Starting phenix.real_space_refine on Mon Mar 11 09:55:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvo_32146/03_2024/7vvo_32146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvo_32146/03_2024/7vvo_32146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvo_32146/03_2024/7vvo_32146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvo_32146/03_2024/7vvo_32146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvo_32146/03_2024/7vvo_32146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvo_32146/03_2024/7vvo_32146.pdb" } resolution = 4.1 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= 0.004 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 39 5.16 5 C 5019 2.51 5 N 1393 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7942 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1895 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2551 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN%COO:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2076 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 6 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 302 Time building chain proxies: 4.70, per 1000 atoms: 0.59 Number of scatterers: 7942 At special positions: 0 Unit cell: (126.16, 102.92, 128.374, 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 39 16.00 O 1491 8.00 N 1393 7.00 C 5019 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=2.11 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 38.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.736A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.605A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.345A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.517A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.506A pdb=" N ASP A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.805A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.811A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.524A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.778A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.771A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.027A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 52 Processing helix chain 'R' and resid 187 through 211 Processing helix chain 'R' and resid 217 through 241 removed outlier: 3.584A pdb=" N ILE R 222 " --> pdb=" O THR R 218 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 285 Processing helix chain 'R' and resid 287 through 309 removed outlier: 3.684A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 328 removed outlier: 3.541A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 345 removed outlier: 3.511A pdb=" N ALA R 337 " --> pdb=" O ALA R 333 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL R 338 " --> pdb=" O VAL R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.645A pdb=" N VAL R 384 " --> pdb=" O ASN R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 418 removed outlier: 3.624A pdb=" N LEU R 407 " --> pdb=" O TYR R 403 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.833A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 443 through 460 removed outlier: 4.559A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR R 459 " --> pdb=" O VAL R 455 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS R 460 " --> pdb=" O ALA R 456 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 removed outlier: 3.653A pdb=" N TRP R 477 " --> pdb=" O SER R 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.252A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.053A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.511A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.805A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.249A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.902A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.183A 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: 6.255A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.537A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.515A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 127 through 130 363 hydrogen bonds defined for protein. 1002 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: 2.10 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1375 1.32 - 1.45: 2165 1.45 - 1.58: 4496 1.58 - 1.71: 0 1.71 - 1.84: 54 Bond restraints: 8090 Sorted by residual: bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.05e+01 bond pdb=" C THR B 329 " pdb=" O THR B 329 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.14e-02 7.69e+03 1.72e+01 bond pdb=" CG HIS B 142 " pdb=" ND1 HIS B 142 " ideal model delta sigma weight residual 1.378 1.333 0.045 1.10e-02 8.26e+03 1.70e+01 bond pdb=" N VAL N 64 " pdb=" CA VAL N 64 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.04e-02 9.25e+03 1.55e+01 bond pdb=" C SER R 449 " pdb=" O SER R 449 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.26e-02 6.30e+03 1.54e+01 ... (remaining 8085 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.42: 37 103.42 - 111.26: 2759 111.26 - 119.10: 4586 119.10 - 126.94: 3523 126.94 - 134.78: 86 Bond angle restraints: 10991 Sorted by residual: angle pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " pdb=" CG ASP B 186 " ideal model delta sigma weight residual 112.60 118.03 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" C TYR R 211 " pdb=" CA TYR R 211 " pdb=" CB TYR R 211 " ideal model delta sigma weight residual 111.17 119.09 -7.92 1.53e+00 4.27e-01 2.68e+01 angle pdb=" N TYR A 381 " pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " ideal model delta sigma weight residual 110.35 115.99 -5.64 1.15e+00 7.56e-01 2.41e+01 angle pdb=" CA MET R 445 " pdb=" C MET R 445 " pdb=" O MET R 445 " ideal model delta sigma weight residual 120.70 115.77 4.93 1.03e+00 9.43e-01 2.29e+01 angle pdb=" N VAL R 204 " pdb=" CA VAL R 204 " pdb=" CB VAL R 204 " ideal model delta sigma weight residual 110.55 116.05 -5.50 1.17e+00 7.31e-01 2.21e+01 ... (remaining 10986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4229 17.21 - 34.41: 431 34.41 - 51.62: 91 51.62 - 68.83: 24 68.83 - 86.03: 8 Dihedral angle restraints: 4783 sinusoidal: 1712 harmonic: 3071 Sorted by residual: dihedral pdb=" CA TYR R 429 " pdb=" C TYR R 429 " pdb=" N THR R 430 " pdb=" CA THR R 430 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA THR A 359 " pdb=" C THR A 359 " pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PHE B 278 " pdb=" C PHE B 278 " pdb=" N SER B 279 " pdb=" CA SER B 279 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 4780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 680 0.069 - 0.137: 412 0.137 - 0.206: 149 0.206 - 0.274: 24 0.274 - 0.343: 3 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA ILE N 51 " pdb=" N ILE N 51 " pdb=" C ILE N 51 " pdb=" CB ILE N 51 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL A 324 " pdb=" CA VAL A 324 " pdb=" CG1 VAL A 324 " pdb=" CG2 VAL A 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL B 200 " pdb=" CA VAL B 200 " pdb=" CG1 VAL B 200 " pdb=" CG2 VAL B 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1265 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 298 " 0.048 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP R 298 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP R 298 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP R 298 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 298 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 298 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP R 298 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 298 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 298 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP R 298 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 378 " -0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C LEU A 378 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 378 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 379 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.034 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR B 105 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.032 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 290 2.71 - 3.25: 7979 3.25 - 3.80: 12603 3.80 - 4.35: 16517 4.35 - 4.90: 26859 Nonbonded interactions: 64248 Sorted by model distance: nonbonded pdb=" OD2 ASP A 215 " pdb=" NH1 ARG A 363 " model vdw 2.158 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.214 2.440 nonbonded pdb=" O TYR R 305 " pdb=" OG SER R 308 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.289 2.440 nonbonded pdb=" OG SER N 52 " pdb=" OG SER N 57 " model vdw 2.376 2.440 ... (remaining 64243 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: 0.100 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: 0.000 Extract box with map and model: 1.150 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.230 Find NCS groups from input model: 0.230 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.014 0.073 8090 Z= 0.924 Angle : 1.879 10.863 10991 Z= 1.360 Chirality : 0.092 0.343 1268 Planarity : 0.008 0.038 1418 Dihedral : 15.541 86.034 2785 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 3.81 % Allowed : 8.13 % Favored : 88.06 % 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: -1.84 (0.24), residues: 1033 helix: -0.35 (0.25), residues: 348 sheet: -1.73 (0.33), residues: 186 loop : -1.59 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.009 TRP R 298 HIS 0.021 0.006 HIS B 54 PHE 0.043 0.007 PHE R 238 TYR 0.038 0.009 TYR A 381 ARG 0.024 0.003 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 56 ILE cc_start: 0.8423 (mt) cc_final: 0.8004 (mt) REVERT: A 60 MET cc_start: 0.7060 (mpp) cc_final: 0.5341 (mtm) REVERT: A 379 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.8003 (ptm-80) REVERT: B 52 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7186 (mtp-110) REVERT: B 68 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.8293 (ttt90) REVERT: B 75 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: B 111 TYR cc_start: 0.8784 (m-80) cc_final: 0.8556 (m-80) REVERT: B 130 GLU cc_start: 0.4808 (pt0) cc_final: 0.4561 (pt0) REVERT: B 137 ARG cc_start: 0.6309 (mmm-85) cc_final: 0.5991 (mmt90) REVERT: B 145 TYR cc_start: 0.8242 (p90) cc_final: 0.7926 (p90) REVERT: B 172 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7447 (mm-30) REVERT: B 217 MET cc_start: 0.7587 (tpp) cc_final: 0.7123 (tmm) REVERT: B 255 LEU cc_start: 0.8073 (mt) cc_final: 0.7829 (tt) REVERT: B 284 LEU cc_start: 0.9171 (mt) cc_final: 0.8965 (mt) REVERT: B 325 MET cc_start: 0.6982 (mmp) cc_final: 0.6487 (mtt) REVERT: G 11 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6373 (pp30) REVERT: G 61 PHE cc_start: 0.7397 (m-80) cc_final: 0.7154 (m-80) REVERT: N 19 ARG cc_start: 0.6915 (ttm-80) cc_final: 0.6619 (ttm-80) REVERT: N 32 TYR cc_start: 0.8628 (m-80) cc_final: 0.8402 (m-10) REVERT: N 34 MET cc_start: 0.8790 (mpp) cc_final: 0.8357 (mmm) REVERT: N 47 TRP cc_start: 0.7729 (t60) cc_final: 0.6341 (t60) REVERT: N 61 THR cc_start: 0.7940 (t) cc_final: 0.7409 (t) REVERT: N 73 ASP cc_start: 0.8486 (t70) cc_final: 0.8087 (t70) REVERT: N 82 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7864 (tp-100) REVERT: N 83 MET cc_start: 0.8259 (mpp) cc_final: 0.7507 (mpp) REVERT: N 89 GLU cc_start: 0.8793 (tt0) cc_final: 0.8162 (mp0) REVERT: R 219 ARG cc_start: 0.7550 (tmm160) cc_final: 0.7191 (ptt90) REVERT: R 302 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7876 (tp30) REVERT: R 339 TRP cc_start: 0.6908 (t60) cc_final: 0.6518 (t60) REVERT: R 371 ILE cc_start: 0.8308 (mm) cc_final: 0.7767 (mt) REVERT: R 383 ARG cc_start: 0.8467 (tmm-80) cc_final: 0.8164 (ttp-170) REVERT: R 401 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7574 (mp10) REVERT: R 404 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7668 (tpt90) REVERT: R 405 LYS cc_start: 0.7903 (tppp) cc_final: 0.7531 (tppt) REVERT: R 422 ILE cc_start: 0.8595 (tp) cc_final: 0.8311 (mm) REVERT: R 444 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8299 (mm-30) REVERT: R 448 ASN cc_start: 0.8129 (m-40) cc_final: 0.7904 (m110) outliers start: 30 outliers final: 11 residues processed: 232 average time/residue: 0.2091 time to fit residues: 63.7475 Evaluate side-chains 156 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 93 optimal weight: 0.0070 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN G 44 HIS N 31 ASN N 84 ASN ** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8090 Z= 0.247 Angle : 0.639 9.142 10991 Z= 0.338 Chirality : 0.044 0.174 1268 Planarity : 0.004 0.075 1418 Dihedral : 4.506 20.170 1135 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -0.66 (0.25), residues: 1033 helix: 0.79 (0.27), residues: 368 sheet: -1.43 (0.31), residues: 219 loop : -0.84 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS R 420 PHE 0.031 0.002 PHE R 230 TYR 0.052 0.002 TYR B 59 ARG 0.004 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8392 (mt) cc_final: 0.8168 (mt) REVERT: A 57 VAL cc_start: 0.7890 (t) cc_final: 0.6860 (t) REVERT: A 304 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7334 (pm20) REVERT: B 130 GLU cc_start: 0.4540 (pt0) cc_final: 0.4309 (pt0) REVERT: B 145 TYR cc_start: 0.8325 (p90) cc_final: 0.7830 (p90) REVERT: B 217 MET cc_start: 0.7432 (tpp) cc_final: 0.7037 (tmm) REVERT: B 258 ASP cc_start: 0.7834 (t0) cc_final: 0.7598 (t0) REVERT: B 325 MET cc_start: 0.6694 (mmp) cc_final: 0.6317 (mtt) REVERT: G 21 MET cc_start: 0.7073 (tmm) cc_final: 0.6828 (tmm) REVERT: N 5 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8398 (mt0) REVERT: N 34 MET cc_start: 0.8524 (mpp) cc_final: 0.8058 (mmm) REVERT: N 47 TRP cc_start: 0.7865 (t60) cc_final: 0.6938 (t60) REVERT: N 61 THR cc_start: 0.7783 (t) cc_final: 0.7445 (t) REVERT: N 68 PHE cc_start: 0.8750 (m-80) cc_final: 0.8212 (m-80) REVERT: N 73 ASP cc_start: 0.8553 (t70) cc_final: 0.8144 (t0) REVERT: N 82 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8066 (tp-100) REVERT: N 83 MET cc_start: 0.8102 (mpp) cc_final: 0.7395 (mpp) REVERT: N 89 GLU cc_start: 0.8853 (tt0) cc_final: 0.8192 (mp0) REVERT: R 219 ARG cc_start: 0.7483 (tmm160) cc_final: 0.7094 (ptt90) REVERT: R 302 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7355 (tp30) REVERT: R 339 TRP cc_start: 0.6996 (t60) cc_final: 0.6666 (t60) REVERT: R 383 ARG cc_start: 0.8476 (tmm-80) cc_final: 0.8256 (ttp-170) REVERT: R 444 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8450 (mm-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2075 time to fit residues: 50.2133 Evaluate side-chains 131 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 75 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 367 ASN B 91 HIS B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 84 ASN ** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8090 Z= 0.164 Angle : 0.555 12.341 10991 Z= 0.291 Chirality : 0.042 0.162 1268 Planarity : 0.004 0.053 1418 Dihedral : 4.120 16.734 1135 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % 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: -0.23 (0.26), residues: 1033 helix: 1.16 (0.27), residues: 363 sheet: -0.89 (0.33), residues: 219 loop : -0.78 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.005 0.001 HIS R 420 PHE 0.039 0.002 PHE R 238 TYR 0.028 0.002 TYR A 381 ARG 0.004 0.000 ARG R 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8163 (mt) cc_final: 0.7851 (mt) REVERT: A 57 VAL cc_start: 0.7869 (t) cc_final: 0.7660 (t) REVERT: A 60 MET cc_start: 0.6064 (mpp) cc_final: 0.5755 (mtm) REVERT: A 378 LEU cc_start: 0.8648 (mt) cc_final: 0.8441 (mt) REVERT: B 44 GLN cc_start: 0.7086 (mt0) cc_final: 0.6685 (mm-40) REVERT: B 61 MET cc_start: 0.8970 (ppp) cc_final: 0.8648 (ppp) REVERT: B 111 TYR cc_start: 0.8962 (m-80) cc_final: 0.8698 (m-80) REVERT: B 130 GLU cc_start: 0.4505 (pt0) cc_final: 0.4288 (pt0) REVERT: B 143 THR cc_start: 0.8836 (p) cc_final: 0.8460 (t) REVERT: B 172 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7683 (mm-30) REVERT: B 217 MET cc_start: 0.7419 (tpp) cc_final: 0.7060 (tmm) REVERT: B 258 ASP cc_start: 0.7623 (t0) cc_final: 0.7181 (t0) REVERT: B 291 ASP cc_start: 0.7967 (p0) cc_final: 0.7756 (p0) REVERT: B 325 MET cc_start: 0.6702 (mmp) cc_final: 0.6341 (mtt) REVERT: G 21 MET cc_start: 0.7038 (tmm) cc_final: 0.6724 (tmm) REVERT: N 19 ARG cc_start: 0.7184 (ttm-80) cc_final: 0.6912 (ttm-80) REVERT: N 47 TRP cc_start: 0.7561 (t60) cc_final: 0.7030 (t60) REVERT: N 73 ASP cc_start: 0.8560 (t70) cc_final: 0.8197 (t70) REVERT: N 82 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7842 (tp-100) REVERT: N 83 MET cc_start: 0.8031 (mpp) cc_final: 0.7587 (mpp) REVERT: N 89 GLU cc_start: 0.8883 (tt0) cc_final: 0.8230 (mp0) REVERT: R 215 LEU cc_start: 0.6980 (pt) cc_final: 0.6495 (pt) REVERT: R 219 ARG cc_start: 0.7625 (tmm160) cc_final: 0.7252 (ptt90) REVERT: R 302 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7305 (tp30) REVERT: R 339 TRP cc_start: 0.6938 (t60) cc_final: 0.6440 (t60) REVERT: R 383 ARG cc_start: 0.8477 (tmm-80) cc_final: 0.8269 (ttp-170) REVERT: R 444 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8375 (mm-30) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2170 time to fit residues: 50.2452 Evaluate side-chains 134 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN R 295 ASN R 307 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8090 Z= 0.267 Angle : 0.625 11.213 10991 Z= 0.325 Chirality : 0.044 0.195 1268 Planarity : 0.004 0.046 1418 Dihedral : 4.389 19.918 1135 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % 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: -0.30 (0.26), residues: 1033 helix: 1.00 (0.27), residues: 369 sheet: -0.76 (0.33), residues: 209 loop : -0.85 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 298 HIS 0.008 0.001 HIS B 225 PHE 0.014 0.002 PHE R 287 TYR 0.013 0.002 TYR A 253 ARG 0.007 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7183 (mtm-85) cc_final: 0.6907 (mtm-85) REVERT: B 61 MET cc_start: 0.9094 (ppp) cc_final: 0.8754 (ppp) REVERT: B 111 TYR cc_start: 0.9047 (m-80) cc_final: 0.8762 (m-80) REVERT: B 130 GLU cc_start: 0.4624 (pt0) cc_final: 0.4232 (pt0) REVERT: B 145 TYR cc_start: 0.8473 (p90) cc_final: 0.8114 (p90) REVERT: B 217 MET cc_start: 0.7527 (tpp) cc_final: 0.7196 (tmm) REVERT: B 325 MET cc_start: 0.6842 (mmp) cc_final: 0.6438 (mtt) REVERT: G 21 MET cc_start: 0.7005 (tmm) cc_final: 0.6683 (tmm) REVERT: N 5 GLN cc_start: 0.8223 (mp10) cc_final: 0.7760 (pp30) REVERT: N 34 MET cc_start: 0.8439 (mpp) cc_final: 0.8161 (mmm) REVERT: N 47 TRP cc_start: 0.7672 (t60) cc_final: 0.7283 (t60) REVERT: N 73 ASP cc_start: 0.8467 (t70) cc_final: 0.8051 (t0) REVERT: N 82 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8090 (tp-100) REVERT: N 89 GLU cc_start: 0.8878 (tt0) cc_final: 0.8253 (mp0) REVERT: R 215 LEU cc_start: 0.7172 (pt) cc_final: 0.6682 (pt) REVERT: R 219 ARG cc_start: 0.7488 (tmm160) cc_final: 0.7213 (ptt90) REVERT: R 302 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7549 (tp30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1975 time to fit residues: 40.4596 Evaluate side-chains 117 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8090 Z= 0.158 Angle : 0.549 10.654 10991 Z= 0.282 Chirality : 0.041 0.141 1268 Planarity : 0.003 0.041 1418 Dihedral : 4.112 22.023 1135 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.02 (0.26), residues: 1033 helix: 1.32 (0.28), residues: 367 sheet: -0.61 (0.32), residues: 231 loop : -0.69 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.010 0.001 PHE R 335 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 VAL cc_start: 0.7935 (t) cc_final: 0.7622 (t) REVERT: A 378 LEU cc_start: 0.8655 (mt) cc_final: 0.8347 (mt) REVERT: B 61 MET cc_start: 0.9033 (ppp) cc_final: 0.8723 (ppp) REVERT: B 75 GLN cc_start: 0.7909 (mt0) cc_final: 0.7106 (pp30) REVERT: B 111 TYR cc_start: 0.9049 (m-80) cc_final: 0.8801 (m-10) REVERT: B 130 GLU cc_start: 0.4618 (pt0) cc_final: 0.4224 (pt0) REVERT: B 217 MET cc_start: 0.7498 (tpp) cc_final: 0.7141 (tmm) REVERT: B 291 ASP cc_start: 0.7689 (p0) cc_final: 0.7426 (p0) REVERT: B 325 MET cc_start: 0.6727 (mmp) cc_final: 0.6370 (mtt) REVERT: N 5 GLN cc_start: 0.8222 (mp10) cc_final: 0.7800 (pp30) REVERT: N 47 TRP cc_start: 0.7577 (t60) cc_final: 0.7084 (t60) REVERT: N 73 ASP cc_start: 0.8471 (t70) cc_final: 0.8070 (t0) REVERT: N 82 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8097 (tp-100) REVERT: N 83 MET cc_start: 0.7885 (mpp) cc_final: 0.7531 (mpp) REVERT: N 89 GLU cc_start: 0.8816 (tt0) cc_final: 0.8189 (mp0) REVERT: R 215 LEU cc_start: 0.7347 (pt) cc_final: 0.6860 (pt) REVERT: R 219 ARG cc_start: 0.7498 (tmm160) cc_final: 0.7169 (ptt90) REVERT: R 302 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7237 (tp30) REVERT: R 339 TRP cc_start: 0.7263 (t60) cc_final: 0.6717 (t60) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1910 time to fit residues: 44.0991 Evaluate side-chains 124 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8090 Z= 0.151 Angle : 0.535 10.886 10991 Z= 0.275 Chirality : 0.041 0.169 1268 Planarity : 0.003 0.036 1418 Dihedral : 3.972 19.160 1135 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 0.29 (0.27), residues: 1033 helix: 1.68 (0.28), residues: 358 sheet: -0.56 (0.32), residues: 230 loop : -0.54 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 297 HIS 0.004 0.001 HIS R 420 PHE 0.009 0.001 PHE R 314 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.7149 (ttp) cc_final: 0.6921 (ptt) REVERT: A 378 LEU cc_start: 0.8715 (mt) cc_final: 0.8365 (mt) REVERT: B 61 MET cc_start: 0.8947 (ppp) cc_final: 0.8607 (ppp) REVERT: B 75 GLN cc_start: 0.7879 (mt0) cc_final: 0.7053 (pp30) REVERT: B 111 TYR cc_start: 0.8988 (m-80) cc_final: 0.8689 (m-10) REVERT: B 130 GLU cc_start: 0.4697 (pt0) cc_final: 0.4300 (pt0) REVERT: B 217 MET cc_start: 0.7502 (tpp) cc_final: 0.7188 (tmm) REVERT: B 325 MET cc_start: 0.6588 (mmp) cc_final: 0.6383 (mtt) REVERT: N 5 GLN cc_start: 0.8146 (mp10) cc_final: 0.7676 (pp30) REVERT: N 47 TRP cc_start: 0.7525 (t60) cc_final: 0.7317 (t60) REVERT: N 73 ASP cc_start: 0.8469 (t70) cc_final: 0.8079 (t0) REVERT: N 82 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8066 (tp-100) REVERT: N 83 MET cc_start: 0.7878 (mpp) cc_final: 0.7534 (mpp) REVERT: N 89 GLU cc_start: 0.8785 (tt0) cc_final: 0.8182 (mp0) REVERT: R 215 LEU cc_start: 0.7172 (pt) cc_final: 0.6732 (pt) REVERT: R 219 ARG cc_start: 0.7579 (tmm160) cc_final: 0.7346 (ptt90) REVERT: R 302 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7213 (tp30) REVERT: R 339 TRP cc_start: 0.7272 (t60) cc_final: 0.7039 (t60) REVERT: R 444 GLU cc_start: 0.8461 (tp30) cc_final: 0.8157 (tp30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1954 time to fit residues: 43.9294 Evaluate side-chains 120 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.0050 chunk 72 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8090 Z= 0.173 Angle : 0.555 12.037 10991 Z= 0.286 Chirality : 0.042 0.174 1268 Planarity : 0.003 0.035 1418 Dihedral : 3.980 19.226 1135 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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 (0.27), residues: 1033 helix: 1.60 (0.28), residues: 359 sheet: -0.50 (0.32), residues: 235 loop : -0.56 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 PHE 0.010 0.001 PHE R 314 TYR 0.014 0.001 TYR N 95 ARG 0.005 0.000 ARG R 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.9034 (ppp) cc_final: 0.8711 (ppp) REVERT: B 75 GLN cc_start: 0.7888 (mt0) cc_final: 0.7036 (pp30) REVERT: B 111 TYR cc_start: 0.9080 (m-80) cc_final: 0.8847 (m-10) REVERT: B 130 GLU cc_start: 0.4920 (pt0) cc_final: 0.4407 (pt0) REVERT: B 217 MET cc_start: 0.7370 (tpp) cc_final: 0.7074 (tmm) REVERT: B 325 MET cc_start: 0.6691 (mmp) cc_final: 0.6391 (mtt) REVERT: N 5 GLN cc_start: 0.8150 (mp10) cc_final: 0.7682 (pp30) REVERT: N 73 ASP cc_start: 0.8471 (t70) cc_final: 0.8077 (t0) REVERT: N 82 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8236 (tp-100) REVERT: N 83 MET cc_start: 0.7917 (mpp) cc_final: 0.7613 (mpp) REVERT: N 89 GLU cc_start: 0.8811 (tt0) cc_final: 0.8160 (mp0) REVERT: R 215 LEU cc_start: 0.7243 (pt) cc_final: 0.6810 (pt) REVERT: R 219 ARG cc_start: 0.7594 (tmm160) cc_final: 0.7235 (ptt90) REVERT: R 339 TRP cc_start: 0.7322 (t60) cc_final: 0.6858 (t60) REVERT: R 444 GLU cc_start: 0.8494 (tp30) cc_final: 0.8181 (tp30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1788 time to fit residues: 38.9628 Evaluate side-chains 122 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 39 GLN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8090 Z= 0.155 Angle : 0.543 11.107 10991 Z= 0.278 Chirality : 0.041 0.164 1268 Planarity : 0.003 0.036 1418 Dihedral : 3.892 18.446 1135 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 (0.27), residues: 1033 helix: 1.67 (0.28), residues: 359 sheet: -0.41 (0.32), residues: 235 loop : -0.58 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 339 HIS 0.004 0.001 HIS R 420 PHE 0.011 0.001 PHE R 327 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG R 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.9024 (ppp) cc_final: 0.8713 (ppp) REVERT: B 75 GLN cc_start: 0.7795 (mt0) cc_final: 0.7065 (pp30) REVERT: B 111 TYR cc_start: 0.9086 (m-80) cc_final: 0.8756 (m-10) REVERT: B 130 GLU cc_start: 0.4876 (pt0) cc_final: 0.4377 (pt0) REVERT: B 217 MET cc_start: 0.7412 (tpp) cc_final: 0.7101 (tmm) REVERT: B 325 MET cc_start: 0.6638 (mmp) cc_final: 0.6419 (mtt) REVERT: N 5 GLN cc_start: 0.8122 (mp10) cc_final: 0.7647 (pp30) REVERT: N 73 ASP cc_start: 0.8466 (t70) cc_final: 0.8073 (t0) REVERT: N 82 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8205 (tp-100) REVERT: N 83 MET cc_start: 0.7829 (mpp) cc_final: 0.7585 (mpp) REVERT: N 89 GLU cc_start: 0.8856 (tt0) cc_final: 0.8165 (mp0) REVERT: R 215 LEU cc_start: 0.7074 (pt) cc_final: 0.6684 (pt) REVERT: R 219 ARG cc_start: 0.7672 (tmm160) cc_final: 0.7210 (ptt90) REVERT: R 444 GLU cc_start: 0.8514 (tp30) cc_final: 0.8207 (tp30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1881 time to fit residues: 41.4905 Evaluate side-chains 126 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8090 Z= 0.255 Angle : 0.614 10.494 10991 Z= 0.318 Chirality : 0.043 0.196 1268 Planarity : 0.004 0.030 1418 Dihedral : 4.332 21.920 1135 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.13 (0.27), residues: 1033 helix: 1.45 (0.28), residues: 360 sheet: -0.50 (0.32), residues: 230 loop : -0.65 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 339 HIS 0.011 0.001 HIS A 220 PHE 0.020 0.002 PHE B 235 TYR 0.016 0.002 TYR N 95 ARG 0.006 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.6712 (t0) cc_final: 0.6465 (t0) REVERT: A 323 ARG cc_start: 0.8586 (ttt180) cc_final: 0.7533 (mtp85) REVERT: B 61 MET cc_start: 0.9146 (ppp) cc_final: 0.8817 (ppp) REVERT: B 111 TYR cc_start: 0.9127 (m-80) cc_final: 0.8895 (m-10) REVERT: B 130 GLU cc_start: 0.4889 (pt0) cc_final: 0.4414 (pt0) REVERT: B 145 TYR cc_start: 0.8476 (p90) cc_final: 0.8151 (p90) REVERT: B 217 MET cc_start: 0.7377 (tpp) cc_final: 0.7106 (tmm) REVERT: B 300 LEU cc_start: 0.8498 (mm) cc_final: 0.8230 (mm) REVERT: B 325 MET cc_start: 0.6790 (mmp) cc_final: 0.6499 (mtt) REVERT: G 36 ASP cc_start: 0.8436 (p0) cc_final: 0.8023 (p0) REVERT: N 5 GLN cc_start: 0.8086 (mp10) cc_final: 0.7825 (mp10) REVERT: N 47 TRP cc_start: 0.7580 (t60) cc_final: 0.6980 (t60) REVERT: N 61 THR cc_start: 0.7421 (t) cc_final: 0.7090 (t) REVERT: N 73 ASP cc_start: 0.8431 (t70) cc_final: 0.8040 (t0) REVERT: N 82 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8142 (tp-100) REVERT: N 89 GLU cc_start: 0.8882 (tt0) cc_final: 0.8187 (mp0) REVERT: R 215 LEU cc_start: 0.6897 (pt) cc_final: 0.6506 (pt) REVERT: R 219 ARG cc_start: 0.7648 (tmm160) cc_final: 0.7179 (ptt90) REVERT: R 339 TRP cc_start: 0.7548 (t60) cc_final: 0.7187 (t60) REVERT: R 371 ILE cc_start: 0.7989 (mm) cc_final: 0.7678 (mt) REVERT: R 444 GLU cc_start: 0.8506 (tp30) cc_final: 0.8233 (tp30) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1940 time to fit residues: 41.2012 Evaluate side-chains 123 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8090 Z= 0.201 Angle : 0.585 10.519 10991 Z= 0.302 Chirality : 0.042 0.189 1268 Planarity : 0.003 0.035 1418 Dihedral : 4.265 24.449 1135 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.49 % 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: 0.13 (0.27), residues: 1033 helix: 1.52 (0.28), residues: 360 sheet: -0.50 (0.32), residues: 239 loop : -0.71 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 339 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.002 PHE R 314 TYR 0.015 0.002 TYR B 264 ARG 0.005 0.000 ARG R 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.6738 (t0) cc_final: 0.6426 (t0) REVERT: A 323 ARG cc_start: 0.8621 (ttt180) cc_final: 0.7577 (mtp85) REVERT: B 61 MET cc_start: 0.9126 (ppp) cc_final: 0.8805 (ppp) REVERT: B 111 TYR cc_start: 0.9115 (m-80) cc_final: 0.8884 (m-10) REVERT: B 130 GLU cc_start: 0.4956 (pt0) cc_final: 0.4370 (pt0) REVERT: B 217 MET cc_start: 0.7391 (tpp) cc_final: 0.7100 (tmm) REVERT: B 314 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7815 (ttt-90) REVERT: B 325 MET cc_start: 0.6810 (mmp) cc_final: 0.6531 (mtt) REVERT: G 36 ASP cc_start: 0.8512 (p0) cc_final: 0.8108 (p0) REVERT: N 5 GLN cc_start: 0.8090 (mp10) cc_final: 0.7828 (mp10) REVERT: N 39 GLN cc_start: 0.7351 (tp40) cc_final: 0.7012 (tt0) REVERT: N 46 GLU cc_start: 0.8397 (mp0) cc_final: 0.8190 (mp0) REVERT: N 47 TRP cc_start: 0.7469 (t60) cc_final: 0.6907 (t60) REVERT: N 61 THR cc_start: 0.7325 (t) cc_final: 0.6952 (t) REVERT: N 73 ASP cc_start: 0.8414 (t70) cc_final: 0.8020 (t0) REVERT: N 82 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8126 (tp-100) REVERT: N 89 GLU cc_start: 0.8869 (tt0) cc_final: 0.8165 (mp0) REVERT: R 215 LEU cc_start: 0.6983 (pt) cc_final: 0.6638 (pt) REVERT: R 219 ARG cc_start: 0.7589 (tmm160) cc_final: 0.7208 (ptt90) REVERT: R 305 TYR cc_start: 0.8148 (t80) cc_final: 0.7945 (t80) REVERT: R 315 PHE cc_start: 0.5333 (t80) cc_final: 0.4908 (t80) REVERT: R 339 TRP cc_start: 0.7454 (t60) cc_final: 0.7041 (t60) REVERT: R 444 GLU cc_start: 0.8408 (tp30) cc_final: 0.8126 (tp30) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2116 time to fit residues: 42.9911 Evaluate side-chains 121 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.114221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099103 restraints weight = 20213.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100652 restraints weight = 13459.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101999 restraints weight = 10144.035| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8090 Z= 0.169 Angle : 0.561 9.501 10991 Z= 0.287 Chirality : 0.042 0.190 1268 Planarity : 0.003 0.035 1418 Dihedral : 4.109 24.151 1135 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.25 (0.27), residues: 1033 helix: 1.67 (0.28), residues: 360 sheet: -0.42 (0.32), residues: 239 loop : -0.72 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 339 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE R 314 TYR 0.013 0.001 TYR B 264 ARG 0.005 0.000 ARG R 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.92 seconds wall clock time: 33 minutes 31.39 seconds (2011.39 seconds total)