Starting phenix.real_space_refine on Wed Feb 14 20:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sz9_10350/02_2024/6sz9_10350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sz9_10350/02_2024/6sz9_10350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sz9_10350/02_2024/6sz9_10350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sz9_10350/02_2024/6sz9_10350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sz9_10350/02_2024/6sz9_10350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sz9_10350/02_2024/6sz9_10350.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.841 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 6520 2.51 5 N 1748 2.21 5 O 1916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 112": "NH1" <-> "NH2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10233 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3665 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 453} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1615 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2284 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 275} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6091 SG CYS C 46 72.511 31.236 60.268 1.00 35.96 S ATOM 6117 SG CYS C 49 75.680 32.328 60.598 1.00 29.67 S ATOM 6346 SG CYS C 78 73.743 35.280 59.358 1.00 29.81 S ATOM 6369 SG CYS C 81 74.403 32.503 57.235 1.00 27.56 S Time building chain proxies: 5.94, per 1000 atoms: 0.58 Number of scatterers: 10233 At special positions: 0 Unit cell: (119.13, 110.77, 122.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 1916 8.00 N 1748 7.00 C 6520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 78 " Number of angles added : 6 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 59.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.702A pdb=" N THR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 152 removed outlier: 3.701A pdb=" N THR A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.939A pdb=" N GLU A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 3.833A pdb=" N ILE A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 303 through 316 removed outlier: 4.063A pdb=" N THR A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 325 through 353 removed outlier: 4.123A pdb=" N SER A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLN A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.537A pdb=" N VAL A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 408 removed outlier: 4.264A pdb=" N LEU A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.714A pdb=" N GLY A 459 " --> pdb=" O ARG A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.677A pdb=" N MET A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.795A pdb=" N SER A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.664A pdb=" N ILE B 141 " --> pdb=" O TRP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 196 through 207 removed outlier: 4.057A pdb=" N ARG B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.550A pdb=" N ASN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 253 removed outlier: 3.729A pdb=" N ALA B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 261 through 266 removed outlier: 3.637A pdb=" N MET B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.858A pdb=" N GLU B 305 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 306 " --> pdb=" O SER B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.998A pdb=" N VAL B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.532A pdb=" N VAL B 323 " --> pdb=" O MET B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.755A pdb=" N MET B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.311A pdb=" N ARG B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.789A pdb=" N ILE C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 43 removed outlier: 3.530A pdb=" N LYS C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 128 through 151 removed outlier: 3.620A pdb=" N ALA C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 191 through 207 removed outlier: 3.523A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 Processing helix chain 'D' and resid 36 through 42 Processing helix chain 'D' and resid 48 through 85 removed outlier: 4.499A pdb=" N ILE D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) Proline residue: D 56 - end of helix removed outlier: 3.754A pdb=" N ASN D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 159 removed outlier: 4.106A pdb=" N GLU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.620A pdb=" N CYS D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 203 removed outlier: 4.101A pdb=" N LYS D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 266 removed outlier: 5.421A pdb=" N GLU D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'E' and resid 8 through 19 removed outlier: 3.713A pdb=" N GLY E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 39 removed outlier: 3.602A pdb=" N ALA E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.924A pdb=" N GLY A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE A 120 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE A 107 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 558 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 464 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 466 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.407A pdb=" N LEU A 186 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 380 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE A 188 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR A 159 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 158 " --> pdb=" O ILE A 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.715A pdb=" N VAL A 297 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 60 Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 101 521 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3327 1.34 - 1.46: 1857 1.46 - 1.58: 5151 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10415 Sorted by residual: bond pdb=" N PHE C 48 " pdb=" CA PHE C 48 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.25e+00 bond pdb=" N CYS C 78 " pdb=" CA CYS C 78 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.31e-02 5.83e+03 6.20e+00 bond pdb=" N CYS C 49 " pdb=" CA CYS C 49 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.50e-02 4.44e+03 5.57e+00 bond pdb=" N GLN C 47 " pdb=" CA GLN C 47 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.57e+00 bond pdb=" N GLY C 50 " pdb=" CA GLY C 50 " ideal model delta sigma weight residual 1.446 1.479 -0.032 1.50e-02 4.44e+03 4.68e+00 ... (remaining 10410 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.76: 204 105.76 - 112.82: 5450 112.82 - 119.88: 3686 119.88 - 126.94: 4621 126.94 - 134.00: 97 Bond angle restraints: 14058 Sorted by residual: angle pdb=" C ASP A 286 " pdb=" N LYS A 287 " pdb=" CA LYS A 287 " ideal model delta sigma weight residual 122.07 127.34 -5.27 1.43e+00 4.89e-01 1.36e+01 angle pdb=" C TYR D 29 " pdb=" N ASN D 30 " pdb=" CA ASN D 30 " ideal model delta sigma weight residual 122.40 127.55 -5.15 1.45e+00 4.76e-01 1.26e+01 angle pdb=" N ASP A 308 " pdb=" CA ASP A 308 " pdb=" C ASP A 308 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.81e+00 angle pdb=" CA LYS A 287 " pdb=" CB LYS A 287 " pdb=" CG LYS A 287 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.65e+00 angle pdb=" CA CYS C 79 " pdb=" C CYS C 79 " pdb=" O CYS C 79 " ideal model delta sigma weight residual 120.55 117.34 3.21 1.06e+00 8.90e-01 9.15e+00 ... (remaining 14053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5605 17.86 - 35.71: 642 35.71 - 53.56: 100 53.56 - 71.42: 24 71.42 - 89.27: 11 Dihedral angle restraints: 6382 sinusoidal: 2612 harmonic: 3770 Sorted by residual: dihedral pdb=" CA GLU A 591 " pdb=" C GLU A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LYS A 474 " pdb=" C LYS A 474 " pdb=" N ALA A 475 " pdb=" CA ALA A 475 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP A 366 " pdb=" C ASP A 366 " pdb=" N PHE A 367 " pdb=" CA PHE A 367 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1244 0.056 - 0.111: 280 0.111 - 0.167: 45 0.167 - 0.223: 9 0.223 - 0.278: 3 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE A 131 " pdb=" CA ILE A 131 " pdb=" CG1 ILE A 131 " pdb=" CG2 ILE A 131 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE D 44 " pdb=" CA ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CG2 ILE D 44 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1578 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 44 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO D 45 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 289 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO A 290 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 362 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C GLU B 362 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 362 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 363 " -0.012 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2983 2.81 - 3.34: 9194 3.34 - 3.86: 16595 3.86 - 4.38: 18277 4.38 - 4.90: 31998 Nonbonded interactions: 79047 Sorted by model distance: nonbonded pdb=" OG1 THR A 114 " pdb=" OE1 GLU A 116 " model vdw 2.293 2.440 nonbonded pdb=" O ALA A 150 " pdb=" OG SER A 155 " model vdw 2.298 2.440 nonbonded pdb=" O ILE A 483 " pdb=" OG1 THR A 487 " model vdw 2.300 2.440 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 271 " model vdw 2.316 2.440 nonbonded pdb=" OD1 ASN C 124 " pdb=" OG1 THR D 21 " model vdw 2.319 2.440 ... (remaining 79042 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.270 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 32.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10415 Z= 0.295 Angle : 0.817 9.511 14058 Z= 0.459 Chirality : 0.050 0.278 1581 Planarity : 0.006 0.060 1809 Dihedral : 15.573 89.271 3938 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.27 % Allowed : 9.90 % Favored : 89.83 % 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: -3.82 (0.18), residues: 1274 helix: -2.19 (0.15), residues: 717 sheet: -2.04 (0.69), residues: 54 loop : -2.96 (0.22), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.005 0.001 HIS B 281 PHE 0.027 0.002 PHE D 254 TYR 0.025 0.002 TYR A 440 ARG 0.005 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8440 (ttm) cc_final: 0.8230 (ttm) REVERT: A 179 MET cc_start: 0.8538 (mmm) cc_final: 0.8014 (mmt) REVERT: A 240 TRP cc_start: 0.5607 (m-10) cc_final: 0.4781 (p90) REVERT: A 266 LEU cc_start: 0.8524 (tp) cc_final: 0.8321 (tp) REVERT: A 405 MET cc_start: 0.6748 (mtp) cc_final: 0.6373 (mtp) REVERT: B 145 VAL cc_start: 0.8790 (p) cc_final: 0.8579 (m) REVERT: B 161 MET cc_start: 0.7753 (ttp) cc_final: 0.7014 (ttp) REVERT: B 173 ASN cc_start: 0.8364 (m-40) cc_final: 0.7971 (t0) REVERT: B 363 ILE cc_start: 0.8738 (mm) cc_final: 0.8218 (mt) REVERT: C 10 LEU cc_start: 0.7938 (mt) cc_final: 0.7699 (mp) REVERT: C 166 ASP cc_start: 0.8109 (t0) cc_final: 0.7807 (t0) REVERT: D 66 ILE cc_start: 0.8906 (pt) cc_final: 0.8280 (mt) REVERT: D 83 TYR cc_start: 0.7525 (t80) cc_final: 0.7234 (t80) REVERT: E 27 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7448 (tm-30) REVERT: E 28 TYR cc_start: 0.8689 (t80) cc_final: 0.8437 (t80) REVERT: E 56 TYR cc_start: 0.7830 (t80) cc_final: 0.7147 (t80) REVERT: E 63 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7638 (tptt) REVERT: E 75 GLU cc_start: 0.8179 (pm20) cc_final: 0.7583 (mm-30) REVERT: E 76 ARG cc_start: 0.6513 (mmm-85) cc_final: 0.6063 (mmt90) outliers start: 3 outliers final: 2 residues processed: 207 average time/residue: 0.2321 time to fit residues: 66.0988 Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 300 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.0370 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 0.0020 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 222 GLN A 321 ASN A 331 GLN A 342 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN A 602 GLN B 133 GLN C 36 GLN C 57 GLN C 108 GLN C 124 ASN C 162 GLN D 59 ASN D 62 ASN D 200 ASN D 218 ASN D 241 ASN D 245 GLN D 281 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10415 Z= 0.175 Angle : 0.566 9.340 14058 Z= 0.293 Chirality : 0.039 0.176 1581 Planarity : 0.004 0.043 1809 Dihedral : 4.657 18.943 1400 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.07 % Allowed : 15.03 % Favored : 82.90 % 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: -2.00 (0.22), residues: 1274 helix: -0.37 (0.19), residues: 720 sheet: -2.27 (0.59), residues: 66 loop : -2.60 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 71 HIS 0.003 0.001 HIS A 559 PHE 0.017 0.001 PHE C 31 TYR 0.011 0.001 TYR D 83 ARG 0.004 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5550 (m-10) cc_final: 0.4693 (p90) REVERT: A 252 MET cc_start: 0.7710 (mmp) cc_final: 0.7494 (mmp) REVERT: A 266 LEU cc_start: 0.8540 (tp) cc_final: 0.8214 (tp) REVERT: A 405 MET cc_start: 0.7035 (mtp) cc_final: 0.6715 (mtp) REVERT: B 173 ASN cc_start: 0.8371 (m-40) cc_final: 0.7991 (t0) REVERT: C 10 LEU cc_start: 0.7916 (mt) cc_final: 0.7601 (mp) REVERT: C 62 LEU cc_start: 0.7071 (mt) cc_final: 0.6811 (mt) REVERT: D 66 ILE cc_start: 0.8854 (pt) cc_final: 0.8205 (mt) REVERT: E 12 LEU cc_start: 0.8843 (tt) cc_final: 0.8626 (mm) REVERT: E 14 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8202 (mtpp) REVERT: E 27 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 28 TYR cc_start: 0.8771 (t80) cc_final: 0.8566 (t80) REVERT: E 51 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 62 PHE cc_start: 0.7249 (m-80) cc_final: 0.6752 (m-80) REVERT: E 63 LYS cc_start: 0.8362 (ttpp) cc_final: 0.7697 (tptt) REVERT: E 75 GLU cc_start: 0.8172 (pm20) cc_final: 0.7573 (mm-30) REVERT: E 76 ARG cc_start: 0.6432 (mmm-85) cc_final: 0.6103 (mmt90) outliers start: 23 outliers final: 11 residues processed: 175 average time/residue: 0.2197 time to fit residues: 54.1732 Evaluate side-chains 156 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain E residue 41 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 189 GLN D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10415 Z= 0.215 Angle : 0.559 10.054 14058 Z= 0.287 Chirality : 0.039 0.166 1581 Planarity : 0.004 0.036 1809 Dihedral : 4.475 19.466 1400 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 16.47 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1274 helix: 0.29 (0.19), residues: 720 sheet: -1.99 (0.69), residues: 55 loop : -2.36 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.003 0.001 HIS B 281 PHE 0.012 0.001 PHE C 179 TYR 0.014 0.001 TYR E 56 ARG 0.005 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5593 (m-10) cc_final: 0.4657 (p90) REVERT: A 266 LEU cc_start: 0.8510 (tp) cc_final: 0.8177 (tp) REVERT: A 405 MET cc_start: 0.6948 (mtp) cc_final: 0.6606 (mtp) REVERT: B 173 ASN cc_start: 0.8337 (m-40) cc_final: 0.7926 (t0) REVERT: C 10 LEU cc_start: 0.7908 (mt) cc_final: 0.7542 (mp) REVERT: C 62 LEU cc_start: 0.7087 (mt) cc_final: 0.6832 (mt) REVERT: D 66 ILE cc_start: 0.8862 (pt) cc_final: 0.8244 (mt) REVERT: E 12 LEU cc_start: 0.8932 (tt) cc_final: 0.8660 (mm) REVERT: E 14 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8302 (mtpp) REVERT: E 16 MET cc_start: 0.8327 (tpp) cc_final: 0.8115 (tpp) REVERT: E 27 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7627 (tm-30) REVERT: E 28 TYR cc_start: 0.8809 (t80) cc_final: 0.8584 (t80) REVERT: E 51 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7883 (tm-30) REVERT: E 55 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7721 (mt-10) REVERT: E 62 PHE cc_start: 0.7417 (m-80) cc_final: 0.6850 (m-80) REVERT: E 63 LYS cc_start: 0.8366 (ttpp) cc_final: 0.7653 (tptt) REVERT: E 75 GLU cc_start: 0.8163 (pm20) cc_final: 0.7581 (mm-30) outliers start: 26 outliers final: 20 residues processed: 162 average time/residue: 0.2360 time to fit residues: 53.1947 Evaluate side-chains 160 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN C 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10415 Z= 0.199 Angle : 0.542 9.261 14058 Z= 0.277 Chirality : 0.039 0.167 1581 Planarity : 0.003 0.035 1809 Dihedral : 4.347 19.792 1400 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.70 % Allowed : 17.73 % Favored : 79.57 % 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: -0.87 (0.23), residues: 1274 helix: 0.65 (0.20), residues: 712 sheet: -2.23 (0.61), residues: 66 loop : -2.19 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.004 0.001 HIS A 559 PHE 0.014 0.001 PHE C 179 TYR 0.022 0.001 TYR E 56 ARG 0.006 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5541 (m-10) cc_final: 0.4611 (p90) REVERT: A 266 LEU cc_start: 0.8538 (tp) cc_final: 0.8211 (tp) REVERT: A 405 MET cc_start: 0.6843 (mtp) cc_final: 0.6523 (mtp) REVERT: B 173 ASN cc_start: 0.8325 (m-40) cc_final: 0.7904 (t0) REVERT: B 265 MET cc_start: 0.8465 (tpp) cc_final: 0.8142 (tpt) REVERT: B 318 TYR cc_start: 0.8125 (m-10) cc_final: 0.7811 (m-10) REVERT: C 62 LEU cc_start: 0.7133 (mt) cc_final: 0.6928 (mt) REVERT: D 66 ILE cc_start: 0.8868 (pt) cc_final: 0.8263 (mt) REVERT: E 12 LEU cc_start: 0.8852 (tt) cc_final: 0.8621 (mm) REVERT: E 14 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8302 (mtpp) REVERT: E 16 MET cc_start: 0.8201 (tpp) cc_final: 0.7922 (tpt) REVERT: E 27 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7576 (tm-30) REVERT: E 28 TYR cc_start: 0.8814 (t80) cc_final: 0.8588 (t80) REVERT: E 51 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8172 (tm-30) REVERT: E 55 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 56 TYR cc_start: 0.7667 (t80) cc_final: 0.7464 (t80) REVERT: E 62 PHE cc_start: 0.7390 (m-80) cc_final: 0.6813 (m-80) REVERT: E 75 GLU cc_start: 0.7985 (pm20) cc_final: 0.7507 (mm-30) outliers start: 30 outliers final: 19 residues processed: 176 average time/residue: 0.2236 time to fit residues: 55.6721 Evaluate side-chains 161 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 36 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10415 Z= 0.249 Angle : 0.577 9.218 14058 Z= 0.293 Chirality : 0.040 0.161 1581 Planarity : 0.003 0.036 1809 Dihedral : 4.344 19.653 1400 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.33 % Allowed : 18.54 % Favored : 78.13 % 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: -0.74 (0.24), residues: 1274 helix: 0.79 (0.20), residues: 712 sheet: -2.28 (0.61), residues: 66 loop : -2.17 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 159 HIS 0.005 0.001 HIS A 559 PHE 0.011 0.001 PHE C 160 TYR 0.015 0.001 TYR E 56 ARG 0.003 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5551 (m-10) cc_final: 0.4522 (p90) REVERT: A 266 LEU cc_start: 0.8630 (tp) cc_final: 0.8379 (tp) REVERT: A 405 MET cc_start: 0.6825 (mtp) cc_final: 0.6486 (mtp) REVERT: B 173 ASN cc_start: 0.8345 (m-40) cc_final: 0.7892 (t0) REVERT: B 265 MET cc_start: 0.8490 (tpp) cc_final: 0.8160 (tpt) REVERT: B 318 TYR cc_start: 0.8236 (m-10) cc_final: 0.7914 (m-10) REVERT: C 62 LEU cc_start: 0.7125 (mt) cc_final: 0.6916 (mt) REVERT: D 66 ILE cc_start: 0.8873 (pt) cc_final: 0.8299 (mt) REVERT: E 12 LEU cc_start: 0.8914 (tt) cc_final: 0.8674 (mm) REVERT: E 14 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8354 (mtpp) REVERT: E 16 MET cc_start: 0.8223 (tpp) cc_final: 0.7815 (tpt) REVERT: E 27 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 28 TYR cc_start: 0.8810 (t80) cc_final: 0.8592 (t80) REVERT: E 51 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8203 (tm-30) REVERT: E 55 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7910 (mt-10) REVERT: E 56 TYR cc_start: 0.7758 (t80) cc_final: 0.7354 (t80) REVERT: E 62 PHE cc_start: 0.7536 (m-80) cc_final: 0.7018 (m-80) REVERT: E 63 LYS cc_start: 0.8749 (tttt) cc_final: 0.7893 (tptt) REVERT: E 75 GLU cc_start: 0.8012 (pm20) cc_final: 0.7558 (mm-30) outliers start: 37 outliers final: 24 residues processed: 176 average time/residue: 0.2202 time to fit residues: 55.1500 Evaluate side-chains 166 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN D 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10415 Z= 0.174 Angle : 0.555 10.665 14058 Z= 0.276 Chirality : 0.039 0.161 1581 Planarity : 0.003 0.035 1809 Dihedral : 4.204 18.224 1400 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.42 % Allowed : 19.89 % Favored : 76.69 % 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 (0.24), residues: 1274 helix: 1.01 (0.20), residues: 714 sheet: -2.24 (0.61), residues: 66 loop : -2.07 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 159 HIS 0.005 0.001 HIS A 559 PHE 0.008 0.001 PHE A 347 TYR 0.014 0.001 TYR D 83 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5586 (m-10) cc_final: 0.4508 (p90) REVERT: A 266 LEU cc_start: 0.8615 (tp) cc_final: 0.8367 (tp) REVERT: A 405 MET cc_start: 0.6719 (mtp) cc_final: 0.6461 (mtp) REVERT: B 173 ASN cc_start: 0.8318 (m-40) cc_final: 0.7891 (t0) REVERT: B 265 MET cc_start: 0.8455 (tpp) cc_final: 0.8088 (tpt) REVERT: C 62 LEU cc_start: 0.7136 (mt) cc_final: 0.6922 (mt) REVERT: D 66 ILE cc_start: 0.8874 (pt) cc_final: 0.8247 (mt) REVERT: D 261 ILE cc_start: 0.8046 (tt) cc_final: 0.7747 (tt) REVERT: E 12 LEU cc_start: 0.8913 (tt) cc_final: 0.8680 (mm) REVERT: E 14 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8347 (mtpp) REVERT: E 16 MET cc_start: 0.8212 (tpp) cc_final: 0.7911 (tpt) REVERT: E 27 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7494 (tm-30) REVERT: E 28 TYR cc_start: 0.8777 (t80) cc_final: 0.8556 (t80) REVERT: E 51 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8203 (tm-30) REVERT: E 55 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7886 (mt-10) REVERT: E 56 TYR cc_start: 0.7706 (t80) cc_final: 0.7358 (t80) REVERT: E 62 PHE cc_start: 0.7506 (m-80) cc_final: 0.7018 (m-80) REVERT: E 63 LYS cc_start: 0.8727 (tttt) cc_final: 0.7922 (tptt) REVERT: E 75 GLU cc_start: 0.8079 (pm20) cc_final: 0.7593 (mm-30) outliers start: 38 outliers final: 27 residues processed: 184 average time/residue: 0.2095 time to fit residues: 55.1589 Evaluate side-chains 170 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10415 Z= 0.171 Angle : 0.562 8.638 14058 Z= 0.278 Chirality : 0.039 0.159 1581 Planarity : 0.003 0.035 1809 Dihedral : 4.128 19.122 1398 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.33 % Allowed : 19.80 % Favored : 76.87 % 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: -0.38 (0.24), residues: 1274 helix: 1.08 (0.20), residues: 721 sheet: -2.18 (0.61), residues: 66 loop : -2.06 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.005 0.001 HIS A 559 PHE 0.007 0.001 PHE C 160 TYR 0.015 0.001 TYR D 83 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5583 (m-10) cc_final: 0.4495 (p90) REVERT: B 173 ASN cc_start: 0.8309 (m-40) cc_final: 0.7869 (t0) REVERT: B 265 MET cc_start: 0.8463 (tpp) cc_final: 0.8118 (tpt) REVERT: C 62 LEU cc_start: 0.7144 (mt) cc_final: 0.6934 (mt) REVERT: D 66 ILE cc_start: 0.8848 (pt) cc_final: 0.8220 (mt) REVERT: D 261 ILE cc_start: 0.8046 (tt) cc_final: 0.7772 (tt) REVERT: E 12 LEU cc_start: 0.8912 (tt) cc_final: 0.8693 (mm) REVERT: E 14 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8359 (mtpp) REVERT: E 27 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7437 (tm-30) REVERT: E 28 TYR cc_start: 0.8734 (t80) cc_final: 0.8485 (t80) REVERT: E 51 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 55 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7858 (mt-10) REVERT: E 56 TYR cc_start: 0.7713 (t80) cc_final: 0.7431 (t80) REVERT: E 62 PHE cc_start: 0.7557 (m-80) cc_final: 0.7059 (m-80) REVERT: E 63 LYS cc_start: 0.8811 (tttt) cc_final: 0.7901 (tptt) REVERT: E 75 GLU cc_start: 0.8087 (pm20) cc_final: 0.7589 (mm-30) outliers start: 37 outliers final: 28 residues processed: 181 average time/residue: 0.2065 time to fit residues: 54.6310 Evaluate side-chains 174 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10415 Z= 0.187 Angle : 0.569 9.105 14058 Z= 0.283 Chirality : 0.039 0.166 1581 Planarity : 0.003 0.035 1809 Dihedral : 4.124 17.883 1398 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.97 % Allowed : 21.06 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1274 helix: 1.14 (0.20), residues: 723 sheet: -2.13 (0.61), residues: 66 loop : -2.01 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.005 0.001 HIS A 559 PHE 0.020 0.001 PHE A 275 TYR 0.022 0.001 TYR D 83 ARG 0.004 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5607 (m-10) cc_final: 0.4485 (p90) REVERT: B 173 ASN cc_start: 0.8316 (m-40) cc_final: 0.7862 (t0) REVERT: B 265 MET cc_start: 0.8480 (tpp) cc_final: 0.8134 (tpt) REVERT: C 62 LEU cc_start: 0.7149 (mt) cc_final: 0.6936 (mt) REVERT: D 66 ILE cc_start: 0.8858 (pt) cc_final: 0.8239 (mt) REVERT: D 261 ILE cc_start: 0.8046 (tt) cc_final: 0.7780 (tt) REVERT: E 14 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8283 (mtpp) REVERT: E 27 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7435 (tm-30) REVERT: E 28 TYR cc_start: 0.8724 (t80) cc_final: 0.8497 (t80) REVERT: E 51 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 55 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7852 (mt-10) REVERT: E 62 PHE cc_start: 0.7547 (m-80) cc_final: 0.7062 (m-80) REVERT: E 63 LYS cc_start: 0.8805 (tttt) cc_final: 0.7957 (tptt) REVERT: E 75 GLU cc_start: 0.8109 (pm20) cc_final: 0.7603 (mm-30) outliers start: 33 outliers final: 28 residues processed: 172 average time/residue: 0.2070 time to fit residues: 51.2222 Evaluate side-chains 167 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN C 36 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10415 Z= 0.266 Angle : 0.615 8.461 14058 Z= 0.307 Chirality : 0.041 0.165 1581 Planarity : 0.004 0.043 1809 Dihedral : 4.281 19.387 1398 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.24 % Allowed : 20.70 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1274 helix: 0.99 (0.20), residues: 723 sheet: -2.03 (0.62), residues: 66 loop : -2.06 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.006 0.001 HIS A 559 PHE 0.018 0.001 PHE C 31 TYR 0.029 0.002 TYR E 56 ARG 0.011 0.000 ARG D 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5553 (m-10) cc_final: 0.4410 (p90) REVERT: B 173 ASN cc_start: 0.8326 (m-40) cc_final: 0.7851 (t0) REVERT: B 265 MET cc_start: 0.8531 (tpp) cc_final: 0.8093 (tpt) REVERT: D 66 ILE cc_start: 0.8870 (pt) cc_final: 0.8323 (mt) REVERT: E 14 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8235 (mtpp) REVERT: E 16 MET cc_start: 0.7940 (tpt) cc_final: 0.7296 (tpt) REVERT: E 27 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7421 (tm-30) REVERT: E 28 TYR cc_start: 0.8794 (t80) cc_final: 0.8546 (t80) REVERT: E 51 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8245 (tm-30) REVERT: E 55 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7877 (mt-10) REVERT: E 56 TYR cc_start: 0.7654 (t80) cc_final: 0.7387 (t80) REVERT: E 62 PHE cc_start: 0.7690 (m-80) cc_final: 0.7186 (m-80) REVERT: E 63 LYS cc_start: 0.8754 (tttt) cc_final: 0.7839 (tptt) REVERT: E 75 GLU cc_start: 0.8119 (pm20) cc_final: 0.7591 (mm-30) outliers start: 36 outliers final: 33 residues processed: 168 average time/residue: 0.1984 time to fit residues: 49.3020 Evaluate side-chains 170 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10415 Z= 0.204 Angle : 0.596 8.157 14058 Z= 0.296 Chirality : 0.040 0.172 1581 Planarity : 0.003 0.043 1809 Dihedral : 4.194 18.339 1398 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.97 % Allowed : 20.97 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.24), residues: 1274 helix: 1.09 (0.20), residues: 723 sheet: -2.00 (0.62), residues: 66 loop : -2.00 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 138 HIS 0.006 0.001 HIS A 559 PHE 0.009 0.001 PHE A 275 TYR 0.026 0.001 TYR D 83 ARG 0.009 0.000 ARG D 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 TRP cc_start: 0.5637 (m-10) cc_final: 0.4482 (p90) REVERT: B 125 TYR cc_start: 0.8230 (m-10) cc_final: 0.8027 (m-10) REVERT: B 173 ASN cc_start: 0.8309 (m-40) cc_final: 0.7847 (t0) REVERT: B 265 MET cc_start: 0.8508 (tpp) cc_final: 0.8070 (tpt) REVERT: D 66 ILE cc_start: 0.8871 (pt) cc_final: 0.8289 (mt) REVERT: E 16 MET cc_start: 0.7884 (tpt) cc_final: 0.7236 (tpt) REVERT: E 27 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7454 (tm-30) REVERT: E 28 TYR cc_start: 0.8730 (t80) cc_final: 0.8497 (t80) REVERT: E 51 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8256 (tm-30) REVERT: E 55 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7865 (mt-10) REVERT: E 56 TYR cc_start: 0.7756 (t80) cc_final: 0.7464 (t80) REVERT: E 62 PHE cc_start: 0.7683 (m-80) cc_final: 0.7218 (m-80) REVERT: E 75 GLU cc_start: 0.8114 (pm20) cc_final: 0.7588 (mm-30) outliers start: 33 outliers final: 30 residues processed: 166 average time/residue: 0.1981 time to fit residues: 48.7977 Evaluate side-chains 164 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.0060 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.159580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131293 restraints weight = 17510.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133201 restraints weight = 12797.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134036 restraints weight = 10865.019| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10415 Z= 0.156 Angle : 0.581 9.176 14058 Z= 0.288 Chirality : 0.039 0.172 1581 Planarity : 0.003 0.037 1809 Dihedral : 4.056 20.423 1398 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 21.69 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.24), residues: 1274 helix: 1.24 (0.20), residues: 721 sheet: -1.96 (0.62), residues: 66 loop : -1.82 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 119 HIS 0.005 0.001 HIS A 559 PHE 0.012 0.001 PHE C 31 TYR 0.026 0.001 TYR D 83 ARG 0.009 0.000 ARG D 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.54 seconds wall clock time: 38 minutes 7.83 seconds (2287.83 seconds total)