Starting phenix.real_space_refine on Wed Feb 14 22:08:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c60_16449/02_2024/8c60_16449.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c60_16449/02_2024/8c60_16449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c60_16449/02_2024/8c60_16449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c60_16449/02_2024/8c60_16449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c60_16449/02_2024/8c60_16449.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c60_16449/02_2024/8c60_16449.pdb" } resolution = 3.4 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= 0.002 sd= 0.032 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 S 71 5.16 5 C 6618 2.51 5 N 1791 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "B TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 191} Chain breaks: 3 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8431 SG CYS C 289 37.156 60.679 44.363 1.00 98.27 S ATOM 8457 SG CYS C 292 34.484 59.125 42.002 1.00 76.90 S ATOM 8640 SG CYS C 315 38.214 58.340 41.438 1.00 99.87 S ATOM 8315 SG CYS C 274 37.578 47.560 46.382 1.00 76.54 S ATOM 8339 SG CYS C 277 38.854 43.874 45.997 1.00 76.10 S ATOM 8523 SG CYS C 300 41.127 46.197 47.023 1.00 52.30 S ATOM 7590 SG CYS C 71 45.057 96.067 75.745 1.00157.09 S ATOM 7614 SG CYS C 74 42.007 94.820 73.799 1.00171.24 S ATOM 7806 SG CYS C 99 44.586 97.004 72.093 1.00151.70 S ATOM 7833 SG CYS C 102 42.314 98.532 74.632 1.00154.53 S ATOM 7508 SG CYS C 59 47.178 87.777 66.516 1.00171.80 S ATOM 7528 SG CYS C 62 47.624 85.720 63.345 1.00149.40 S ATOM 7675 SG CYS C 82 49.675 88.925 63.768 1.00152.27 S Time building chain proxies: 6.08, per 1000 atoms: 0.59 Number of scatterers: 10393 At special positions: 0 Unit cell: (121.338, 127.008, 108.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 71 16.00 O 1906 8.00 N 1791 7.00 C 6618 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: 4.35 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 99 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 102 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 74 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 71 " pdb=" ZN C1104 " pdb="ZN ZN C1104 " - pdb=" ND1 HIS C 79 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 62 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 59 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 82 " Number of angles added : 15 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 59.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.722A pdb=" N PHE A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 340 through 353 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.673A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.088A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 Processing helix chain 'A' and resid 530 through 561 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.916A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.527A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.711A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.537A pdb=" N ARG A 792 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.348A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 removed outlier: 3.518A pdb=" N LEU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 888 removed outlier: 3.662A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 5.169A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 33 through 46 removed outlier: 4.044A pdb=" N ARG B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.072A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.576A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.501A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.508A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 263 through 267 removed outlier: 4.038A pdb=" N SER B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 267 " --> pdb=" O ALA B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 267' Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.952A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.683A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.854A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.513A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.510A pdb=" N CYS C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 4.061A pdb=" N VAL C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.605A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 205 through 216 removed outlier: 3.786A pdb=" N ASP D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 249 through 266 removed outlier: 4.339A pdb=" N GLU D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 298 through 313 removed outlier: 3.925A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.741A pdb=" N ILE A 397 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.030A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.732A pdb=" N TYR B 14 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 258 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU B 299 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 260 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 171 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL B 197 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 173 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE B 199 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 175 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N LYS B 201 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'C' and resid 287 through 288 523 hydrogen bonds defined for protein. 1521 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: 2.79 Time building geometry restraints manager: 4.63 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: 3402 1.34 - 1.46: 2277 1.46 - 1.58: 4842 1.58 - 1.70: 2 1.70 - 1.82: 104 Bond restraints: 10627 Sorted by residual: bond pdb=" CG LEU A 753 " pdb=" CD2 LEU A 753 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.84e+00 bond pdb=" C LYS D 204 " pdb=" N PRO D 205 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.24e+00 bond pdb=" CB PRO A 664 " pdb=" CG PRO A 664 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.69e+00 bond pdb=" CB PRO C 293 " pdb=" CG PRO C 293 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.51e+00 bond pdb=" C ALA D 299 " pdb=" N PRO D 300 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.44e-02 4.82e+03 3.14e+00 ... (remaining 10622 not shown) Histogram of bond angle deviations from ideal: 92.53 - 100.84: 18 100.84 - 109.14: 696 109.14 - 117.44: 6834 117.44 - 125.74: 6650 125.74 - 134.05: 154 Bond angle restraints: 14352 Sorted by residual: angle pdb=" CA PRO A 664 " pdb=" N PRO A 664 " pdb=" CD PRO A 664 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.03e+01 angle pdb=" CA LEU A 347 " pdb=" CB LEU A 347 " pdb=" CG LEU A 347 " ideal model delta sigma weight residual 116.30 132.58 -16.28 3.50e+00 8.16e-02 2.16e+01 angle pdb=" C GLY D 298 " pdb=" N ALA D 299 " pdb=" CA ALA D 299 " ideal model delta sigma weight residual 120.09 125.59 -5.50 1.25e+00 6.40e-01 1.94e+01 angle pdb=" CA PRO C 293 " pdb=" N PRO C 293 " pdb=" CD PRO C 293 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" CG MET A 934 " pdb=" SD MET A 934 " pdb=" CE MET A 934 " ideal model delta sigma weight residual 100.90 92.53 8.37 2.20e+00 2.07e-01 1.45e+01 ... (remaining 14347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5443 17.29 - 34.59: 701 34.59 - 51.88: 248 51.88 - 69.18: 40 69.18 - 86.47: 17 Dihedral angle restraints: 6449 sinusoidal: 2681 harmonic: 3768 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LYS C 272 " pdb=" C LYS C 272 " pdb=" N VAL C 273 " pdb=" CA VAL C 273 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 16 " pdb=" C TYR B 16 " pdb=" N ASP B 17 " pdb=" CA ASP B 17 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1498 0.107 - 0.215: 33 0.215 - 0.322: 1 0.322 - 0.429: 1 0.429 - 0.537: 1 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CG LEU C 213 " pdb=" CB LEU C 213 " pdb=" CD1 LEU C 213 " pdb=" CD2 LEU C 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CG LEU C 355 " pdb=" CB LEU C 355 " pdb=" CD1 LEU C 355 " pdb=" CD2 LEU C 355 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU D 213 " pdb=" CB LEU D 213 " pdb=" CD1 LEU D 213 " pdb=" CD2 LEU D 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1531 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 663 " 0.079 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 664 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 292 " -0.054 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO C 293 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 293 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 293 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 315 " -0.198 9.50e-02 1.11e+02 8.93e-02 6.15e+00 pdb=" NE ARG A 315 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 315 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 315 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 315 " -0.014 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 33 2.38 - 3.01: 5937 3.01 - 3.64: 16128 3.64 - 4.27: 23576 4.27 - 4.90: 39100 Nonbonded interactions: 84774 Sorted by model distance: nonbonded pdb=" CG HIS B 179 " pdb="ZN ZN B 501 " model vdw 1.750 1.960 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 501 " model vdw 2.136 2.230 nonbonded pdb=" ND2 ASN B 96 " pdb=" O ALA B 148 " model vdw 2.183 2.520 nonbonded pdb=" OG1 THR C 330 " pdb=" OD1 ASN C 333 " model vdw 2.249 2.440 nonbonded pdb=" O ASN D 228 " pdb=" OG SER D 231 " model vdw 2.265 2.440 ... (remaining 84769 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.260 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.200 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 : 0.004 0.096 10627 Z= 0.249 Angle : 0.783 16.276 14352 Z= 0.404 Chirality : 0.047 0.537 1534 Planarity : 0.006 0.114 1862 Dihedral : 17.712 86.471 4015 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.80 % Allowed : 29.15 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 1260 helix: 0.70 (0.20), residues: 671 sheet: -0.50 (0.63), residues: 74 loop : -0.95 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 560 HIS 0.004 0.001 HIS C 297 PHE 0.031 0.002 PHE A 743 TYR 0.036 0.002 TYR D 236 ARG 0.020 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 279 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 LYS cc_start: 0.7588 (tptt) cc_final: 0.7081 (tptm) REVERT: A 557 ASN cc_start: 0.7745 (t0) cc_final: 0.7510 (t0) REVERT: A 570 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8063 (ttpp) REVERT: A 625 GLU cc_start: 0.6413 (pm20) cc_final: 0.5180 (pm20) REVERT: A 771 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7604 (mt0) REVERT: A 776 GLU cc_start: 0.7120 (tp30) cc_final: 0.6705 (tp30) REVERT: A 822 MET cc_start: 0.7800 (ttm) cc_final: 0.7546 (ttm) REVERT: A 843 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7546 (mpp) REVERT: A 922 LYS cc_start: 0.8008 (tmmt) cc_final: 0.7782 (tmmt) REVERT: B 75 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7247 (mmmt) REVERT: B 265 ASP cc_start: 0.6929 (p0) cc_final: 0.6626 (p0) outliers start: 9 outliers final: 1 residues processed: 281 average time/residue: 0.2828 time to fit residues: 105.9592 Evaluate side-chains 272 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 843 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 114 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN A 574 HIS ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10627 Z= 0.215 Angle : 0.624 12.269 14352 Z= 0.310 Chirality : 0.043 0.284 1534 Planarity : 0.004 0.063 1862 Dihedral : 4.307 24.360 1413 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.09 % Allowed : 25.88 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 1260 helix: 1.25 (0.20), residues: 672 sheet: -0.53 (0.62), residues: 75 loop : -0.94 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.009 0.001 HIS B 58 PHE 0.027 0.002 PHE A 743 TYR 0.027 0.002 TYR D 329 ARG 0.009 0.001 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 301 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 GLU cc_start: 0.7846 (tt0) cc_final: 0.7602 (tt0) REVERT: A 457 ASP cc_start: 0.7313 (m-30) cc_final: 0.7042 (m-30) REVERT: A 458 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 503 THR cc_start: 0.7991 (p) cc_final: 0.7640 (m) REVERT: A 540 LYS cc_start: 0.7559 (mttp) cc_final: 0.7340 (mttp) REVERT: A 545 LYS cc_start: 0.7689 (tptt) cc_final: 0.7279 (tptm) REVERT: A 557 ASN cc_start: 0.7788 (t160) cc_final: 0.7528 (t0) REVERT: A 570 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7939 (ttpp) REVERT: A 741 SER cc_start: 0.8120 (t) cc_final: 0.7585 (p) REVERT: A 787 LEU cc_start: 0.4283 (OUTLIER) cc_final: 0.4067 (tt) REVERT: A 814 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6429 (mt-10) REVERT: A 850 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8087 (m) REVERT: A 922 LYS cc_start: 0.8082 (tmmt) cc_final: 0.7649 (tmmt) REVERT: A 925 PHE cc_start: 0.7711 (m-80) cc_final: 0.7438 (m-80) REVERT: B 44 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5894 (mp) REVERT: B 75 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7325 (mmmt) REVERT: B 127 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6965 (mpp80) REVERT: B 151 PHE cc_start: 0.8643 (m-10) cc_final: 0.8243 (m-80) REVERT: B 265 ASP cc_start: 0.7054 (p0) cc_final: 0.6571 (p0) REVERT: B 336 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 305 LEU cc_start: 0.8195 (mt) cc_final: 0.7940 (mp) REVERT: D 303 LEU cc_start: 0.7828 (tp) cc_final: 0.7586 (tp) outliers start: 35 outliers final: 15 residues processed: 320 average time/residue: 0.2837 time to fit residues: 119.2277 Evaluate side-chains 298 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 279 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10627 Z= 0.263 Angle : 0.646 13.528 14352 Z= 0.318 Chirality : 0.044 0.249 1534 Planarity : 0.004 0.053 1862 Dihedral : 4.228 21.663 1408 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.27 % Allowed : 27.12 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.45 (0.24), residues: 1260 helix: 1.31 (0.20), residues: 676 sheet: -0.30 (0.62), residues: 74 loop : -0.96 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 560 HIS 0.007 0.001 HIS C 297 PHE 0.033 0.002 PHE A 751 TYR 0.025 0.002 TYR D 329 ARG 0.006 0.001 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 314 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8230 (t80) cc_final: 0.7993 (t80) REVERT: A 428 TRP cc_start: 0.8630 (m100) cc_final: 0.7989 (m100) REVERT: A 444 LYS cc_start: 0.4961 (mttt) cc_final: 0.3801 (ptpt) REVERT: A 449 GLU cc_start: 0.7936 (tt0) cc_final: 0.7699 (tt0) REVERT: A 456 GLU cc_start: 0.7721 (tp30) cc_final: 0.7506 (tp30) REVERT: A 457 ASP cc_start: 0.7503 (m-30) cc_final: 0.7037 (m-30) REVERT: A 458 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 470 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 475 VAL cc_start: 0.8122 (t) cc_final: 0.7907 (p) REVERT: A 522 GLU cc_start: 0.7342 (mp0) cc_final: 0.7108 (mp0) REVERT: A 559 ILE cc_start: 0.7427 (mt) cc_final: 0.7026 (mt) REVERT: A 582 ASN cc_start: 0.7598 (m-40) cc_final: 0.7310 (m-40) REVERT: A 601 ASP cc_start: 0.6841 (m-30) cc_final: 0.6552 (m-30) REVERT: A 741 SER cc_start: 0.8260 (t) cc_final: 0.7535 (p) REVERT: A 776 GLU cc_start: 0.7231 (tp30) cc_final: 0.6901 (tp30) REVERT: A 814 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6675 (mt-10) REVERT: A 822 MET cc_start: 0.7848 (ttm) cc_final: 0.7432 (ttm) REVERT: A 847 HIS cc_start: 0.7403 (m90) cc_final: 0.7096 (m90) REVERT: A 855 ASP cc_start: 0.7200 (p0) cc_final: 0.6980 (p0) REVERT: A 857 LEU cc_start: 0.7950 (tp) cc_final: 0.7652 (tp) REVERT: A 915 MET cc_start: 0.6193 (mpp) cc_final: 0.5708 (mpp) REVERT: A 924 MET cc_start: 0.6390 (ttm) cc_final: 0.5829 (ttm) REVERT: A 925 PHE cc_start: 0.8083 (m-80) cc_final: 0.7825 (m-80) REVERT: A 935 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7704 (p) REVERT: A 937 GLU cc_start: 0.7347 (mp0) cc_final: 0.7063 (mt-10) REVERT: B 74 ILE cc_start: 0.7532 (mm) cc_final: 0.7234 (mm) REVERT: B 75 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7207 (mmmt) REVERT: B 91 GLN cc_start: 0.8219 (mt0) cc_final: 0.7998 (mt0) REVERT: B 151 PHE cc_start: 0.8681 (m-10) cc_final: 0.8236 (m-80) REVERT: B 211 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6714 (t0) REVERT: B 336 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7149 (tm-30) REVERT: C 21 MET cc_start: 0.8302 (mmm) cc_final: 0.7898 (mmm) REVERT: C 286 LEU cc_start: 0.8420 (mt) cc_final: 0.8131 (mm) REVERT: D 261 LYS cc_start: 0.8251 (mttm) cc_final: 0.7970 (mttm) REVERT: D 265 ASN cc_start: 0.6674 (OUTLIER) cc_final: 0.6430 (m110) REVERT: D 303 LEU cc_start: 0.7929 (tp) cc_final: 0.7657 (tp) outliers start: 37 outliers final: 19 residues processed: 331 average time/residue: 0.2769 time to fit residues: 121.3149 Evaluate side-chains 307 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 557 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10627 Z= 0.236 Angle : 0.631 13.251 14352 Z= 0.309 Chirality : 0.043 0.220 1534 Planarity : 0.004 0.053 1862 Dihedral : 4.214 20.704 1408 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.80 % Allowed : 27.30 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 1260 helix: 1.36 (0.20), residues: 665 sheet: -0.34 (0.62), residues: 74 loop : -0.95 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 560 HIS 0.010 0.001 HIS A 867 PHE 0.025 0.002 PHE A 362 TYR 0.026 0.002 TYR D 329 ARG 0.005 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 308 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.7153 (ptp-170) REVERT: A 428 TRP cc_start: 0.8583 (m100) cc_final: 0.8073 (m100) REVERT: A 444 LYS cc_start: 0.5061 (mttt) cc_final: 0.3854 (ptpt) REVERT: A 449 GLU cc_start: 0.7927 (tt0) cc_final: 0.7697 (tt0) REVERT: A 456 GLU cc_start: 0.7704 (tp30) cc_final: 0.7431 (tp30) REVERT: A 457 ASP cc_start: 0.7489 (m-30) cc_final: 0.6971 (m-30) REVERT: A 458 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7089 (mt-10) REVERT: A 470 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8319 (mm) REVERT: A 475 VAL cc_start: 0.8154 (t) cc_final: 0.7943 (p) REVERT: A 522 GLU cc_start: 0.7444 (mp0) cc_final: 0.7202 (mp0) REVERT: A 559 ILE cc_start: 0.7527 (mt) cc_final: 0.7154 (mt) REVERT: A 582 ASN cc_start: 0.7570 (m-40) cc_final: 0.7324 (m-40) REVERT: A 597 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 601 ASP cc_start: 0.6973 (m-30) cc_final: 0.6663 (m-30) REVERT: A 741 SER cc_start: 0.8241 (t) cc_final: 0.7487 (p) REVERT: A 822 MET cc_start: 0.7815 (ttm) cc_final: 0.7476 (ttm) REVERT: A 855 ASP cc_start: 0.7329 (p0) cc_final: 0.7075 (p0) REVERT: A 915 MET cc_start: 0.6308 (mpp) cc_final: 0.5988 (mpp) REVERT: A 924 MET cc_start: 0.6464 (ttm) cc_final: 0.5863 (ttm) REVERT: A 925 PHE cc_start: 0.8142 (m-80) cc_final: 0.7882 (m-80) REVERT: A 935 THR cc_start: 0.8073 (m) cc_final: 0.7711 (p) REVERT: B 74 ILE cc_start: 0.7603 (mm) cc_final: 0.7381 (mm) REVERT: B 75 LYS cc_start: 0.7637 (mmmt) cc_final: 0.7435 (mtmm) REVERT: B 91 GLN cc_start: 0.8243 (mt0) cc_final: 0.8019 (mt0) REVERT: B 112 GLN cc_start: 0.8353 (mt0) cc_final: 0.8140 (mt0) REVERT: B 132 MET cc_start: 0.7600 (ttt) cc_final: 0.7395 (ttm) REVERT: B 156 ASP cc_start: 0.7921 (p0) cc_final: 0.7533 (p0) REVERT: B 211 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6736 (t0) REVERT: B 222 TYR cc_start: 0.8265 (m-80) cc_final: 0.8001 (m-80) REVERT: B 243 LYS cc_start: 0.8063 (tttp) cc_final: 0.7799 (ttpt) REVERT: B 336 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7095 (tm-30) REVERT: C 21 MET cc_start: 0.8249 (mmm) cc_final: 0.7437 (mmm) REVERT: C 295 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7834 (mt) REVERT: C 329 MET cc_start: 0.6502 (tpp) cc_final: 0.6164 (mpp) REVERT: D 303 LEU cc_start: 0.7917 (tp) cc_final: 0.7662 (tp) outliers start: 43 outliers final: 22 residues processed: 333 average time/residue: 0.2817 time to fit residues: 124.5300 Evaluate side-chains 324 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 299 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 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 480 GLN A 557 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 771 GLN ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN A 867 HIS ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10627 Z= 0.244 Angle : 0.622 12.708 14352 Z= 0.309 Chirality : 0.043 0.327 1534 Planarity : 0.004 0.051 1862 Dihedral : 4.233 22.066 1408 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.71 % Allowed : 28.89 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1260 helix: 1.40 (0.20), residues: 665 sheet: -0.16 (0.63), residues: 74 loop : -0.93 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 206 HIS 0.013 0.001 HIS A 847 PHE 0.027 0.002 PHE A 743 TYR 0.026 0.001 TYR D 329 ARG 0.008 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 300 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.7399 (ptp-170) cc_final: 0.7133 (ptp-170) REVERT: A 428 TRP cc_start: 0.8591 (m100) cc_final: 0.8087 (m100) REVERT: A 444 LYS cc_start: 0.5146 (mttt) cc_final: 0.3949 (ptpt) REVERT: A 457 ASP cc_start: 0.7510 (m-30) cc_final: 0.6920 (m-30) REVERT: A 458 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 463 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.6977 (t0) REVERT: A 470 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8311 (mm) REVERT: A 475 VAL cc_start: 0.8315 (t) cc_final: 0.8001 (p) REVERT: A 505 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 522 GLU cc_start: 0.7388 (mp0) cc_final: 0.7183 (mp0) REVERT: A 546 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 582 ASN cc_start: 0.7575 (m-40) cc_final: 0.7321 (m-40) REVERT: A 597 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 601 ASP cc_start: 0.7018 (m-30) cc_final: 0.6731 (m-30) REVERT: A 741 SER cc_start: 0.8166 (t) cc_final: 0.7471 (p) REVERT: A 748 ASN cc_start: 0.7287 (m110) cc_final: 0.7043 (m110) REVERT: A 752 PHE cc_start: 0.7858 (t80) cc_final: 0.7482 (t80) REVERT: A 768 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7211 (mtt90) REVERT: A 822 MET cc_start: 0.7794 (ttm) cc_final: 0.7402 (ttm) REVERT: A 855 ASP cc_start: 0.7650 (p0) cc_final: 0.7233 (p0) REVERT: A 856 LYS cc_start: 0.8053 (mttm) cc_final: 0.7624 (mptt) REVERT: A 863 ARG cc_start: 0.7177 (ttp-110) cc_final: 0.6896 (ttm-80) REVERT: A 922 LYS cc_start: 0.8095 (tmmt) cc_final: 0.7710 (tmmt) REVERT: A 924 MET cc_start: 0.6472 (ttm) cc_final: 0.5858 (ttm) REVERT: A 935 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7823 (p) REVERT: B 74 ILE cc_start: 0.7706 (mm) cc_final: 0.7488 (mm) REVERT: B 91 GLN cc_start: 0.8248 (mt0) cc_final: 0.8001 (mt0) REVERT: B 156 ASP cc_start: 0.7895 (p0) cc_final: 0.7570 (p0) REVERT: B 211 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6775 (t0) REVERT: B 243 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7801 (ttpt) REVERT: B 336 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7059 (tm-30) REVERT: B 337 TYR cc_start: 0.8236 (m-80) cc_final: 0.7802 (m-80) REVERT: B 360 MET cc_start: 0.8224 (mmm) cc_final: 0.7900 (tpp) REVERT: C 21 MET cc_start: 0.8247 (mmm) cc_final: 0.7469 (mmm) REVERT: C 91 MET cc_start: 0.4965 (tpt) cc_final: 0.4550 (tpt) REVERT: C 295 LEU cc_start: 0.8220 (mm) cc_final: 0.7907 (mt) REVERT: C 329 MET cc_start: 0.6488 (tpp) cc_final: 0.6125 (mpp) outliers start: 42 outliers final: 23 residues processed: 324 average time/residue: 0.2786 time to fit residues: 119.7084 Evaluate side-chains 318 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 773 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 45 ASN B 112 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10627 Z= 0.199 Angle : 0.611 12.820 14352 Z= 0.300 Chirality : 0.042 0.317 1534 Planarity : 0.004 0.050 1862 Dihedral : 4.155 22.917 1408 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.80 % Allowed : 28.53 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.64 (0.24), residues: 1260 helix: 1.45 (0.20), residues: 671 sheet: -0.14 (0.62), residues: 74 loop : -0.84 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 206 HIS 0.005 0.001 HIS C 297 PHE 0.025 0.002 PHE A 362 TYR 0.025 0.001 TYR D 329 ARG 0.007 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 298 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6684 (mmm160) cc_final: 0.6357 (mmp-170) REVERT: A 402 ARG cc_start: 0.7392 (ptp-170) cc_final: 0.7089 (ptp-170) REVERT: A 428 TRP cc_start: 0.8606 (m100) cc_final: 0.8106 (m100) REVERT: A 444 LYS cc_start: 0.5131 (mttt) cc_final: 0.3761 (ptpt) REVERT: A 456 GLU cc_start: 0.7827 (tp30) cc_final: 0.7623 (tp30) REVERT: A 457 ASP cc_start: 0.7518 (m-30) cc_final: 0.6928 (m-30) REVERT: A 458 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 463 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7100 (t0) REVERT: A 470 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 475 VAL cc_start: 0.8442 (t) cc_final: 0.8099 (p) REVERT: A 505 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 546 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 582 ASN cc_start: 0.7499 (m-40) cc_final: 0.7258 (m-40) REVERT: A 597 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 601 ASP cc_start: 0.7166 (m-30) cc_final: 0.6823 (m-30) REVERT: A 768 ARG cc_start: 0.7501 (mtt90) cc_final: 0.7139 (mtt90) REVERT: A 822 MET cc_start: 0.7767 (ttm) cc_final: 0.7253 (ttm) REVERT: A 828 GLU cc_start: 0.8074 (pt0) cc_final: 0.7843 (pt0) REVERT: A 854 MET cc_start: 0.8486 (mmm) cc_final: 0.8193 (mmm) REVERT: A 855 ASP cc_start: 0.7515 (p0) cc_final: 0.7141 (p0) REVERT: A 856 LYS cc_start: 0.7920 (mttm) cc_final: 0.7505 (mptt) REVERT: A 863 ARG cc_start: 0.7135 (ttp-110) cc_final: 0.6853 (ttm-80) REVERT: A 924 MET cc_start: 0.6465 (ttm) cc_final: 0.5891 (ttm) REVERT: A 935 THR cc_start: 0.8232 (m) cc_final: 0.7754 (p) REVERT: B 74 ILE cc_start: 0.7728 (mm) cc_final: 0.7491 (mm) REVERT: B 91 GLN cc_start: 0.8282 (mt0) cc_final: 0.8063 (mt0) REVERT: B 100 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7192 (t0) REVERT: B 156 ASP cc_start: 0.7867 (p0) cc_final: 0.7581 (p0) REVERT: B 211 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6694 (t0) REVERT: B 261 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: B 336 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7067 (tm-30) REVERT: C 21 MET cc_start: 0.8248 (mmm) cc_final: 0.7495 (mmm) REVERT: C 295 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7881 (mt) REVERT: C 329 MET cc_start: 0.6463 (tpp) cc_final: 0.6121 (mpp) outliers start: 43 outliers final: 25 residues processed: 322 average time/residue: 0.2780 time to fit residues: 118.5628 Evaluate side-chains 313 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 0.0040 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.0570 chunk 121 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10627 Z= 0.188 Angle : 0.620 13.121 14352 Z= 0.305 Chirality : 0.043 0.372 1534 Planarity : 0.004 0.051 1862 Dihedral : 4.128 23.080 1408 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.53 % Allowed : 28.53 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.69 (0.24), residues: 1260 helix: 1.48 (0.20), residues: 670 sheet: -0.22 (0.62), residues: 75 loop : -0.78 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 206 HIS 0.004 0.001 HIS C 297 PHE 0.019 0.001 PHE A 743 TYR 0.031 0.001 TYR B 16 ARG 0.008 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 292 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.7047 (ptp-170) REVERT: A 428 TRP cc_start: 0.8603 (m100) cc_final: 0.8113 (m100) REVERT: A 444 LYS cc_start: 0.5197 (mttt) cc_final: 0.4014 (ptpt) REVERT: A 456 GLU cc_start: 0.7777 (tp30) cc_final: 0.7539 (tp30) REVERT: A 457 ASP cc_start: 0.7516 (m-30) cc_final: 0.6931 (m-30) REVERT: A 458 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 470 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 475 VAL cc_start: 0.8453 (t) cc_final: 0.8108 (p) REVERT: A 505 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 546 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 582 ASN cc_start: 0.7475 (m-40) cc_final: 0.7218 (m-40) REVERT: A 597 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 601 ASP cc_start: 0.7152 (m-30) cc_final: 0.6846 (m-30) REVERT: A 625 GLU cc_start: 0.6830 (pm20) cc_final: 0.6591 (pm20) REVERT: A 854 MET cc_start: 0.8422 (mmm) cc_final: 0.8100 (mmt) REVERT: A 855 ASP cc_start: 0.7569 (p0) cc_final: 0.7214 (p0) REVERT: A 856 LYS cc_start: 0.7977 (mttm) cc_final: 0.7603 (mptt) REVERT: A 863 ARG cc_start: 0.7191 (ttp-110) cc_final: 0.6882 (ttm-80) REVERT: A 915 MET cc_start: 0.5983 (mpp) cc_final: 0.5655 (ttt) REVERT: B 91 GLN cc_start: 0.8283 (mt0) cc_final: 0.8059 (mt0) REVERT: B 100 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7239 (t70) REVERT: B 156 ASP cc_start: 0.7847 (p0) cc_final: 0.7591 (p0) REVERT: B 211 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6612 (t0) REVERT: B 261 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: B 307 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7612 (ptt-90) REVERT: B 336 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7048 (tm-30) REVERT: C 21 MET cc_start: 0.8234 (mmm) cc_final: 0.7510 (mmm) REVERT: C 295 LEU cc_start: 0.8178 (mm) cc_final: 0.7868 (mt) REVERT: C 329 MET cc_start: 0.6499 (tpp) cc_final: 0.6162 (mpp) outliers start: 40 outliers final: 29 residues processed: 314 average time/residue: 0.2945 time to fit residues: 122.9563 Evaluate side-chains 314 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 112 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10627 Z= 0.256 Angle : 0.667 12.680 14352 Z= 0.329 Chirality : 0.044 0.382 1534 Planarity : 0.004 0.049 1862 Dihedral : 4.259 23.009 1408 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.15 % Allowed : 28.98 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.38 (0.20), residues: 671 sheet: -0.05 (0.63), residues: 74 loop : -0.73 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 206 HIS 0.005 0.001 HIS C 297 PHE 0.027 0.002 PHE A 362 TYR 0.036 0.002 TYR B 16 ARG 0.009 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 307 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6839 (mmm160) cc_final: 0.6188 (mmp-170) REVERT: A 402 ARG cc_start: 0.7456 (ptp-170) cc_final: 0.7167 (ptp-170) REVERT: A 428 TRP cc_start: 0.8617 (m100) cc_final: 0.8111 (m100) REVERT: A 456 GLU cc_start: 0.7789 (tp30) cc_final: 0.7537 (tp30) REVERT: A 457 ASP cc_start: 0.7554 (m-30) cc_final: 0.6939 (m-30) REVERT: A 458 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 463 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7197 (t0) REVERT: A 470 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 475 VAL cc_start: 0.8416 (t) cc_final: 0.8068 (p) REVERT: A 491 GLN cc_start: 0.6426 (mm-40) cc_final: 0.6177 (mm-40) REVERT: A 505 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 546 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 597 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 601 ASP cc_start: 0.7250 (m-30) cc_final: 0.6953 (m-30) REVERT: A 625 GLU cc_start: 0.6913 (pm20) cc_final: 0.6552 (pm20) REVERT: A 743 PHE cc_start: 0.8175 (t80) cc_final: 0.7961 (t80) REVERT: A 822 MET cc_start: 0.7671 (ttm) cc_final: 0.7434 (ttm) REVERT: A 842 GLU cc_start: 0.7831 (pp20) cc_final: 0.7518 (tm-30) REVERT: A 854 MET cc_start: 0.8448 (mmm) cc_final: 0.8175 (mmt) REVERT: A 855 ASP cc_start: 0.7639 (p0) cc_final: 0.7196 (p0) REVERT: A 856 LYS cc_start: 0.8038 (mttm) cc_final: 0.7591 (mptt) REVERT: A 863 ARG cc_start: 0.7309 (ttp-110) cc_final: 0.7011 (ttm-80) REVERT: A 915 MET cc_start: 0.6182 (mpp) cc_final: 0.5763 (ttt) REVERT: A 922 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7480 (tptm) REVERT: A 926 LEU cc_start: 0.8556 (pp) cc_final: 0.8329 (pp) REVERT: B 91 GLN cc_start: 0.8252 (mt0) cc_final: 0.8024 (mt0) REVERT: B 100 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7282 (t70) REVERT: B 156 ASP cc_start: 0.7856 (p0) cc_final: 0.7588 (p0) REVERT: B 211 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6816 (t0) REVERT: B 248 LYS cc_start: 0.7453 (tppt) cc_final: 0.7184 (tppt) REVERT: B 294 LEU cc_start: 0.8512 (mp) cc_final: 0.8292 (mt) REVERT: B 307 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7490 (ptt-90) REVERT: B 336 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7165 (tm-30) REVERT: B 360 MET cc_start: 0.8067 (mmt) cc_final: 0.7616 (tpp) REVERT: B 372 ARG cc_start: 0.7348 (mmt180) cc_final: 0.6864 (mmt180) REVERT: C 21 MET cc_start: 0.8259 (mmm) cc_final: 0.7521 (mmm) REVERT: C 295 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7958 (mt) REVERT: C 329 MET cc_start: 0.6624 (tpp) cc_final: 0.6260 (mpp) outliers start: 47 outliers final: 29 residues processed: 329 average time/residue: 0.2659 time to fit residues: 117.0560 Evaluate side-chains 325 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10627 Z= 0.241 Angle : 0.675 12.605 14352 Z= 0.332 Chirality : 0.044 0.371 1534 Planarity : 0.004 0.050 1862 Dihedral : 4.259 22.904 1408 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.06 % Allowed : 28.71 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.63 (0.24), residues: 1260 helix: 1.37 (0.20), residues: 670 sheet: -0.06 (0.63), residues: 74 loop : -0.73 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.004 0.001 HIS C 297 PHE 0.017 0.002 PHE A 743 TYR 0.039 0.002 TYR B 16 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 298 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6769 (mmm160) cc_final: 0.6442 (mmp-170) REVERT: A 402 ARG cc_start: 0.7469 (ptp-170) cc_final: 0.7181 (ptp-170) REVERT: A 428 TRP cc_start: 0.8613 (m100) cc_final: 0.8131 (m100) REVERT: A 449 GLU cc_start: 0.7936 (tt0) cc_final: 0.7587 (tt0) REVERT: A 456 GLU cc_start: 0.7755 (tp30) cc_final: 0.7505 (tp30) REVERT: A 457 ASP cc_start: 0.7535 (m-30) cc_final: 0.6861 (m-30) REVERT: A 458 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 463 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7205 (t0) REVERT: A 470 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 475 VAL cc_start: 0.8439 (t) cc_final: 0.8104 (p) REVERT: A 505 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7665 (mt-10) REVERT: A 522 GLU cc_start: 0.7499 (mp0) cc_final: 0.7127 (mp0) REVERT: A 546 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 581 GLN cc_start: 0.7705 (mp10) cc_final: 0.7446 (mp10) REVERT: A 597 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 601 ASP cc_start: 0.7361 (m-30) cc_final: 0.7054 (m-30) REVERT: A 625 GLU cc_start: 0.6925 (pm20) cc_final: 0.6568 (pm20) REVERT: A 743 PHE cc_start: 0.8165 (t80) cc_final: 0.7949 (t80) REVERT: A 842 GLU cc_start: 0.7855 (pp20) cc_final: 0.7540 (tm-30) REVERT: A 854 MET cc_start: 0.8494 (mmm) cc_final: 0.8272 (mmt) REVERT: A 856 LYS cc_start: 0.8001 (mttm) cc_final: 0.7780 (mptt) REVERT: A 863 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.7036 (ttm-80) REVERT: A 915 MET cc_start: 0.6332 (mpp) cc_final: 0.5863 (ttt) REVERT: A 922 LYS cc_start: 0.7908 (tmmt) cc_final: 0.7295 (tmmt) REVERT: A 926 LEU cc_start: 0.8557 (pp) cc_final: 0.8262 (pp) REVERT: A 928 ARG cc_start: 0.6746 (ptm160) cc_final: 0.6542 (ptm160) REVERT: B 73 TYR cc_start: 0.8080 (t80) cc_final: 0.7735 (t80) REVERT: B 91 GLN cc_start: 0.8248 (mt0) cc_final: 0.8023 (mt0) REVERT: B 100 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7282 (t70) REVERT: B 127 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7243 (mtp85) REVERT: B 211 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6868 (t0) REVERT: B 248 LYS cc_start: 0.7588 (tppt) cc_final: 0.7207 (tppt) REVERT: B 261 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 294 LEU cc_start: 0.8546 (mp) cc_final: 0.8278 (mt) REVERT: B 307 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7633 (ptt-90) REVERT: B 336 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7097 (tm-30) REVERT: B 360 MET cc_start: 0.8077 (mmt) cc_final: 0.7723 (tpp) REVERT: B 372 ARG cc_start: 0.7410 (mmt180) cc_final: 0.6398 (mmt180) REVERT: C 21 MET cc_start: 0.8251 (mmm) cc_final: 0.7524 (mmm) REVERT: C 295 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7956 (mt) REVERT: C 308 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6223 (mmp) REVERT: C 329 MET cc_start: 0.6640 (tpp) cc_final: 0.6275 (mpp) outliers start: 46 outliers final: 28 residues processed: 321 average time/residue: 0.2612 time to fit residues: 112.6656 Evaluate side-chains 329 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 835 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 112 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10627 Z= 0.233 Angle : 0.681 12.752 14352 Z= 0.335 Chirality : 0.044 0.334 1534 Planarity : 0.004 0.048 1862 Dihedral : 4.256 25.943 1408 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.62 % Allowed : 29.51 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1260 helix: 1.27 (0.20), residues: 674 sheet: -0.10 (0.63), residues: 74 loop : -0.79 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 313 HIS 0.005 0.001 HIS B 40 PHE 0.031 0.002 PHE A 362 TYR 0.031 0.002 TYR B 16 ARG 0.008 0.000 ARG A 643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 302 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6936 (mmm160) cc_final: 0.6669 (mmm160) REVERT: A 402 ARG cc_start: 0.7473 (ptp-170) cc_final: 0.7194 (ptp-170) REVERT: A 428 TRP cc_start: 0.8614 (m100) cc_final: 0.8131 (m100) REVERT: A 448 TYR cc_start: 0.7178 (m-80) cc_final: 0.6861 (m-80) REVERT: A 449 GLU cc_start: 0.7934 (tt0) cc_final: 0.7582 (tt0) REVERT: A 457 ASP cc_start: 0.7475 (m-30) cc_final: 0.6823 (m-30) REVERT: A 458 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 463 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7183 (t0) REVERT: A 470 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 475 VAL cc_start: 0.8432 (t) cc_final: 0.8097 (p) REVERT: A 483 LEU cc_start: 0.8044 (mp) cc_final: 0.7580 (tt) REVERT: A 491 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6510 (mm-40) REVERT: A 505 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 522 GLU cc_start: 0.7474 (mp0) cc_final: 0.7035 (mp0) REVERT: A 546 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 581 GLN cc_start: 0.7719 (mp10) cc_final: 0.7453 (mp10) REVERT: A 597 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 601 ASP cc_start: 0.7380 (m-30) cc_final: 0.7074 (m-30) REVERT: A 625 GLU cc_start: 0.6899 (pm20) cc_final: 0.5800 (mt-10) REVERT: A 743 PHE cc_start: 0.8150 (t80) cc_final: 0.7948 (t80) REVERT: A 768 ARG cc_start: 0.7391 (mtt90) cc_final: 0.7106 (mtt90) REVERT: A 776 GLU cc_start: 0.7079 (tp30) cc_final: 0.6628 (tp30) REVERT: A 842 GLU cc_start: 0.7825 (pp20) cc_final: 0.7523 (tm-30) REVERT: A 854 MET cc_start: 0.8551 (mmm) cc_final: 0.8323 (mmt) REVERT: A 856 LYS cc_start: 0.8049 (mttm) cc_final: 0.7801 (mptt) REVERT: A 863 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.7079 (ttm-80) REVERT: A 915 MET cc_start: 0.6411 (mpp) cc_final: 0.5809 (ttt) REVERT: A 922 LYS cc_start: 0.7873 (tmmt) cc_final: 0.7232 (tmmt) REVERT: A 926 LEU cc_start: 0.8562 (pp) cc_final: 0.8251 (pp) REVERT: A 928 ARG cc_start: 0.6750 (ptm160) cc_final: 0.6537 (ptm160) REVERT: B 91 GLN cc_start: 0.8245 (mt0) cc_final: 0.8029 (mt0) REVERT: B 100 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7236 (t70) REVERT: B 211 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6863 (t0) REVERT: B 253 TYR cc_start: 0.8009 (t80) cc_final: 0.7801 (t80) REVERT: B 261 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: B 307 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7624 (ptt-90) REVERT: B 360 MET cc_start: 0.8052 (mmt) cc_final: 0.7593 (tpp) REVERT: B 366 ARG cc_start: 0.7490 (ttt-90) cc_final: 0.7233 (ttt180) REVERT: B 372 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7115 (mmt180) REVERT: C 21 MET cc_start: 0.8237 (mmm) cc_final: 0.7528 (mmm) REVERT: C 295 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7886 (mt) REVERT: C 316 PRO cc_start: 0.8634 (Cg_endo) cc_final: 0.8340 (Cg_exo) REVERT: C 329 MET cc_start: 0.6650 (tpp) cc_final: 0.6292 (mpp) outliers start: 41 outliers final: 30 residues processed: 320 average time/residue: 0.2632 time to fit residues: 113.6795 Evaluate side-chains 331 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 294 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 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 = 0.4157 r_free = 0.4157 target = 0.169216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140960 restraints weight = 16003.692| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.54 r_work: 0.3656 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10627 Z= 0.217 Angle : 0.688 12.781 14352 Z= 0.335 Chirality : 0.044 0.341 1534 Planarity : 0.004 0.051 1862 Dihedral : 4.218 22.662 1408 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.18 % Allowed : 30.30 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.51 (0.24), residues: 1260 helix: 1.28 (0.20), residues: 676 sheet: -0.17 (0.62), residues: 74 loop : -0.82 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 313 HIS 0.007 0.001 HIS B 40 PHE 0.017 0.002 PHE A 743 TYR 0.028 0.002 TYR B 16 ARG 0.007 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.43 seconds wall clock time: 53 minutes 25.58 seconds (3205.58 seconds total)