Starting phenix.real_space_refine on Fri Jul 3 00:19:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2026/7ydi_33748.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1490 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6144 2.51 5 N 1602 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1530 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 182} Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.83, per 1000 atoms: 0.19 Number of scatterers: 9675 At special positions: 0 Unit cell: (108.416, 160.512, 95.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1878 8.00 N 1602 7.00 C 6144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 53 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 281.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 35.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 83 removed outlier: 3.802A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.726A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.750A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.975A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.535A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.800A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.902A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.582A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.667A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.852A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.039A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.512A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.206A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.736A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.676A pdb=" N ASP A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.594A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 127 through 133 removed outlier: 3.717A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.091A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.571A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.177A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 361 through 362 removed outlier: 7.476A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.511A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.520A pdb=" N GLU H 10 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.548A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS H 151 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.743A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER H 164 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN H 208 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL H 209 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 218 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 216 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.980A pdb=" N ALA L 86 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L 87 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN L 40 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.980A pdb=" N ALA L 86 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 23 Processing sheet with id=AB5, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.176A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 141 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 179 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP L 143 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.646A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1071 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: 1.28 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3101 1.35 - 1.46: 2498 1.46 - 1.58: 4259 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9931 Sorted by residual: bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C GLU H 159 " pdb=" N PRO H 160 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CB GLN H 65 " pdb=" CG GLN H 65 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 ... (remaining 9926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 13284 2.32 - 4.65: 183 4.65 - 6.97: 36 6.97 - 9.29: 13 9.29 - 11.62: 3 Bond angle restraints: 13519 Sorted by residual: angle pdb=" CB MET A 557 " pdb=" CG MET A 557 " pdb=" SD MET A 557 " ideal model delta sigma weight residual 112.70 124.32 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA GLU A 110 " pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET A 82 " pdb=" CB MET A 82 " pdb=" CG MET A 82 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET A 332 " pdb=" CG MET A 332 " pdb=" SD MET A 332 " ideal model delta sigma weight residual 112.70 123.39 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB LYS E 458 " pdb=" CG LYS E 458 " pdb=" CD LYS E 458 " ideal model delta sigma weight residual 111.30 119.23 -7.93 2.30e+00 1.89e-01 1.19e+01 ... (remaining 13514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5260 17.87 - 35.74: 448 35.74 - 53.61: 122 53.61 - 71.47: 18 71.47 - 89.34: 9 Dihedral angle restraints: 5857 sinusoidal: 2281 harmonic: 3576 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 198 " pdb=" CB CYS L 198 " ideal model delta sinusoidal sigma weight residual 93.00 139.36 -46.36 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -47.98 -38.02 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CA ILE H 51 " pdb=" C ILE H 51 " pdb=" N ILE H 52 " pdb=" CA ILE H 52 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1310 0.073 - 0.145: 155 0.145 - 0.218: 3 0.218 - 0.290: 1 0.290 - 0.363: 1 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB THR A 334 " pdb=" CA THR A 334 " pdb=" OG1 THR A 334 " pdb=" CG2 THR A 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 1467 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " 0.022 2.00e-02 2.50e+03 4.38e-02 1.91e+01 pdb=" C GLY L 112 " -0.076 2.00e-02 2.50e+03 pdb=" O GLY L 112 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN L 113 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 159 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO H 160 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 160 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 110 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" CD GLU A 110 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU A 110 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 110 " 0.014 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 61 2.53 - 3.12: 6859 3.12 - 3.72: 15478 3.72 - 4.31: 20678 4.31 - 4.90: 34224 Nonbonded interactions: 77300 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 1.938 2.230 nonbonded pdb=" OE1 GLU H 6 " pdb=" N GLY H 117 " model vdw 2.086 3.120 nonbonded pdb=" O TYR A 515 " pdb=" OG1 THR A 519 " model vdw 2.288 3.040 nonbonded pdb=" O LYS A 114 " pdb=" OG1 THR A 118 " model vdw 2.310 3.040 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.316 3.040 ... (remaining 77295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9949 Z= 0.154 Angle : 0.701 11.618 13555 Z= 0.346 Chirality : 0.045 0.363 1470 Planarity : 0.005 0.057 1744 Dihedral : 14.654 89.344 3537 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.67 % Allowed : 20.53 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1223 helix: 0.22 (0.25), residues: 403 sheet: -0.29 (0.38), residues: 186 loop : -1.09 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 346 TYR 0.023 0.001 TYR H 32 PHE 0.014 0.001 PHE E 486 TRP 0.015 0.001 TRP H 47 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9931) covalent geometry : angle 0.69839 / 0.35 (13519) SS BOND : bond 0.00094 / 0.07 ( 12) SS BOND : angle 0.56956 / 0.32 ( 24) hydrogen bonds : bond 0.17796 / 11.60 ( 378) hydrogen bonds : angle 7.02040 / 4.87 ( 1071) metal coordination : bond 0.00064 / 0.03 ( 2) link_NAG-ASN : bond 0.00256 / 0.12 ( 4) link_NAG-ASN : angle 2.19484 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7813 (t80) cc_final: 0.7459 (t80) REVERT: A 45 LEU cc_start: 0.7500 (tp) cc_final: 0.7258 (mt) REVERT: A 49 ASN cc_start: 0.7790 (m-40) cc_final: 0.7234 (m-40) REVERT: A 90 ASN cc_start: 0.5282 (OUTLIER) cc_final: 0.4943 (t0) REVERT: A 121 ASN cc_start: 0.8153 (m-40) cc_final: 0.7819 (m-40) REVERT: A 150 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6657 (mm-30) REVERT: A 198 ASP cc_start: 0.7134 (p0) cc_final: 0.6916 (p0) REVERT: A 213 ASP cc_start: 0.7902 (p0) cc_final: 0.7583 (m-30) REVERT: A 245 ARG cc_start: 0.5956 (ttp-170) cc_final: 0.5477 (ttp80) REVERT: A 323 MET cc_start: 0.8302 (mmm) cc_final: 0.7989 (mmm) REVERT: A 328 TRP cc_start: 0.7696 (m100) cc_final: 0.6868 (m100) REVERT: A 330 ASN cc_start: 0.8205 (t0) cc_final: 0.7969 (t0) REVERT: A 355 ASP cc_start: 0.7684 (t0) cc_final: 0.6990 (t0) REVERT: A 390 PHE cc_start: 0.6364 (t80) cc_final: 0.6120 (t80) REVERT: A 434 THR cc_start: 0.4862 (p) cc_final: 0.4263 (t) REVERT: A 435 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5501 (pm20) REVERT: A 462 MET cc_start: 0.6783 (ptp) cc_final: 0.6529 (mpp) REVERT: A 471 ASP cc_start: 0.7606 (t0) cc_final: 0.6176 (p0) REVERT: A 472 GLN cc_start: 0.6912 (mt0) cc_final: 0.6485 (tm-30) REVERT: A 480 MET cc_start: 0.7141 (ptm) cc_final: 0.6506 (ptp) REVERT: A 534 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7536 (mmtt) REVERT: A 546 ASN cc_start: 0.5202 (m-40) cc_final: 0.4490 (t0) REVERT: A 582 ARG cc_start: 0.6646 (mmp80) cc_final: 0.5371 (tpm170) REVERT: E 338 PHE cc_start: 0.6314 (m-80) cc_final: 0.5382 (m-80) REVERT: E 406 GLU cc_start: 0.7264 (mp0) cc_final: 0.6814 (mp0) REVERT: E 424 LYS cc_start: 0.7421 (tttm) cc_final: 0.7190 (tttm) REVERT: E 428 ASP cc_start: 0.8414 (p0) cc_final: 0.8186 (p0) REVERT: E 467 ASP cc_start: 0.8139 (t0) cc_final: 0.7853 (t0) REVERT: H 59 ASN cc_start: 0.8435 (p0) cc_final: 0.8047 (p0) REVERT: H 60 TYR cc_start: 0.8523 (m-80) cc_final: 0.8131 (m-10) REVERT: H 65 GLN cc_start: 0.7363 (pm20) cc_final: 0.6687 (tp40) REVERT: H 90 ASP cc_start: 0.7019 (m-30) cc_final: 0.6706 (t0) REVERT: H 94 TYR cc_start: 0.7823 (m-80) cc_final: 0.7604 (m-80) REVERT: H 103 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.6939 (m) REVERT: L 37 TRP cc_start: 0.8188 (m100) cc_final: 0.7884 (m100) REVERT: L 64 PHE cc_start: 0.6393 (m-80) cc_final: 0.5992 (m-80) REVERT: L 87 ASP cc_start: 0.6840 (p0) cc_final: 0.6571 (p0) outliers start: 6 outliers final: 1 residues processed: 283 average time/residue: 0.0800 time to fit residues: 31.6037 Evaluate side-chains 178 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain H residue 103 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN A 81 GLN A 101 GLN A 330 ASN E 394 ASN E 409 GLN E 437 ASN E 506 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182235 restraints weight = 21736.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169819 restraints weight = 39534.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167569 restraints weight = 34774.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168049 restraints weight = 34423.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168394 restraints weight = 23600.749| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9949 Z= 0.149 Angle : 0.624 8.243 13555 Z= 0.314 Chirality : 0.044 0.174 1470 Planarity : 0.004 0.051 1744 Dihedral : 4.223 57.134 1334 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.37 % Allowed : 18.73 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1223 helix: 0.48 (0.26), residues: 414 sheet: 0.27 (0.36), residues: 201 loop : -0.97 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 357 TYR 0.015 0.001 TYR A 510 PHE 0.016 0.002 PHE A 504 TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9931) covalent geometry : angle 0.62080 / 0.31 (13519) SS BOND : bond 0.00330 / 0.22 ( 12) SS BOND : angle 1.09409 / 0.76 ( 24) hydrogen bonds : bond 0.03972 / 2.62 ( 378) hydrogen bonds : angle 4.86770 / 3.40 ( 1071) metal coordination : bond 0.00467 / 0.23 ( 2) link_NAG-ASN : bond 0.00311 / 0.15 ( 4) link_NAG-ASN : angle 1.71171 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.7516 (m-40) cc_final: 0.6913 (m-40) REVERT: A 117 ASN cc_start: 0.7911 (p0) cc_final: 0.7410 (p0) REVERT: A 279 TYR cc_start: 0.7356 (t80) cc_final: 0.7138 (t80) REVERT: A 328 TRP cc_start: 0.8006 (m100) cc_final: 0.6833 (m100) REVERT: A 355 ASP cc_start: 0.8288 (t0) cc_final: 0.7370 (t0) REVERT: A 359 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7249 (mm) REVERT: A 434 THR cc_start: 0.5491 (p) cc_final: 0.5218 (t) REVERT: A 480 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7692 (ptp) REVERT: A 582 ARG cc_start: 0.6810 (mmp80) cc_final: 0.6507 (tpm170) REVERT: E 406 GLU cc_start: 0.8061 (mp0) cc_final: 0.7193 (mp0) REVERT: E 418 ILE cc_start: 0.7825 (mt) cc_final: 0.7254 (mt) REVERT: E 428 ASP cc_start: 0.7861 (p0) cc_final: 0.7649 (p0) REVERT: E 467 ASP cc_start: 0.8849 (t0) cc_final: 0.8389 (t0) REVERT: H 59 ASN cc_start: 0.9014 (p0) cc_final: 0.8556 (p0) REVERT: H 60 TYR cc_start: 0.8688 (m-80) cc_final: 0.8376 (m-10) REVERT: L 19 THR cc_start: 0.7362 (m) cc_final: 0.6530 (p) outliers start: 45 outliers final: 14 residues processed: 219 average time/residue: 0.0751 time to fit residues: 23.9130 Evaluate side-chains 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 353 TRP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 182 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 105 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN E 409 GLN ** E 422 ASN ** 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 = 0.4224 r_free = 0.4224 target = 0.190430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.186832 restraints weight = 20024.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172580 restraints weight = 29450.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170503 restraints weight = 27811.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.170473 restraints weight = 31281.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170795 restraints weight = 26034.119| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9949 Z= 0.123 Angle : 0.616 20.498 13555 Z= 0.302 Chirality : 0.045 0.404 1470 Planarity : 0.004 0.046 1744 Dihedral : 3.878 53.433 1331 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.19 % Allowed : 21.10 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1223 helix: 0.65 (0.27), residues: 414 sheet: 0.34 (0.37), residues: 192 loop : -1.00 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.014 0.001 TYR A 510 PHE 0.026 0.001 PHE H 64 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9931) covalent geometry : angle 0.57666 / 0.29 (13519) SS BOND : bond 0.00399 / 0.25 ( 12) SS BOND : angle 0.88888 / 0.58 ( 24) hydrogen bonds : bond 0.03601 / 2.41 ( 378) hydrogen bonds : angle 4.52123 / 3.17 ( 1071) metal coordination : bond 0.00088 / 0.05 ( 2) link_NAG-ASN : bond 0.02588 / 1.29 ( 4) link_NAG-ASN : angle 7.25102 / 4.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 TRP cc_start: 0.8262 (m100) cc_final: 0.7574 (m100) REVERT: A 330 ASN cc_start: 0.7675 (m-40) cc_final: 0.6932 (m110) REVERT: A 366 MET cc_start: 0.6926 (tpp) cc_final: 0.6416 (mmm) REVERT: A 434 THR cc_start: 0.5662 (p) cc_final: 0.5397 (t) REVERT: A 435 GLU cc_start: 0.7233 (pm20) cc_final: 0.6940 (pm20) REVERT: E 406 GLU cc_start: 0.7988 (mp0) cc_final: 0.7185 (mp0) REVERT: E 467 ASP cc_start: 0.8766 (t0) cc_final: 0.8383 (t0) REVERT: H 59 ASN cc_start: 0.9055 (p0) cc_final: 0.8649 (p0) REVERT: H 60 TYR cc_start: 0.8869 (m-80) cc_final: 0.8520 (m-10) REVERT: L 19 THR cc_start: 0.7168 (m) cc_final: 0.6345 (p) outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 0.0708 time to fit residues: 17.2915 Evaluate side-chains 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 360 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN H 175 HIS L 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158896 restraints weight = 32837.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162841 restraints weight = 40727.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161112 restraints weight = 33924.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161730 restraints weight = 27211.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161687 restraints weight = 22993.988| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9949 Z= 0.152 Angle : 0.649 13.108 13555 Z= 0.319 Chirality : 0.045 0.267 1470 Planarity : 0.004 0.045 1744 Dihedral : 4.110 50.923 1331 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.71 % Allowed : 20.82 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1223 helix: 0.74 (0.26), residues: 406 sheet: 0.27 (0.36), residues: 198 loop : -0.97 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.018 0.001 TYR E 380 PHE 0.023 0.002 PHE A 555 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9931) covalent geometry : angle 0.62796 / 0.31 (13519) SS BOND : bond 0.00700 / 0.53 ( 12) SS BOND : angle 1.45467 / 0.84 ( 24) hydrogen bonds : bond 0.03787 / 2.57 ( 378) hydrogen bonds : angle 4.42466 / 3.13 ( 1071) metal coordination : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : bond 0.00819 / 0.41 ( 4) link_NAG-ASN : angle 5.27889 / 3.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7409 (tmm) cc_final: 0.6955 (tmm) REVERT: A 328 TRP cc_start: 0.8307 (m100) cc_final: 0.7275 (m100) REVERT: A 366 MET cc_start: 0.7216 (tpp) cc_final: 0.6998 (tpp) REVERT: A 434 THR cc_start: 0.6402 (p) cc_final: 0.6147 (t) REVERT: A 435 GLU cc_start: 0.7037 (pm20) cc_final: 0.6789 (pm20) REVERT: A 479 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: E 406 GLU cc_start: 0.8518 (mp0) cc_final: 0.7615 (mp0) REVERT: H 59 ASN cc_start: 0.9241 (p0) cc_final: 0.9018 (p0) REVERT: H 60 TYR cc_start: 0.8949 (m-80) cc_final: 0.8686 (m-10) REVERT: L 19 THR cc_start: 0.7221 (m) cc_final: 0.6552 (p) REVERT: L 107 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8183 (mtpp) outliers start: 38 outliers final: 21 residues processed: 184 average time/residue: 0.0959 time to fit residues: 25.0491 Evaluate side-chains 145 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 119 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157955 restraints weight = 27242.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157571 restraints weight = 31595.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157940 restraints weight = 31418.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.158282 restraints weight = 25887.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158450 restraints weight = 25504.785| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9949 Z= 0.140 Angle : 0.612 9.393 13555 Z= 0.307 Chirality : 0.044 0.213 1470 Planarity : 0.004 0.041 1744 Dihedral : 4.155 51.684 1331 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.80 % Allowed : 20.91 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1223 helix: 0.79 (0.27), residues: 406 sheet: 0.25 (0.36), residues: 198 loop : -0.95 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 357 TYR 0.022 0.001 TYR A 279 PHE 0.013 0.001 PHE A 428 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9931) covalent geometry : angle 0.60601 / 0.31 (13519) SS BOND : bond 0.00559 / 0.40 ( 12) SS BOND : angle 1.09069 / 0.69 ( 24) hydrogen bonds : bond 0.03584 / 2.42 ( 378) hydrogen bonds : angle 4.41400 / 3.12 ( 1071) metal coordination : bond 0.00054 / 0.03 ( 2) link_NAG-ASN : bond 0.00338 / 0.17 ( 4) link_NAG-ASN : angle 2.72309 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7368 (tmm) cc_final: 0.7021 (tmm) REVERT: A 310 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 328 TRP cc_start: 0.8273 (m100) cc_final: 0.7916 (m100) REVERT: A 330 ASN cc_start: 0.8096 (m-40) cc_final: 0.7328 (m-40) REVERT: A 434 THR cc_start: 0.7011 (p) cc_final: 0.6689 (t) REVERT: A 435 GLU cc_start: 0.6844 (pm20) cc_final: 0.6589 (pm20) REVERT: A 479 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: E 406 GLU cc_start: 0.8610 (mp0) cc_final: 0.7648 (mp0) REVERT: H 60 TYR cc_start: 0.8930 (m-80) cc_final: 0.8657 (m-10) REVERT: L 19 THR cc_start: 0.7641 (m) cc_final: 0.6980 (p) REVERT: L 107 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8116 (mtpp) outliers start: 39 outliers final: 27 residues processed: 165 average time/residue: 0.0848 time to fit residues: 20.2890 Evaluate side-chains 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN E 370 ASN E 394 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149782 restraints weight = 26114.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151433 restraints weight = 32583.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150860 restraints weight = 30603.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150862 restraints weight = 26068.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150940 restraints weight = 23531.367| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9949 Z= 0.159 Angle : 0.634 7.128 13555 Z= 0.318 Chirality : 0.045 0.199 1470 Planarity : 0.004 0.048 1744 Dihedral : 4.299 50.392 1331 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.61 % Allowed : 21.10 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1223 helix: 0.71 (0.26), residues: 408 sheet: 0.25 (0.38), residues: 184 loop : -0.98 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.018 0.002 TYR H 205 PHE 0.021 0.002 PHE A 555 TRP 0.012 0.002 TRP H 165 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9931) covalent geometry : angle 0.62823 / 0.32 (13519) SS BOND : bond 0.00476 / 0.34 ( 12) SS BOND : angle 1.08157 / 0.71 ( 24) hydrogen bonds : bond 0.03788 / 2.57 ( 378) hydrogen bonds : angle 4.47817 / 3.18 ( 1071) metal coordination : bond 0.00064 / 0.03 ( 2) link_NAG-ASN : bond 0.00441 / 0.21 ( 4) link_NAG-ASN : angle 2.53836 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.7610 (t80) cc_final: 0.7052 (t80) REVERT: A 330 ASN cc_start: 0.8060 (m-40) cc_final: 0.7275 (m110) REVERT: A 434 THR cc_start: 0.7880 (p) cc_final: 0.7315 (t) REVERT: A 435 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: A 479 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: E 406 GLU cc_start: 0.8747 (mp0) cc_final: 0.7666 (mp0) REVERT: H 29 PHE cc_start: 0.7160 (t80) cc_final: 0.6776 (t80) REVERT: H 60 TYR cc_start: 0.9008 (m-80) cc_final: 0.8752 (m-10) REVERT: L 107 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8087 (mtpp) outliers start: 37 outliers final: 26 residues processed: 164 average time/residue: 0.0822 time to fit residues: 19.5746 Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 104 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.154547 restraints weight = 21460.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153131 restraints weight = 47542.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153566 restraints weight = 35090.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153956 restraints weight = 24210.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153802 restraints weight = 22916.801| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9949 Z= 0.127 Angle : 0.611 12.851 13555 Z= 0.305 Chirality : 0.044 0.200 1470 Planarity : 0.003 0.030 1744 Dihedral : 4.171 49.723 1331 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.42 % Allowed : 22.34 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1223 helix: 0.74 (0.26), residues: 408 sheet: 0.29 (0.38), residues: 184 loop : -0.93 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.011 0.001 TYR A 41 PHE 0.015 0.001 PHE A 428 TRP 0.010 0.001 TRP A 459 HIS 0.005 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9931) covalent geometry : angle 0.60670 / 0.30 (13519) SS BOND : bond 0.00388 / 0.29 ( 12) SS BOND : angle 0.94509 / 0.64 ( 24) hydrogen bonds : bond 0.03604 / 2.44 ( 378) hydrogen bonds : angle 4.45223 / 3.14 ( 1071) metal coordination : bond 0.00035 / 0.02 ( 2) link_NAG-ASN : bond 0.00435 / 0.21 ( 4) link_NAG-ASN : angle 2.35225 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.7779 (t80) cc_final: 0.7385 (t80) REVERT: A 330 ASN cc_start: 0.7975 (m-40) cc_final: 0.7049 (m-40) REVERT: A 434 THR cc_start: 0.7840 (p) cc_final: 0.7299 (t) REVERT: A 435 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: A 479 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: E 406 GLU cc_start: 0.8725 (mp0) cc_final: 0.7715 (mp0) REVERT: H 60 TYR cc_start: 0.8982 (m-80) cc_final: 0.8721 (m-10) REVERT: L 64 PHE cc_start: 0.7890 (m-80) cc_final: 0.7670 (m-80) REVERT: L 107 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8110 (mtpp) outliers start: 35 outliers final: 27 residues processed: 159 average time/residue: 0.0777 time to fit residues: 18.1400 Evaluate side-chains 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 chunk 64 optimal weight: 0.0170 chunk 68 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN ** E 487 ASN ** 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 = 0.4007 r_free = 0.4007 target = 0.171053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150881 restraints weight = 25845.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150059 restraints weight = 31200.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150071 restraints weight = 30933.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150339 restraints weight = 28013.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150824 restraints weight = 24917.823| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9949 Z= 0.121 Angle : 0.608 11.118 13555 Z= 0.304 Chirality : 0.043 0.187 1470 Planarity : 0.003 0.034 1744 Dihedral : 4.059 49.138 1331 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.61 % Allowed : 22.34 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1223 helix: 0.68 (0.26), residues: 415 sheet: 0.38 (0.38), residues: 182 loop : -0.88 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 357 TYR 0.011 0.001 TYR A 510 PHE 0.033 0.002 PHE E 486 TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9931) covalent geometry : angle 0.60443 / 0.30 (13519) SS BOND : bond 0.00351 / 0.26 ( 12) SS BOND : angle 0.88822 / 0.60 ( 24) hydrogen bonds : bond 0.03535 / 2.40 ( 378) hydrogen bonds : angle 4.40885 / 3.11 ( 1071) metal coordination : bond 0.00038 / 0.02 ( 2) link_NAG-ASN : bond 0.00458 / 0.22 ( 4) link_NAG-ASN : angle 2.24225 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9132 (mmm) cc_final: 0.8766 (mmp) REVERT: A 347 THR cc_start: 0.6568 (m) cc_final: 0.6295 (m) REVERT: A 434 THR cc_start: 0.8328 (p) cc_final: 0.7947 (t) REVERT: A 435 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6669 (pm20) REVERT: A 479 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: A 526 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7964 (tp40) REVERT: A 582 ARG cc_start: 0.7539 (tpm170) cc_final: 0.7259 (tpm170) REVERT: E 406 GLU cc_start: 0.8675 (mp0) cc_final: 0.7692 (mp0) REVERT: H 29 PHE cc_start: 0.7112 (t80) cc_final: 0.6731 (t80) REVERT: H 60 TYR cc_start: 0.8967 (m-80) cc_final: 0.8730 (m-10) REVERT: L 64 PHE cc_start: 0.7916 (m-80) cc_final: 0.7625 (m-80) outliers start: 37 outliers final: 30 residues processed: 161 average time/residue: 0.0774 time to fit residues: 18.3981 Evaluate side-chains 151 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 63 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 chunk 120 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166978 restraints weight = 14907.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151526 restraints weight = 26332.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151347 restraints weight = 30354.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151389 restraints weight = 24280.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151440 restraints weight = 22445.253| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9949 Z= 0.113 Angle : 0.592 8.327 13555 Z= 0.298 Chirality : 0.043 0.173 1470 Planarity : 0.003 0.031 1744 Dihedral : 4.069 50.592 1331 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.04 % Allowed : 23.10 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1223 helix: 0.78 (0.26), residues: 415 sheet: 0.47 (0.38), residues: 182 loop : -0.90 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 357 TYR 0.020 0.001 TYR A 279 PHE 0.027 0.001 PHE E 486 TRP 0.015 0.001 TRP A 478 HIS 0.007 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9931) covalent geometry : angle 0.58847 / 0.30 (13519) SS BOND : bond 0.00416 / 0.29 ( 12) SS BOND : angle 0.91866 / 0.62 ( 24) hydrogen bonds : bond 0.03469 / 2.34 ( 378) hydrogen bonds : angle 4.31039 / 3.03 ( 1071) metal coordination : bond 0.00068 / 0.04 ( 2) link_NAG-ASN : bond 0.00511 / 0.25 ( 4) link_NAG-ASN : angle 2.16146 / 1.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 TRP cc_start: 0.8012 (m100) cc_final: 0.7800 (m100) REVERT: A 347 THR cc_start: 0.6544 (m) cc_final: 0.6329 (m) REVERT: A 434 THR cc_start: 0.8264 (p) cc_final: 0.7858 (t) REVERT: A 435 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: A 479 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: E 406 GLU cc_start: 0.8536 (mp0) cc_final: 0.7633 (mp0) REVERT: H 60 TYR cc_start: 0.8920 (m-80) cc_final: 0.8678 (m-10) REVERT: L 64 PHE cc_start: 0.7867 (m-80) cc_final: 0.7580 (m-80) outliers start: 31 outliers final: 27 residues processed: 142 average time/residue: 0.0887 time to fit residues: 18.5645 Evaluate side-chains 141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 182 TYR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.168711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.162942 restraints weight = 19471.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151945 restraints weight = 35823.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148947 restraints weight = 33169.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148295 restraints weight = 29190.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148564 restraints weight = 26479.977| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9949 Z= 0.145 Angle : 0.631 8.116 13555 Z= 0.316 Chirality : 0.044 0.162 1470 Planarity : 0.004 0.034 1744 Dihedral : 4.196 49.133 1331 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.52 % Allowed : 23.19 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1223 helix: 0.80 (0.26), residues: 413 sheet: 0.31 (0.38), residues: 182 loop : -0.91 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 357 TYR 0.018 0.001 TYR A 510 PHE 0.027 0.002 PHE E 486 TRP 0.016 0.001 TRP H 47 HIS 0.007 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 9931) covalent geometry : angle 0.62661 / 0.31 (13519) SS BOND : bond 0.00427 / 0.29 ( 12) SS BOND : angle 1.12077 / 0.75 ( 24) hydrogen bonds : bond 0.03734 / 2.52 ( 378) hydrogen bonds : angle 4.44248 / 3.14 ( 1071) metal coordination : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : bond 0.00431 / 0.21 ( 4) link_NAG-ASN : angle 2.18912 / 1.35 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.7573 (t80) cc_final: 0.7023 (t80) REVERT: A 347 THR cc_start: 0.6987 (m) cc_final: 0.6783 (m) REVERT: A 434 THR cc_start: 0.8365 (p) cc_final: 0.7991 (t) REVERT: A 435 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: A 479 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: A 526 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8293 (tp40) REVERT: A 582 ARG cc_start: 0.7685 (tpm170) cc_final: 0.7454 (tpm170) REVERT: E 406 GLU cc_start: 0.8662 (mp0) cc_final: 0.7700 (mp0) REVERT: H 29 PHE cc_start: 0.7155 (t80) cc_final: 0.6813 (t80) REVERT: H 60 TYR cc_start: 0.9003 (m-80) cc_final: 0.8744 (m-10) REVERT: L 107 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8153 (mtpp) outliers start: 36 outliers final: 30 residues processed: 143 average time/residue: 0.0783 time to fit residues: 16.3273 Evaluate side-chains 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 182 TYR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149017 restraints weight = 29173.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149608 restraints weight = 45172.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149001 restraints weight = 33935.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149420 restraints weight = 30437.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149551 restraints weight = 25807.060| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9949 Z= 0.158 Angle : 0.649 8.147 13555 Z= 0.326 Chirality : 0.045 0.158 1470 Planarity : 0.004 0.034 1744 Dihedral : 4.214 49.021 1331 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.33 % Allowed : 23.48 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1223 helix: 0.70 (0.26), residues: 416 sheet: 0.38 (0.38), residues: 185 loop : -0.90 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 357 TYR 0.016 0.001 TYR H 205 PHE 0.026 0.002 PHE E 486 TRP 0.014 0.001 TRP H 47 HIS 0.007 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9931) covalent geometry : angle 0.64444 / 0.32 (13519) SS BOND : bond 0.00394 / 0.27 ( 12) SS BOND : angle 1.36540 / 0.92 ( 24) hydrogen bonds : bond 0.03845 / 2.63 ( 378) hydrogen bonds : angle 4.51484 / 3.20 ( 1071) metal coordination : bond 0.00114 / 0.06 ( 2) link_NAG-ASN : bond 0.00396 / 0.19 ( 4) link_NAG-ASN : angle 2.04979 / 1.25 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1504.84 seconds wall clock time: 26 minutes 52.21 seconds (1612.21 seconds total)