p0) REVERT: B 225 ARG cc_start: 0.6989 (mmt-90) cc_final: 0.6584 (mmt-90) REVERT: R 145 MET cc_start: 0.6513 (ptt) cc_final: 0.6166 (ptm) outliers start: 24 outliers final: 16 residues processed: 118 average time/residue: 1.3066 time to fit residues: 163.4255 Evaluate side-chains 119 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN R 197 GLN R 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8418 Z= 0.129 Angle : 0.485 8.186 11395 Z= 0.253 Chirality : 0.041 0.179 1282 Planarity : 0.004 0.058 1450 Dihedral : 5.322 35.828 1169 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.48 % Allowed : 15.99 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 1033 helix: 2.52 (0.28), residues: 389 sheet: 0.35 (0.36), residues: 206 loop : -1.02 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.011 0.001 TYR R 185 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6572 (mm-30) REVERT: A 60 MET cc_start: 0.4394 (mmp) cc_final: 0.4001 (mmp) REVERT: B 70 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 206 ASP cc_start: 0.7377 (p0) cc_final: 0.7147 (p0) REVERT: R 112 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7154 (ptp90) REVERT: R 145 MET cc_start: 0.6503 (ptt) cc_final: 0.6132 (ptm) outliers start: 22 outliers final: 13 residues processed: 119 average time/residue: 1.2361 time to fit residues: 156.3952 Evaluate side-chains 115 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 112 ARG Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN R 197 GLN R 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8418 Z= 0.136 Angle : 0.491 8.419 11395 Z= 0.256 Chirality : 0.041 0.174 1282 Planarity : 0.004 0.057 1450 Dihedral : 5.140 39.645 1169 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.48 % Allowed : 15.88 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 1033 helix: 2.55 (0.28), residues: 389 sheet: 0.48 (0.36), residues: 199 loop : -1.02 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.012 0.001 TYR R 185 ARG 0.002 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 70 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 206 ASP cc_start: 0.7471 (p0) cc_final: 0.7200 (p0) REVERT: B 208 ARG cc_start: 0.6989 (mmm160) cc_final: 0.6688 (mtp180) REVERT: B 271 GLU cc_start: 0.8025 (tt0) cc_final: 0.7702 (tt0) REVERT: R 145 MET cc_start: 0.6500 (ptt) cc_final: 0.6139 (ptm) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 1.2248 time to fit residues: 154.9770 Evaluate side-chains 116 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 257 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 0.0170 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN R 147 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8418 Z= 0.214 Angle : 0.553 10.059 11395 Z= 0.286 Chirality : 0.044 0.201 1282 Planarity : 0.004 0.058 1450 Dihedral : 5.323 38.683 1169 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.82 % Allowed : 15.99 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 1033 helix: 2.37 (0.28), residues: 390 sheet: 0.21 (0.36), residues: 207 loop : -1.00 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.016 0.002 TYR R 185 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.981 Fit side-chains REVERT: A 27 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6595 (mm-30) REVERT: B 70 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: B 206 ASP cc_start: 0.7360 (p0) cc_final: 0.7089 (p0) REVERT: B 230 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7134 (mtt-85) REVERT: R 36 ASN cc_start: 0.6265 (m-40) cc_final: 0.5321 (m-40) REVERT: R 145 MET cc_start: 0.6512 (ptt) cc_final: 0.6148 (ptm) REVERT: R 283 GLN cc_start: 0.7169 (mt0) cc_final: 0.6935 (mt0) outliers start: 25 outliers final: 16 residues processed: 117 average time/residue: 1.3440 time to fit residues: 166.7413 Evaluate side-chains 117 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 11 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: A 35 GLN N 5 GLN R 147 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8418 Z= 0.159 Angle : 0.519 9.058 11395 Z= 0.269 Chirality : 0.042 0.188 1282 Planarity : 0.004 0.057 1450 Dihedral : 5.157 40.013 1169 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.36 % Allowed : 16.67 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 1033 helix: 2.45 (0.28), residues: 390 sheet: 0.39 (0.36), residues: 203 loop : -1.03 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.013 0.001 TYR R 281 ARG 0.003 0.000 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6614 (mm-30) REVERT: B 70 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: B 72 MET cc_start: 0.8384 (ppp) cc_final: 0.8116 (pp-130) REVERT: B 206 ASP cc_start: 0.7375 (p0) cc_final: 0.7101 (p0) REVERT: B 230 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7187 (mtt-85) REVERT: R 36 ASN cc_start: 0.6246 (m-40) cc_final: 0.5274 (m-40) REVERT: R 112 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7195 (ptp90) REVERT: R 145 MET cc_start: 0.6545 (ptt) cc_final: 0.6184 (ptm) REVERT: R 283 GLN cc_start: 0.7139 (mt0) cc_final: 0.6902 (mt0) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 1.3199 time to fit residues: 160.9973 Evaluate side-chains 119 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 112 ARG Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 5 GLN R 147 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111736 restraints weight = 8895.257| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.06 r_work: 0.3131 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8418 Z= 0.170 Angle : 0.526 9.118 11395 Z= 0.273 Chirality : 0.043 0.186 1282 Planarity : 0.004 0.057 1450 Dihedral : 5.102 40.161 1169 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 16.10 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 1033 helix: 2.45 (0.28), residues: 390 sheet: 0.31 (0.36), residues: 206 loop : -0.99 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.014 0.001 TYR R 185 ARG 0.002 0.000 ARG B 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.74 seconds wall clock time: 58 minutes 49.17 seconds (3529.17 seconds total)