Starting phenix.real_space_refine on Sat Apr 6 19:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/04_2024/8hbd_34619_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/04_2024/8hbd_34619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/04_2024/8hbd_34619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/04_2024/8hbd_34619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/04_2024/8hbd_34619_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbd_34619/04_2024/8hbd_34619_neut.pdb" } resolution = 2.99 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= 0.001 sd= 0.026 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 63 5.16 5 C 5635 2.51 5 N 1481 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1717 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2540 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1726 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 123 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2293 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 4.66, per 1000 atoms: 0.53 Number of scatterers: 8803 At special positions: 0 Unit cell: (107.12, 112.32, 130, 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 63 16.00 O 1624 8.00 N 1481 7.00 C 5635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.05 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.4% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.520A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.587A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.107A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.365A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.881A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.660A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.970A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'L' and resid 10 through 18 removed outlier: 4.143A pdb=" N PHE L 14 " --> pdb=" O GLU L 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU L 17 " --> pdb=" O TYR L 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 129 removed outlier: 3.982A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN R 104 " --> pdb=" O PHE R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 Processing helix chain 'R' and resid 154 through 165 Processing helix chain 'R' and resid 176 through 205 removed outlier: 3.610A pdb=" N LEU R 192 " --> pdb=" O THR R 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS R 193 " --> pdb=" O VAL R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 233 removed outlier: 3.576A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP R 226 " --> pdb=" O ILE R 222 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 237 Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 272 through 280 removed outlier: 3.594A pdb=" N PHE R 280 " --> pdb=" O TRP R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 removed outlier: 4.362A pdb=" N ALA R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR R 297 " --> pdb=" O TYR R 293 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS R 298 " --> pdb=" O THR R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 349 removed outlier: 4.000A pdb=" N LYS R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU R 320 " --> pdb=" O LYS R 316 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 321 " --> pdb=" O GLN R 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU R 328 " --> pdb=" O THR R 324 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Proline residue: R 338 - end of helix removed outlier: 3.933A pdb=" N ARG R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 344 " --> pdb=" O HIS R 340 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 345 " --> pdb=" O LEU R 341 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS R 346 " --> pdb=" O SER R 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU R 347 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 380 removed outlier: 3.892A pdb=" N PHE R 363 " --> pdb=" O GLU R 359 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 389 removed outlier: 3.723A pdb=" N ILE R 384 " --> pdb=" O CYS R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 399 removed outlier: 4.075A pdb=" N CYS R 396 " --> pdb=" O ARG R 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.921A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.589A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.154A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 7.014A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.751A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.909A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.819A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.551A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.904A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.538A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.659A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'R' and resid 240 through 246 removed outlier: 3.683A pdb=" N ASP R 241 " --> pdb=" O LEU R 256 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU R 256 " --> pdb=" O ASP R 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET R 245 " --> pdb=" O LEU R 252 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU R 252 " --> pdb=" O MET R 245 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1143 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: 2.61 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1528 1.32 - 1.45: 2385 1.45 - 1.57: 4983 1.57 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 8984 Sorted by residual: bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.23e-02 6.61e+03 8.69e+00 bond pdb=" C PRO R 178 " pdb=" O PRO R 178 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.30e-02 5.92e+03 7.43e+00 bond pdb=" N ARG A 313 " pdb=" CA ARG A 313 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.77e+00 bond pdb=" N PRO R 178 " pdb=" CA PRO R 178 " ideal model delta sigma weight residual 1.469 1.439 0.030 1.28e-02 6.10e+03 5.35e+00 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.94: 210 106.94 - 113.75: 4981 113.75 - 120.57: 3624 120.57 - 127.38: 3295 127.38 - 134.19: 93 Bond angle restraints: 12203 Sorted by residual: angle pdb=" N GLN A 52 " pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 112.04 102.46 9.58 1.44e+00 4.82e-01 4.43e+01 angle pdb=" N TRP R 206 " pdb=" CA TRP R 206 " pdb=" C TRP R 206 " ideal model delta sigma weight residual 113.20 104.38 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" N ARG R 343 " pdb=" CA ARG R 343 " pdb=" C ARG R 343 " ideal model delta sigma weight residual 114.75 108.35 6.40 1.26e+00 6.30e-01 2.58e+01 angle pdb=" N ILE R 209 " pdb=" CA ILE R 209 " pdb=" C ILE R 209 " ideal model delta sigma weight residual 109.34 118.89 -9.55 2.08e+00 2.31e-01 2.11e+01 angle pdb=" N THR B 184 " pdb=" CA THR B 184 " pdb=" C THR B 184 " ideal model delta sigma weight residual 113.61 106.75 6.86 1.50e+00 4.44e-01 2.09e+01 ... (remaining 12198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4556 17.51 - 35.01: 545 35.01 - 52.52: 156 52.52 - 70.03: 24 70.03 - 87.53: 7 Dihedral angle restraints: 5288 sinusoidal: 1929 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 139.64 -46.64 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" C ARG R 208 " pdb=" N ARG R 208 " pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " ideal model delta harmonic sigma weight residual -122.60 -132.34 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA LEU B 14 " pdb=" C LEU B 14 " pdb=" N LYS B 15 " pdb=" CA LYS B 15 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1251 0.062 - 0.125: 146 0.125 - 0.187: 16 0.187 - 0.249: 4 0.249 - 0.311: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ARG R 208 " pdb=" N ARG R 208 " pdb=" C ARG R 208 " pdb=" CB ARG R 208 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL R 177 " pdb=" CA VAL R 177 " pdb=" CG1 VAL R 177 " pdb=" CG2 VAL R 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLN A 52 " pdb=" N GLN A 52 " pdb=" C GLN A 52 " pdb=" CB GLN A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1416 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 313 " -0.038 2.00e-02 2.50e+03 7.40e-02 5.47e+01 pdb=" C ASN B 313 " 0.128 2.00e-02 2.50e+03 pdb=" O ASN B 313 " -0.048 2.00e-02 2.50e+03 pdb=" N ARG B 314 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 307 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C PHE A 307 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 307 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU A 308 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 180 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C PHE B 180 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 181 " 0.023 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 68 2.51 - 3.11: 6276 3.11 - 3.70: 13791 3.70 - 4.30: 19315 4.30 - 4.90: 31914 Nonbonded interactions: 71364 Sorted by model distance: nonbonded pdb=" CE1 TYR A 296 " pdb=" OE1 GLU A 297 " model vdw 1.912 3.340 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.034 2.440 nonbonded pdb=" OE1 GLU A 289 " pdb=" OH TYR A 302 " model vdw 2.212 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.232 2.440 ... (remaining 71359 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: 3.770 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.150 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: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8984 Z= 0.194 Angle : 0.709 9.582 12203 Z= 0.408 Chirality : 0.044 0.311 1419 Planarity : 0.004 0.074 1536 Dihedral : 16.471 87.532 3110 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 29.55 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.26), residues: 1134 helix: 0.26 (0.27), residues: 397 sheet: 1.16 (0.32), residues: 281 loop : -0.42 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE A 336 TYR 0.011 0.001 TYR H 175 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6956 (tp30) cc_final: 0.6466 (tp30) REVERT: A 274 PHE cc_start: 0.8423 (t80) cc_final: 0.8209 (t80) REVERT: A 289 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 308 GLU cc_start: 0.7807 (mp0) cc_final: 0.7243 (mp0) REVERT: B 19 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.6866 (mtm-85) REVERT: B 114 CYS cc_start: 0.7945 (t) cc_final: 0.7727 (t) REVERT: B 183 HIS cc_start: 0.8509 (m-70) cc_final: 0.8144 (m-70) REVERT: B 262 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7689 (tpp) REVERT: B 313 ASN cc_start: 0.8352 (t0) cc_final: 0.8074 (t0) REVERT: H 230 MET cc_start: 0.8051 (ttm) cc_final: 0.7717 (ttp) REVERT: R 175 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8264 (tttp) REVERT: R 374 MET cc_start: 0.7887 (mmm) cc_final: 0.7450 (mmm) outliers start: 17 outliers final: 8 residues processed: 252 average time/residue: 0.9759 time to fit residues: 266.3466 Evaluate side-chains 241 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 207 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 102 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8984 Z= 0.197 Angle : 0.553 8.618 12203 Z= 0.287 Chirality : 0.041 0.193 1419 Planarity : 0.004 0.034 1536 Dihedral : 5.498 57.309 1257 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.78 % Allowed : 25.19 % Favored : 69.03 % 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: 0.49 (0.25), residues: 1134 helix: 0.61 (0.27), residues: 401 sheet: 1.05 (0.32), residues: 272 loop : -0.26 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 111 HIS 0.004 0.001 HIS G 44 PHE 0.027 0.002 PHE A 336 TYR 0.018 0.001 TYR A 296 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 268 time to evaluate : 0.882 Fit side-chains REVERT: A 245 GLU cc_start: 0.7176 (tp30) cc_final: 0.6683 (tp30) REVERT: A 274 PHE cc_start: 0.8443 (t80) cc_final: 0.7940 (t80) REVERT: A 276 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 289 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 304 GLN cc_start: 0.7379 (mt0) cc_final: 0.6081 (tt0) REVERT: A 308 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 71 VAL cc_start: 0.8453 (t) cc_final: 0.8039 (p) REVERT: B 75 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.6436 (pm20) REVERT: B 214 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7580 (mmm-85) REVERT: B 217 MET cc_start: 0.8093 (pmm) cc_final: 0.7803 (pmm) REVERT: B 243 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8178 (p) REVERT: B 313 ASN cc_start: 0.8330 (t0) cc_final: 0.7822 (t0) REVERT: H 30 SER cc_start: 0.8593 (p) cc_final: 0.8231 (t) REVERT: H 60 TYR cc_start: 0.8815 (m-80) cc_final: 0.8558 (m-80) REVERT: L 14 PHE cc_start: 0.8452 (t80) cc_final: 0.8176 (t80) REVERT: R 102 TYR cc_start: 0.7464 (m-80) cc_final: 0.6932 (m-80) REVERT: R 230 VAL cc_start: 0.8540 (t) cc_final: 0.8248 (m) REVERT: R 243 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7724 (pp) REVERT: R 254 ILE cc_start: 0.7904 (mt) cc_final: 0.7603 (mp) REVERT: R 268 PHE cc_start: 0.8141 (t80) cc_final: 0.7824 (t80) REVERT: R 374 MET cc_start: 0.7966 (mmm) cc_final: 0.7548 (mmm) outliers start: 53 outliers final: 21 residues processed: 291 average time/residue: 0.8111 time to fit residues: 258.6787 Evaluate side-chains 294 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 269 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 243 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 125 ASN B 156 GLN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8984 Z= 0.213 Angle : 0.578 10.075 12203 Z= 0.293 Chirality : 0.041 0.169 1419 Planarity : 0.004 0.059 1536 Dihedral : 4.848 49.643 1243 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.54 % Allowed : 26.83 % Favored : 66.63 % 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: 0.48 (0.26), residues: 1134 helix: 0.60 (0.27), residues: 406 sheet: 0.87 (0.31), residues: 281 loop : -0.15 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.004 0.001 HIS R 150 PHE 0.018 0.002 PHE A 189 TYR 0.034 0.002 TYR H 190 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 303 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7382 (tp30) cc_final: 0.6888 (tp30) REVERT: A 289 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 336 PHE cc_start: 0.8606 (t80) cc_final: 0.8405 (t80) REVERT: B 45 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: B 49 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.8172 (mmt90) REVERT: B 68 ARG cc_start: 0.8269 (ttt180) cc_final: 0.7882 (ttt180) REVERT: B 110 ASN cc_start: 0.7986 (m110) cc_final: 0.7579 (m110) REVERT: B 217 MET cc_start: 0.8091 (pmm) cc_final: 0.7683 (pmm) REVERT: B 239 ASN cc_start: 0.8312 (m-40) cc_final: 0.8045 (m110) REVERT: B 243 THR cc_start: 0.8676 (m) cc_final: 0.8265 (p) REVERT: B 251 ARG cc_start: 0.8300 (mtt90) cc_final: 0.8006 (mtt90) REVERT: B 258 ASP cc_start: 0.7954 (t0) cc_final: 0.7710 (t70) REVERT: B 313 ASN cc_start: 0.8287 (t0) cc_final: 0.7856 (t0) REVERT: H 30 SER cc_start: 0.8681 (p) cc_final: 0.8350 (t) REVERT: H 32 PHE cc_start: 0.8488 (m-80) cc_final: 0.8217 (m-80) REVERT: H 60 TYR cc_start: 0.8829 (m-80) cc_final: 0.8525 (m-80) REVERT: H 156 SER cc_start: 0.8197 (m) cc_final: 0.7923 (t) REVERT: L 14 PHE cc_start: 0.8594 (t80) cc_final: 0.8228 (t80) REVERT: R 102 TYR cc_start: 0.7532 (m-80) cc_final: 0.6972 (m-80) REVERT: R 140 ILE cc_start: 0.8903 (mt) cc_final: 0.8553 (tt) REVERT: R 221 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: R 225 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8310 (OUTLIER) REVERT: R 254 ILE cc_start: 0.8164 (mt) cc_final: 0.7897 (mp) REVERT: R 325 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8479 (p) REVERT: R 364 LEU cc_start: 0.8608 (mm) cc_final: 0.8389 (tp) REVERT: R 374 MET cc_start: 0.8072 (mmm) cc_final: 0.7614 (mmm) outliers start: 60 outliers final: 19 residues processed: 326 average time/residue: 0.8420 time to fit residues: 299.2590 Evaluate side-chains 301 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 279 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 17 GLN B 125 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8984 Z= 0.187 Angle : 0.562 8.734 12203 Z= 0.283 Chirality : 0.041 0.175 1419 Planarity : 0.004 0.053 1536 Dihedral : 4.657 51.258 1240 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.02 % Allowed : 29.88 % Favored : 65.10 % 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: 0.55 (0.26), residues: 1134 helix: 0.72 (0.27), residues: 403 sheet: 0.86 (0.31), residues: 282 loop : -0.15 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 111 HIS 0.004 0.001 HIS R 314 PHE 0.015 0.001 PHE A 189 TYR 0.024 0.001 TYR H 190 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 282 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7424 (tp30) cc_final: 0.6955 (tp30) REVERT: A 262 THR cc_start: 0.8571 (m) cc_final: 0.8235 (p) REVERT: A 289 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7269 (tm-30) REVERT: B 32 GLN cc_start: 0.8323 (mt0) cc_final: 0.8093 (mm-40) REVERT: B 68 ARG cc_start: 0.8224 (ttt180) cc_final: 0.7933 (ttt180) REVERT: B 71 VAL cc_start: 0.8527 (t) cc_final: 0.8165 (p) REVERT: B 75 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6478 (pm20) REVERT: B 146 LEU cc_start: 0.8548 (tt) cc_final: 0.8265 (tp) REVERT: B 217 MET cc_start: 0.8115 (pmm) cc_final: 0.7683 (pmm) REVERT: B 243 THR cc_start: 0.8671 (m) cc_final: 0.8280 (p) REVERT: B 314 ARG cc_start: 0.8491 (ptp-170) cc_final: 0.8069 (ptm160) REVERT: H 30 SER cc_start: 0.8590 (p) cc_final: 0.8273 (m) REVERT: H 32 PHE cc_start: 0.8528 (m-80) cc_final: 0.8226 (m-80) REVERT: H 60 TYR cc_start: 0.8825 (m-80) cc_final: 0.8496 (m-80) REVERT: H 156 SER cc_start: 0.8218 (m) cc_final: 0.7945 (t) REVERT: H 235 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7056 (t80) REVERT: L 14 PHE cc_start: 0.8530 (t80) cc_final: 0.8249 (t80) REVERT: R 94 ILE cc_start: 0.7436 (mm) cc_final: 0.7142 (mp) REVERT: R 102 TYR cc_start: 0.7556 (m-80) cc_final: 0.7091 (m-80) REVERT: R 138 ILE cc_start: 0.8383 (pt) cc_final: 0.8156 (pp) REVERT: R 140 ILE cc_start: 0.8874 (mt) cc_final: 0.8518 (tt) REVERT: R 176 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7599 (mm) REVERT: R 221 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: R 225 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8264 (mm) REVERT: R 254 ILE cc_start: 0.8103 (mt) cc_final: 0.7821 (mp) REVERT: R 325 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (p) REVERT: R 374 MET cc_start: 0.8105 (mmm) cc_final: 0.7655 (mmm) REVERT: R 380 CYS cc_start: 0.8081 (m) cc_final: 0.7806 (m) outliers start: 46 outliers final: 21 residues processed: 306 average time/residue: 0.8829 time to fit residues: 293.8489 Evaluate side-chains 294 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 337 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8984 Z= 0.228 Angle : 0.573 9.037 12203 Z= 0.293 Chirality : 0.042 0.193 1419 Planarity : 0.004 0.051 1536 Dihedral : 4.770 51.877 1240 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.54 % Allowed : 30.21 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.26), residues: 1134 helix: 0.83 (0.28), residues: 399 sheet: 0.92 (0.31), residues: 276 loop : -0.32 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.004 0.001 HIS R 314 PHE 0.015 0.002 PHE R 292 TYR 0.023 0.001 TYR H 190 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 275 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8264 (mt) cc_final: 0.8058 (mm) REVERT: A 245 GLU cc_start: 0.7468 (tp30) cc_final: 0.7037 (tp30) REVERT: A 289 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 304 GLN cc_start: 0.8165 (tt0) cc_final: 0.7947 (tt0) REVERT: A 337 ASP cc_start: 0.7580 (m-30) cc_final: 0.7278 (m-30) REVERT: B 15 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7840 (ttmm) REVERT: B 19 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7279 (mtm-85) REVERT: B 75 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: B 146 LEU cc_start: 0.8567 (tt) cc_final: 0.8330 (tt) REVERT: B 243 THR cc_start: 0.8668 (m) cc_final: 0.8268 (p) REVERT: B 329 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8283 (p) REVERT: H 30 SER cc_start: 0.8537 (p) cc_final: 0.8301 (m) REVERT: H 32 PHE cc_start: 0.8517 (m-80) cc_final: 0.8251 (m-80) REVERT: H 103 TYR cc_start: 0.8519 (t80) cc_final: 0.8110 (t80) REVERT: H 156 SER cc_start: 0.8305 (m) cc_final: 0.8013 (t) REVERT: H 230 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7695 (tpt) REVERT: H 235 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7336 (t80) REVERT: L 14 PHE cc_start: 0.8561 (t80) cc_final: 0.8242 (t80) REVERT: R 102 TYR cc_start: 0.7662 (m-80) cc_final: 0.7172 (m-80) REVERT: R 138 ILE cc_start: 0.8408 (pt) cc_final: 0.8136 (pp) REVERT: R 176 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7581 (mm) REVERT: R 292 PHE cc_start: 0.7395 (m-10) cc_final: 0.7116 (m-10) REVERT: R 325 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8521 (p) REVERT: R 346 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8339 (ttpp) REVERT: R 374 MET cc_start: 0.8119 (mmm) cc_final: 0.7643 (mmm) REVERT: R 380 CYS cc_start: 0.8078 (m) cc_final: 0.7812 (m) outliers start: 60 outliers final: 31 residues processed: 305 average time/residue: 0.7946 time to fit residues: 265.3983 Evaluate side-chains 301 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 262 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 346 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.0020 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 50 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8984 Z= 0.204 Angle : 0.590 11.178 12203 Z= 0.293 Chirality : 0.042 0.182 1419 Planarity : 0.004 0.052 1536 Dihedral : 4.785 55.818 1240 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 7.42 % Allowed : 29.88 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.26), residues: 1134 helix: 0.86 (0.27), residues: 398 sheet: 0.84 (0.30), residues: 286 loop : -0.32 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 111 HIS 0.004 0.001 HIS R 314 PHE 0.019 0.001 PHE H 27 TYR 0.020 0.001 TYR H 190 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 275 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8246 (mt) cc_final: 0.8014 (mm) REVERT: A 245 GLU cc_start: 0.7470 (tp30) cc_final: 0.7038 (tp30) REVERT: A 262 THR cc_start: 0.8573 (m) cc_final: 0.8145 (p) REVERT: A 272 ASP cc_start: 0.7608 (t0) cc_final: 0.7210 (t70) REVERT: A 289 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 304 GLN cc_start: 0.8146 (tt0) cc_final: 0.7924 (tt0) REVERT: A 337 ASP cc_start: 0.7526 (m-30) cc_final: 0.7270 (m-30) REVERT: B 15 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7827 (ttmm) REVERT: B 19 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7216 (mtm-85) REVERT: B 75 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: B 146 LEU cc_start: 0.8547 (tt) cc_final: 0.8299 (tt) REVERT: B 243 THR cc_start: 0.8705 (m) cc_final: 0.8293 (p) REVERT: B 255 LEU cc_start: 0.8515 (mt) cc_final: 0.8242 (mp) REVERT: B 329 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8254 (p) REVERT: H 30 SER cc_start: 0.8493 (p) cc_final: 0.8282 (m) REVERT: H 103 TYR cc_start: 0.8522 (t80) cc_final: 0.8128 (t80) REVERT: H 156 SER cc_start: 0.8271 (m) cc_final: 0.7972 (t) REVERT: H 174 LEU cc_start: 0.8535 (tp) cc_final: 0.8270 (tp) REVERT: H 230 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7796 (tpt) REVERT: H 235 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7406 (t80) REVERT: L 14 PHE cc_start: 0.8513 (t80) cc_final: 0.8229 (t80) REVERT: R 102 TYR cc_start: 0.7662 (m-80) cc_final: 0.7179 (m-80) REVERT: R 138 ILE cc_start: 0.8408 (pt) cc_final: 0.8121 (pp) REVERT: R 225 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8258 (OUTLIER) REVERT: R 254 ILE cc_start: 0.8042 (mt) cc_final: 0.7820 (mp) REVERT: R 257 LEU cc_start: 0.8712 (mt) cc_final: 0.8499 (mp) REVERT: R 301 LEU cc_start: 0.7674 (mm) cc_final: 0.7463 (mp) REVERT: R 325 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8557 (p) REVERT: R 374 MET cc_start: 0.8110 (mmm) cc_final: 0.7677 (mmm) REVERT: R 380 CYS cc_start: 0.8053 (m) cc_final: 0.7789 (m) outliers start: 68 outliers final: 34 residues processed: 307 average time/residue: 0.8071 time to fit residues: 272.4842 Evaluate side-chains 317 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 277 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 337 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 ASN ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8984 Z= 0.204 Angle : 0.599 11.496 12203 Z= 0.297 Chirality : 0.042 0.177 1419 Planarity : 0.004 0.051 1536 Dihedral : 4.827 58.513 1240 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.11 % Allowed : 32.06 % Favored : 61.83 % 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: 0.55 (0.26), residues: 1134 helix: 0.89 (0.27), residues: 397 sheet: 0.86 (0.30), residues: 284 loop : -0.32 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 111 HIS 0.005 0.001 HIS R 314 PHE 0.025 0.002 PHE H 27 TYR 0.018 0.001 TYR H 190 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 285 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7484 (tp30) cc_final: 0.7051 (tp30) REVERT: A 262 THR cc_start: 0.8568 (m) cc_final: 0.8347 (p) REVERT: A 272 ASP cc_start: 0.7653 (t0) cc_final: 0.7249 (t70) REVERT: A 289 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 304 GLN cc_start: 0.8160 (tt0) cc_final: 0.7928 (tt0) REVERT: A 337 ASP cc_start: 0.7469 (m-30) cc_final: 0.7249 (m-30) REVERT: B 15 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7848 (ttmm) REVERT: B 19 ARG cc_start: 0.7883 (mtp-110) cc_final: 0.7233 (mtm-85) REVERT: B 71 VAL cc_start: 0.8618 (t) cc_final: 0.8330 (p) REVERT: B 75 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: B 93 ILE cc_start: 0.8859 (mt) cc_final: 0.8637 (mm) REVERT: B 134 ARG cc_start: 0.7798 (ptt90) cc_final: 0.7594 (ptp90) REVERT: B 146 LEU cc_start: 0.8536 (tt) cc_final: 0.8276 (tt) REVERT: B 243 THR cc_start: 0.8678 (m) cc_final: 0.8229 (p) REVERT: B 255 LEU cc_start: 0.8541 (mt) cc_final: 0.8274 (mp) REVERT: B 329 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8249 (p) REVERT: G 20 LYS cc_start: 0.8596 (ptmt) cc_final: 0.8338 (ptpp) REVERT: H 32 PHE cc_start: 0.8460 (m-80) cc_final: 0.8211 (m-80) REVERT: H 103 TYR cc_start: 0.8530 (t80) cc_final: 0.8153 (t80) REVERT: H 144 THR cc_start: 0.7386 (t) cc_final: 0.7167 (p) REVERT: H 156 SER cc_start: 0.8305 (m) cc_final: 0.8003 (t) REVERT: H 178 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8209 (tt) REVERT: H 230 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7832 (tpt) REVERT: H 235 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7435 (t80) REVERT: L 14 PHE cc_start: 0.8480 (t80) cc_final: 0.8234 (t80) REVERT: R 102 TYR cc_start: 0.7667 (m-80) cc_final: 0.7172 (m-80) REVERT: R 138 ILE cc_start: 0.8420 (pt) cc_final: 0.8120 (pp) REVERT: R 176 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7609 (mm) REVERT: R 225 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8258 (OUTLIER) REVERT: R 254 ILE cc_start: 0.8067 (mt) cc_final: 0.7811 (mp) REVERT: R 257 LEU cc_start: 0.8717 (mt) cc_final: 0.8505 (mp) REVERT: R 301 LEU cc_start: 0.7720 (mm) cc_final: 0.7494 (mp) REVERT: R 325 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8560 (p) REVERT: R 380 CYS cc_start: 0.8059 (m) cc_final: 0.7794 (m) outliers start: 56 outliers final: 37 residues processed: 315 average time/residue: 0.7912 time to fit residues: 273.6782 Evaluate side-chains 319 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 274 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 337 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 ASN ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8984 Z= 0.234 Angle : 0.616 12.257 12203 Z= 0.307 Chirality : 0.043 0.237 1419 Planarity : 0.004 0.052 1536 Dihedral : 4.410 27.853 1236 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.78 % Allowed : 33.59 % Favored : 60.63 % 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: 0.52 (0.26), residues: 1134 helix: 0.77 (0.27), residues: 404 sheet: 0.90 (0.31), residues: 275 loop : -0.29 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 111 HIS 0.005 0.001 HIS R 314 PHE 0.026 0.002 PHE H 27 TYR 0.021 0.001 TYR R 247 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 296 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7684 (t0) cc_final: 0.7014 (t70) REVERT: A 276 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6991 (mt-10) REVERT: A 289 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 304 GLN cc_start: 0.8173 (tt0) cc_final: 0.7940 (tt0) REVERT: A 313 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7013 (mmp-170) REVERT: A 318 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6779 (mm-30) REVERT: A 319 ILE cc_start: 0.8679 (mm) cc_final: 0.8472 (mp) REVERT: A 337 ASP cc_start: 0.7547 (m-30) cc_final: 0.7238 (m-30) REVERT: B 15 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7801 (ttmm) REVERT: B 19 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7273 (mtm-85) REVERT: B 61 MET cc_start: 0.8356 (ppp) cc_final: 0.7848 (ppp) REVERT: B 75 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: B 93 ILE cc_start: 0.8844 (mt) cc_final: 0.8632 (mm) REVERT: B 243 THR cc_start: 0.8673 (m) cc_final: 0.8272 (p) REVERT: B 246 ASP cc_start: 0.7857 (t0) cc_final: 0.7310 (t0) REVERT: B 329 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8305 (p) REVERT: G 20 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8355 (ptpp) REVERT: H 103 TYR cc_start: 0.8547 (t80) cc_final: 0.8208 (t80) REVERT: H 144 THR cc_start: 0.7447 (t) cc_final: 0.7218 (p) REVERT: H 178 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8295 (tp) REVERT: H 180 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8309 (mtt90) REVERT: H 230 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7805 (tpt) REVERT: H 235 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7398 (t80) REVERT: L 14 PHE cc_start: 0.8484 (t80) cc_final: 0.8227 (t80) REVERT: R 102 TYR cc_start: 0.7708 (m-80) cc_final: 0.7215 (m-80) REVERT: R 138 ILE cc_start: 0.8396 (pt) cc_final: 0.8116 (pp) REVERT: R 176 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7617 (mm) REVERT: R 225 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8271 (OUTLIER) REVERT: R 254 ILE cc_start: 0.8104 (mt) cc_final: 0.7847 (mp) REVERT: R 268 PHE cc_start: 0.8098 (t80) cc_final: 0.7799 (t80) REVERT: R 301 LEU cc_start: 0.7813 (mm) cc_final: 0.7607 (mp) REVERT: R 320 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7501 (mp0) REVERT: R 325 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8574 (p) REVERT: R 347 LEU cc_start: 0.8349 (mm) cc_final: 0.8111 (mm) REVERT: R 350 TYR cc_start: 0.7709 (t80) cc_final: 0.7403 (t80) REVERT: R 374 MET cc_start: 0.8186 (mmm) cc_final: 0.7761 (mmm) REVERT: R 380 CYS cc_start: 0.8074 (m) cc_final: 0.7798 (m) outliers start: 53 outliers final: 33 residues processed: 321 average time/residue: 0.8235 time to fit residues: 289.0463 Evaluate side-chains 322 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8984 Z= 0.250 Angle : 0.637 10.950 12203 Z= 0.318 Chirality : 0.043 0.285 1419 Planarity : 0.004 0.053 1536 Dihedral : 4.506 28.109 1236 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.34 % Allowed : 34.90 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.26), residues: 1134 helix: 0.75 (0.27), residues: 404 sheet: 0.70 (0.30), residues: 287 loop : -0.27 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 111 HIS 0.005 0.001 HIS R 314 PHE 0.027 0.002 PHE H 27 TYR 0.021 0.002 TYR R 247 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 THR cc_start: 0.8667 (m) cc_final: 0.8322 (p) REVERT: A 272 ASP cc_start: 0.7694 (t0) cc_final: 0.6823 (t0) REVERT: A 276 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 289 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 297 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 304 GLN cc_start: 0.8177 (tt0) cc_final: 0.7958 (tt0) REVERT: A 313 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6997 (mmp-170) REVERT: A 337 ASP cc_start: 0.7524 (m-30) cc_final: 0.7237 (m-30) REVERT: B 15 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7819 (ttmm) REVERT: B 19 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7282 (mtm-85) REVERT: B 37 ILE cc_start: 0.8624 (tp) cc_final: 0.8220 (pp) REVERT: B 43 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.7997 (pp) REVERT: B 61 MET cc_start: 0.8373 (ppp) cc_final: 0.7969 (ppp) REVERT: B 75 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: B 146 LEU cc_start: 0.8622 (tt) cc_final: 0.8292 (tp) REVERT: B 243 THR cc_start: 0.8685 (m) cc_final: 0.8261 (p) REVERT: B 246 ASP cc_start: 0.7883 (t0) cc_final: 0.7326 (t0) REVERT: B 329 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8304 (p) REVERT: G 20 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8380 (ptpp) REVERT: H 72 ARG cc_start: 0.8695 (ptm-80) cc_final: 0.8156 (mtp85) REVERT: H 103 TYR cc_start: 0.8585 (t80) cc_final: 0.8260 (t80) REVERT: H 144 THR cc_start: 0.7519 (t) cc_final: 0.7273 (p) REVERT: H 178 LEU cc_start: 0.8513 (tt) cc_final: 0.8198 (tt) REVERT: H 180 ARG cc_start: 0.8678 (mtt90) cc_final: 0.8305 (mtt90) REVERT: H 230 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7989 (tpt) REVERT: H 235 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7365 (t80) REVERT: L 14 PHE cc_start: 0.8423 (t80) cc_final: 0.8213 (t80) REVERT: R 102 TYR cc_start: 0.7702 (m-80) cc_final: 0.7219 (m-80) REVERT: R 138 ILE cc_start: 0.8392 (pt) cc_final: 0.8112 (pp) REVERT: R 176 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7643 (mm) REVERT: R 254 ILE cc_start: 0.8125 (mt) cc_final: 0.7838 (mp) REVERT: R 320 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7478 (mp0) REVERT: R 325 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8586 (p) REVERT: R 347 LEU cc_start: 0.8371 (mm) cc_final: 0.8132 (mm) REVERT: R 350 TYR cc_start: 0.7728 (t80) cc_final: 0.7419 (t80) REVERT: R 374 MET cc_start: 0.8147 (mmm) cc_final: 0.7679 (mmm) REVERT: R 380 CYS cc_start: 0.8083 (m) cc_final: 0.7810 (m) outliers start: 49 outliers final: 32 residues processed: 300 average time/residue: 0.8646 time to fit residues: 282.4847 Evaluate side-chains 320 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.0010 chunk 112 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8984 Z= 0.181 Angle : 0.602 11.289 12203 Z= 0.300 Chirality : 0.042 0.197 1419 Planarity : 0.004 0.049 1536 Dihedral : 4.364 27.635 1236 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.36 % Allowed : 35.99 % Favored : 59.65 % 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: 0.55 (0.26), residues: 1134 helix: 0.81 (0.27), residues: 403 sheet: 0.79 (0.30), residues: 280 loop : -0.20 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 111 HIS 0.005 0.001 HIS R 314 PHE 0.029 0.002 PHE R 280 TYR 0.024 0.001 TYR R 247 ARG 0.009 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7484 (tp30) cc_final: 0.7021 (tp30) REVERT: A 262 THR cc_start: 0.8550 (m) cc_final: 0.8336 (p) REVERT: A 272 ASP cc_start: 0.7657 (t0) cc_final: 0.6960 (t70) REVERT: A 276 GLU cc_start: 0.7623 (mm-30) cc_final: 0.6939 (mm-30) REVERT: A 289 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 313 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6958 (mmp-170) REVERT: A 318 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6694 (mm-30) REVERT: B 15 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7848 (ttmm) REVERT: B 16 ASN cc_start: 0.8041 (m-40) cc_final: 0.7797 (m-40) REVERT: B 19 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7316 (mtm-85) REVERT: B 61 MET cc_start: 0.8382 (ppp) cc_final: 0.7973 (ppp) REVERT: B 71 VAL cc_start: 0.8585 (t) cc_final: 0.8310 (p) REVERT: B 75 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: B 146 LEU cc_start: 0.8598 (tt) cc_final: 0.8292 (tp) REVERT: B 219 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7007 (mtt-85) REVERT: B 243 THR cc_start: 0.8665 (m) cc_final: 0.8215 (p) REVERT: B 246 ASP cc_start: 0.7869 (t0) cc_final: 0.7346 (t0) REVERT: B 329 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8276 (p) REVERT: G 20 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8365 (ptpp) REVERT: H 72 ARG cc_start: 0.8628 (ptm-80) cc_final: 0.8120 (mtp85) REVERT: H 103 TYR cc_start: 0.8527 (t80) cc_final: 0.8195 (t80) REVERT: H 140 MET cc_start: 0.8242 (mmm) cc_final: 0.7550 (mmm) REVERT: H 144 THR cc_start: 0.7498 (t) cc_final: 0.7247 (p) REVERT: H 230 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.8006 (tpt) REVERT: H 235 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7425 (t80) REVERT: R 102 TYR cc_start: 0.7692 (m-80) cc_final: 0.7185 (m-80) REVERT: R 110 LEU cc_start: 0.8545 (tp) cc_final: 0.8307 (tm) REVERT: R 138 ILE cc_start: 0.8392 (pt) cc_final: 0.8091 (pp) REVERT: R 176 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7602 (mm) REVERT: R 225 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8236 (mm) REVERT: R 254 ILE cc_start: 0.8076 (mt) cc_final: 0.7803 (mp) REVERT: R 268 PHE cc_start: 0.8096 (t80) cc_final: 0.7785 (t80) REVERT: R 325 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8573 (p) REVERT: R 350 TYR cc_start: 0.7718 (t80) cc_final: 0.7405 (t80) REVERT: R 374 MET cc_start: 0.8116 (mmm) cc_final: 0.7689 (mmm) REVERT: R 380 CYS cc_start: 0.8015 (m) cc_final: 0.7755 (m) outliers start: 40 outliers final: 29 residues processed: 293 average time/residue: 0.8505 time to fit residues: 272.2190 Evaluate side-chains 309 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.0030 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109753 restraints weight = 14112.783| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.12 r_work: 0.3443 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8984 Z= 0.229 Angle : 0.633 12.221 12203 Z= 0.316 Chirality : 0.043 0.299 1419 Planarity : 0.004 0.052 1536 Dihedral : 4.442 27.962 1236 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.47 % Allowed : 36.31 % Favored : 59.21 % 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: 0.44 (0.25), residues: 1134 helix: 0.80 (0.27), residues: 403 sheet: 0.70 (0.30), residues: 283 loop : -0.33 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 111 HIS 0.005 0.001 HIS R 314 PHE 0.037 0.002 PHE H 212 TYR 0.032 0.002 TYR R 247 ARG 0.009 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.14 seconds wall clock time: 80 minutes 15.34 seconds (4815.34 seconds total)