Starting phenix.real_space_refine on Wed Sep 17 21:33:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mt6_48601/09_2025/9mt6_48601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mt6_48601/09_2025/9mt6_48601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mt6_48601/09_2025/9mt6_48601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mt6_48601/09_2025/9mt6_48601.map" model { file = "/net/cci-nas-00/data/ceres_data/9mt6_48601/09_2025/9mt6_48601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mt6_48601/09_2025/9mt6_48601.cif" } resolution = 3.0 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 87 5.16 5 C 7238 2.51 5 N 1876 2.21 5 O 2036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11243 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1526 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 11, 'TRANS': 176} Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "I" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1526 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 11, 'TRANS': 176} Chain: "H" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1526 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 11, 'TRANS': 176} Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 196} Chain breaks: 1 Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' ZN': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' ZN': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1955 SG CYS D 57 20.217 25.911 135.538 1.00 83.03 S ATOM 3903 SG CYS I 467 16.961 27.856 135.784 1.00158.49 S ATOM 3920 SG CYS I 469 17.039 24.139 136.642 1.00158.33 S ATOM 3816 SG CYS I 455 28.561 34.187 137.017 1.00150.27 S ATOM 2384 SG CYS G 57 71.551 30.739 135.239 1.00 83.35 S ATOM 8629 SG CYS C 467 71.801 26.947 135.250 1.00172.43 S ATOM 8646 SG CYS C 469 74.560 28.938 136.769 1.00160.19 S ATOM 8542 SG CYS C 455 60.103 33.683 136.906 1.00139.09 S ATOM 10303 SG CYS F 467 44.129 75.139 135.154 1.00177.44 S ATOM 10320 SG CYS F 469 41.133 76.248 137.280 1.00169.29 S ATOM 10887 SG CYS A 57 41.059 72.925 135.440 1.00 85.03 S ATOM 10216 SG CYS F 455 44.052 61.340 136.919 1.00172.35 S Time building chain proxies: 3.15, per 1000 atoms: 0.28 Number of scatterers: 11243 At special positions: 0 Unit cell: (87.98, 87.15, 149.4, 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 6 29.99 S 87 16.00 O 2036 8.00 N 1876 7.00 C 7238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 226 " distance=2.02 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS I 271 " - pdb=" SG CYS I 284 " distance=2.03 Simple disulfide: pdb=" SG CYS I 293 " - pdb=" SG CYS I 302 " distance=2.03 Simple disulfide: pdb=" SG CYS I 356 " - pdb=" SG CYS I 377 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 226 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 207 " - pdb=" SG CYS E 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 226 " distance=2.02 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 207 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS F 271 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 293 " - pdb=" SG CYS F 302 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F 377 " 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 BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG B 501 " - " ASN B 166 " " NAG C 501 " - " ASN C 382 " " NAG E 501 " - " ASN E 166 " " NAG F 501 " - " ASN F 382 " " NAG H 501 " - " ASN H 166 " " NAG I 501 " - " ASN I 382 " " NAG I 502 " - " ASN I 387 " " NAG J 1 " - " ASN B 178 " " NAG K 1 " - " ASN I 357 " " NAG L 1 " - " ASN I 365 " " NAG M 1 " - " ASN E 178 " " NAG N 1 " - " ASN H 178 " " NAG O 1 " - " ASN C 357 " " NAG P 1 " - " ASN C 365 " " NAG Q 1 " - " ASN F 357 " " NAG R 1 " - " ASN F 365 " Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 712.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 459 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 467 " pdb="ZN ZN C 502 " - pdb=" SG CYS G 57 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 469 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 447 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 485 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 449 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 455 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 459 " pdb="ZN ZN F 502 " - pdb=" SG CYS A 57 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 467 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 469 " pdb=" ZN F 503 " pdb="ZN ZN F 503 " - pdb=" NE2 HIS F 447 " pdb="ZN ZN F 503 " - pdb=" NE2 HIS F 485 " pdb="ZN ZN F 503 " - pdb=" NE2 HIS F 449 " pdb="ZN ZN F 503 " - pdb=" SG CYS F 455 " pdb=" ZN I 503 " pdb="ZN ZN I 503 " - pdb=" ND1 HIS I 459 " pdb="ZN ZN I 503 " - pdb=" SG CYS D 57 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 467 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 469 " pdb=" ZN I 504 " pdb="ZN ZN I 504 " - pdb=" NE2 HIS I 447 " pdb="ZN ZN I 504 " - pdb=" NE2 HIS I 485 " pdb="ZN ZN I 504 " - pdb=" NE2 HIS I 449 " pdb="ZN ZN I 504 " - pdb=" SG CYS I 455 " Number of angles added : 18 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 12 sheets defined 47.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.752A pdb=" N LEU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.537A pdb=" N SER B 133 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.595A pdb=" N ILE B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.616A pdb=" N GLN D 9 " --> pdb=" O ILE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 42 Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'G' and resid 3 through 15 Proline residue: G 12 - end of helix Processing helix chain 'G' and resid 17 through 42 Processing helix chain 'G' and resid 42 through 52 Processing helix chain 'I' and resid 273 through 277 Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 291 through 296 removed outlier: 4.173A pdb=" N LEU I 295 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.512A pdb=" N ASP I 303 " --> pdb=" O SER I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 337 Processing helix chain 'I' and resid 338 through 351 Processing helix chain 'I' and resid 391 through 416 Processing helix chain 'I' and resid 419 through 443 Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.699A pdb=" N LEU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 removed outlier: 3.635A pdb=" N TRP E 134 " --> pdb=" O ASP E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 removed outlier: 3.599A pdb=" N ILE E 142 " --> pdb=" O SER E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 Processing helix chain 'E' and resid 230 through 240 Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 128 through 135 removed outlier: 3.573A pdb=" N TRP H 134 " --> pdb=" O ASP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 152 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 185 through 200 Processing helix chain 'H' and resid 230 through 240 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.899A pdb=" N CYS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 Processing helix chain 'C' and resid 332 through 337 removed outlier: 3.566A pdb=" N ILE C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 Processing helix chain 'C' and resid 391 through 416 Processing helix chain 'C' and resid 419 through 443 Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.851A pdb=" N CYS F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 338 through 351 Processing helix chain 'F' and resid 391 through 416 Processing helix chain 'F' and resid 419 through 443 Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.752A pdb=" N GLN A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 17 through 42 Processing helix chain 'A' and resid 42 through 52 Processing sheet with id=AA1, first strand: chain 'B' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.739A pdb=" N LEU B 99 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 101 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 218 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 175 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'I' and resid 376 through 377 Processing sheet with id=AA5, first strand: chain 'I' and resid 380 through 381 Processing sheet with id=AA6, first strand: chain 'I' and resid 447 through 449 removed outlier: 3.692A pdb=" N HIS I 447 " --> pdb=" O ARG I 482 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG I 482 " --> pdb=" O HIS I 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 62 through 63 Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 103 removed outlier: 3.618A pdb=" N ILE E 101 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 106 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN E 218 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 175 " --> pdb=" O ALA E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 93 removed outlier: 3.606A pdb=" N CYS H 92 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 99 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN H 218 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE H 175 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AB2, first strand: chain 'C' and resid 447 through 449 removed outlier: 3.652A pdb=" N ARG C 482 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 449 through 450 529 hydrogen bonds defined for protein. 1458 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: 1.75 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3456 1.34 - 1.46: 2867 1.46 - 1.58: 5088 1.58 - 1.70: 0 1.70 - 1.83: 123 Bond restraints: 11534 Sorted by residual: bond pdb=" CA SER F 338 " pdb=" CB SER F 338 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.26e-02 6.30e+03 1.29e+01 bond pdb=" N ILE C 333 " pdb=" CA ILE C 333 " ideal model delta sigma weight residual 1.461 1.501 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N ILE F 333 " pdb=" CA ILE F 333 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" N ILE I 333 " pdb=" CA ILE I 333 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.91e+00 bond pdb=" N ASN H 83 " pdb=" CA ASN H 83 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 7.97e+00 ... (remaining 11529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15221 1.94 - 3.87: 340 3.87 - 5.81: 49 5.81 - 7.75: 12 7.75 - 9.69: 3 Bond angle restraints: 15625 Sorted by residual: angle pdb=" N LEU C 336 " pdb=" CA LEU C 336 " pdb=" C LEU C 336 " ideal model delta sigma weight residual 113.50 107.02 6.48 1.23e+00 6.61e-01 2.78e+01 angle pdb=" N LEU I 336 " pdb=" CA LEU I 336 " pdb=" CB LEU I 336 " ideal model delta sigma weight residual 110.30 102.48 7.82 1.54e+00 4.22e-01 2.58e+01 angle pdb=" C LYS H 241 " pdb=" CA LYS H 241 " pdb=" CB LYS H 241 " ideal model delta sigma weight residual 117.23 110.46 6.77 1.36e+00 5.41e-01 2.48e+01 angle pdb=" N LEU I 386 " pdb=" CA LEU I 386 " pdb=" CB LEU I 386 " ideal model delta sigma weight residual 110.38 116.63 -6.25 1.37e+00 5.33e-01 2.08e+01 angle pdb=" C LEU H 88 " pdb=" N PRO H 89 " pdb=" CA PRO H 89 " ideal model delta sigma weight residual 119.90 124.45 -4.55 1.02e+00 9.61e-01 1.99e+01 ... (remaining 15620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6573 17.95 - 35.91: 477 35.91 - 53.86: 92 53.86 - 71.82: 19 71.82 - 89.77: 6 Dihedral angle restraints: 7167 sinusoidal: 3237 harmonic: 3930 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 -177.23 -89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 164 " pdb=" CB CYS E 164 " ideal model delta sinusoidal sigma weight residual 93.00 178.10 -85.10 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS H 135 " pdb=" SG CYS H 135 " pdb=" SG CYS H 164 " pdb=" CB CYS H 164 " ideal model delta sinusoidal sigma weight residual 93.00 166.63 -73.63 1 1.00e+01 1.00e-02 6.89e+01 ... (remaining 7164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1410 0.049 - 0.098: 272 0.098 - 0.147: 72 0.147 - 0.196: 15 0.196 - 0.245: 6 Chirality restraints: 1775 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.52e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.51e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.51e+00 ... (remaining 1772 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 502 " 0.306 2.00e-02 2.50e+03 2.63e-01 8.63e+02 pdb=" C7 NAG I 502 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG I 502 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG I 502 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG I 502 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 501 " -0.294 2.00e-02 2.50e+03 2.54e-01 8.04e+02 pdb=" C7 NAG H 501 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG H 501 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG H 501 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG H 501 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 387 " -0.139 2.00e-02 2.50e+03 1.61e-01 3.24e+02 pdb=" CG ASN I 387 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN I 387 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN I 387 " 0.263 2.00e-02 2.50e+03 pdb=" C1 NAG I 502 " -0.195 2.00e-02 2.50e+03 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2408 2.78 - 3.31: 10817 3.31 - 3.84: 18709 3.84 - 4.37: 21396 4.37 - 4.90: 37439 Nonbonded interactions: 90769 Sorted by model distance: nonbonded pdb=" NZ LYS B 193 " pdb=" OD2 ASP B 205 " model vdw 2.254 3.120 nonbonded pdb=" OG1 THR B 182 " pdb=" O GLY B 210 " model vdw 2.267 3.040 nonbonded pdb=" O SER B 133 " pdb=" NH1 ARG B 167 " model vdw 2.287 3.120 nonbonded pdb=" NZ LYS F 346 " pdb=" OE2 GLU F 349 " model vdw 2.305 3.120 nonbonded pdb=" N GLN H 225 " pdb=" OE1 GLN H 225 " model vdw 2.308 3.120 ... (remaining 90764 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'C' and (resid 269 through 501 or resid 503)) selection = (chain 'F' and (resid 269 through 501 or resid 503)) selection = (chain 'I' and (resid 269 through 501 or resid 503)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.280 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11601 Z= 0.228 Angle : 0.735 12.375 15754 Z= 0.392 Chirality : 0.046 0.245 1775 Planarity : 0.010 0.263 1933 Dihedral : 12.625 89.410 4563 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.72 (0.23), residues: 1323 helix: 2.17 (0.21), residues: 546 sheet: -1.52 (0.44), residues: 153 loop : -0.50 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 167 TYR 0.013 0.001 TYR I 358 PHE 0.019 0.002 PHE E 175 TRP 0.031 0.002 TRP C 395 HIS 0.010 0.001 HIS H 86 Details of bonding type rmsd covalent geometry : bond 0.00413 (11534) covalent geometry : angle 0.68553 (15625) SS BOND : bond 0.00342 ( 18) SS BOND : angle 1.00842 ( 36) hydrogen bonds : bond 0.15883 ( 529) hydrogen bonds : angle 6.03021 ( 1458) metal coordination : bond 0.01055 ( 24) metal coordination : angle 2.11974 ( 18) link_BETA1-4 : bond 0.02748 ( 9) link_BETA1-4 : angle 4.35082 ( 27) link_NAG-ASN : bond 0.00243 ( 16) link_NAG-ASN : angle 3.32967 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7738 (tt) cc_final: 0.7200 (mp) REVERT: B 196 MET cc_start: 0.8448 (mmm) cc_final: 0.8015 (mmt) REVERT: D 8 MET cc_start: 0.7618 (mmm) cc_final: 0.7236 (mmm) REVERT: I 411 TYR cc_start: 0.8610 (m-80) cc_final: 0.8355 (m-80) REVERT: I 417 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7906 (ttpp) REVERT: E 76 SER cc_start: 0.8135 (t) cc_final: 0.7923 (t) REVERT: E 107 SER cc_start: 0.8428 (p) cc_final: 0.8214 (p) REVERT: E 167 ARG cc_start: 0.7637 (ttp-170) cc_final: 0.7387 (ttp-170) REVERT: H 98 HIS cc_start: 0.6430 (m90) cc_final: 0.6213 (m-70) REVERT: H 100 TYR cc_start: 0.8224 (m-80) cc_final: 0.7760 (m-80) REVERT: H 196 MET cc_start: 0.8688 (mmm) cc_final: 0.8380 (mmt) REVERT: H 228 LEU cc_start: 0.8456 (tp) cc_final: 0.8159 (tt) REVERT: C 274 GLU cc_start: 0.6430 (mp0) cc_final: 0.6217 (mp0) REVERT: C 351 MET cc_start: 0.8344 (mtt) cc_final: 0.8014 (mtm) REVERT: F 272 LEU cc_start: 0.7593 (mt) cc_final: 0.7252 (mp) REVERT: F 282 MET cc_start: 0.6717 (tpt) cc_final: 0.6339 (tmm) REVERT: A 8 MET cc_start: 0.8006 (tpt) cc_final: 0.7575 (tpt) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.3954 time to fit residues: 82.0824 Evaluate side-chains 162 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 149 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN I 313 ASN E 86 HIS C 331 GLN C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128614 restraints weight = 14186.037| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.93 r_work: 0.3479 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11601 Z= 0.165 Angle : 0.629 9.965 15754 Z= 0.303 Chirality : 0.044 0.298 1775 Planarity : 0.004 0.048 1933 Dihedral : 7.210 59.406 1962 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.82 % Allowed : 6.20 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.84 (0.23), residues: 1323 helix: 2.13 (0.21), residues: 558 sheet: -0.64 (0.41), residues: 159 loop : -0.58 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 167 TYR 0.013 0.001 TYR I 270 PHE 0.030 0.002 PHE B 175 TRP 0.029 0.002 TRP I 395 HIS 0.009 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00380 (11534) covalent geometry : angle 0.59884 (15625) SS BOND : bond 0.00366 ( 18) SS BOND : angle 0.95112 ( 36) hydrogen bonds : bond 0.04513 ( 529) hydrogen bonds : angle 4.67020 ( 1458) metal coordination : bond 0.00826 ( 24) metal coordination : angle 2.20184 ( 18) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 2.33183 ( 27) link_NAG-ASN : bond 0.00347 ( 16) link_NAG-ASN : angle 2.72268 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8163 (m) REVERT: B 94 LEU cc_start: 0.7769 (tt) cc_final: 0.7322 (mp) REVERT: B 102 LYS cc_start: 0.8404 (tttm) cc_final: 0.8128 (ttpp) REVERT: B 155 ASP cc_start: 0.8180 (t0) cc_final: 0.7943 (t0) REVERT: B 159 ASP cc_start: 0.8084 (m-30) cc_final: 0.7749 (m-30) REVERT: B 208 LEU cc_start: 0.8009 (mp) cc_final: 0.7770 (mp) REVERT: B 236 PHE cc_start: 0.8423 (t80) cc_final: 0.8170 (t80) REVERT: D 8 MET cc_start: 0.7552 (mmm) cc_final: 0.7192 (mmm) REVERT: I 411 TYR cc_start: 0.8645 (m-80) cc_final: 0.8422 (m-80) REVERT: H 77 MET cc_start: 0.6840 (mmt) cc_final: 0.6477 (mtt) REVERT: H 176 GLN cc_start: 0.8329 (tt0) cc_final: 0.8080 (tt0) REVERT: H 196 MET cc_start: 0.8639 (mmm) cc_final: 0.8368 (mmm) REVERT: C 274 GLU cc_start: 0.6216 (mp0) cc_final: 0.5994 (mp0) REVERT: C 351 MET cc_start: 0.8277 (mtt) cc_final: 0.7964 (mtm) REVERT: F 272 LEU cc_start: 0.7775 (mt) cc_final: 0.7477 (mp) REVERT: F 282 MET cc_start: 0.6617 (tpt) cc_final: 0.6401 (tmm) REVERT: F 304 MET cc_start: 0.8461 (mmm) cc_final: 0.8044 (mmm) REVERT: F 368 LEU cc_start: 0.8597 (mp) cc_final: 0.8384 (mt) REVERT: F 381 LYS cc_start: 0.8208 (tptp) cc_final: 0.7982 (tptp) REVERT: F 383 ASN cc_start: 0.7897 (t0) cc_final: 0.7696 (t0) REVERT: F 417 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8391 (mtmt) REVERT: A 8 MET cc_start: 0.7922 (tpt) cc_final: 0.7554 (tpt) outliers start: 22 outliers final: 10 residues processed: 193 average time/residue: 0.3918 time to fit residues: 84.4339 Evaluate side-chains 175 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 101 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126753 restraints weight = 14204.859| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.93 r_work: 0.3474 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11601 Z= 0.149 Angle : 0.590 9.791 15754 Z= 0.283 Chirality : 0.042 0.293 1775 Planarity : 0.004 0.045 1933 Dihedral : 7.032 59.668 1959 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.15 % Allowed : 8.93 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.95 (0.24), residues: 1323 helix: 2.24 (0.21), residues: 567 sheet: -0.74 (0.40), residues: 159 loop : -0.55 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 448 TYR 0.013 0.001 TYR I 270 PHE 0.025 0.002 PHE B 175 TRP 0.029 0.002 TRP I 395 HIS 0.007 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00344 (11534) covalent geometry : angle 0.56399 (15625) SS BOND : bond 0.00480 ( 18) SS BOND : angle 0.96188 ( 36) hydrogen bonds : bond 0.04261 ( 529) hydrogen bonds : angle 4.42773 ( 1458) metal coordination : bond 0.00892 ( 24) metal coordination : angle 2.15930 ( 18) link_BETA1-4 : bond 0.00369 ( 9) link_BETA1-4 : angle 2.06828 ( 27) link_NAG-ASN : bond 0.00341 ( 16) link_NAG-ASN : angle 2.43603 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7804 (tt) cc_final: 0.7369 (mp) REVERT: B 102 LYS cc_start: 0.8432 (tttm) cc_final: 0.8173 (ttpp) REVERT: B 159 ASP cc_start: 0.8065 (m-30) cc_final: 0.7774 (m-30) REVERT: B 236 PHE cc_start: 0.8446 (t80) cc_final: 0.8176 (t80) REVERT: D 8 MET cc_start: 0.7475 (mmm) cc_final: 0.7153 (mmm) REVERT: E 107 SER cc_start: 0.8619 (p) cc_final: 0.8353 (p) REVERT: H 77 MET cc_start: 0.6978 (mmt) cc_final: 0.6375 (mmt) REVERT: H 134 TRP cc_start: 0.8167 (m100) cc_final: 0.7753 (m100) REVERT: H 155 ASP cc_start: 0.7952 (t0) cc_final: 0.7744 (t0) REVERT: H 196 MET cc_start: 0.8663 (mmm) cc_final: 0.8450 (mmm) REVERT: C 299 SER cc_start: 0.8171 (t) cc_final: 0.7910 (t) REVERT: C 371 GLN cc_start: 0.8245 (mt0) cc_final: 0.8033 (mt0) REVERT: F 304 MET cc_start: 0.8490 (mmm) cc_final: 0.8032 (mmm) REVERT: F 368 LEU cc_start: 0.8599 (mp) cc_final: 0.8390 (mt) REVERT: F 383 ASN cc_start: 0.7898 (t0) cc_final: 0.7687 (t0) REVERT: A 8 MET cc_start: 0.7903 (tpt) cc_final: 0.7539 (tpt) outliers start: 26 outliers final: 17 residues processed: 174 average time/residue: 0.3943 time to fit residues: 76.5630 Evaluate side-chains 173 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 107 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128408 restraints weight = 14226.050| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.95 r_work: 0.3491 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11601 Z= 0.110 Angle : 0.545 9.637 15754 Z= 0.262 Chirality : 0.040 0.273 1775 Planarity : 0.004 0.043 1933 Dihedral : 6.842 57.868 1959 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.49 % Allowed : 10.67 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.07 (0.24), residues: 1323 helix: 2.38 (0.21), residues: 567 sheet: -0.73 (0.41), residues: 153 loop : -0.51 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 482 TYR 0.011 0.001 TYR I 270 PHE 0.024 0.001 PHE B 175 TRP 0.025 0.001 TRP F 395 HIS 0.006 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00244 (11534) covalent geometry : angle 0.52384 (15625) SS BOND : bond 0.00273 ( 18) SS BOND : angle 0.74694 ( 36) hydrogen bonds : bond 0.03831 ( 529) hydrogen bonds : angle 4.21725 ( 1458) metal coordination : bond 0.00963 ( 24) metal coordination : angle 1.91086 ( 18) link_BETA1-4 : bond 0.00371 ( 9) link_BETA1-4 : angle 1.80616 ( 27) link_NAG-ASN : bond 0.00320 ( 16) link_NAG-ASN : angle 2.11391 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7804 (tt) cc_final: 0.7400 (mp) REVERT: B 102 LYS cc_start: 0.8445 (tttm) cc_final: 0.8180 (ttpp) REVERT: B 208 LEU cc_start: 0.7954 (mp) cc_final: 0.7705 (mp) REVERT: B 236 PHE cc_start: 0.8436 (t80) cc_final: 0.8169 (t80) REVERT: D 8 MET cc_start: 0.7323 (mmm) cc_final: 0.7019 (mmm) REVERT: I 307 LEU cc_start: 0.8327 (tp) cc_final: 0.8104 (mt) REVERT: E 107 SER cc_start: 0.8571 (p) cc_final: 0.8328 (p) REVERT: E 196 MET cc_start: 0.8550 (mmm) cc_final: 0.8261 (mmt) REVERT: H 77 MET cc_start: 0.6957 (mmt) cc_final: 0.6392 (mmt) REVERT: H 134 TRP cc_start: 0.8156 (m100) cc_final: 0.7792 (m100) REVERT: H 196 MET cc_start: 0.8665 (mmm) cc_final: 0.8405 (mmm) REVERT: H 201 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8068 (ttp80) REVERT: H 208 LEU cc_start: 0.8036 (mt) cc_final: 0.7800 (mp) REVERT: C 272 LEU cc_start: 0.7849 (mt) cc_final: 0.7615 (mp) REVERT: C 299 SER cc_start: 0.8143 (t) cc_final: 0.7884 (t) REVERT: C 368 LEU cc_start: 0.7605 (mp) cc_final: 0.7293 (mt) REVERT: F 304 MET cc_start: 0.8475 (mmm) cc_final: 0.8074 (mmm) REVERT: F 368 LEU cc_start: 0.8572 (mp) cc_final: 0.8370 (mt) REVERT: F 383 ASN cc_start: 0.7868 (t0) cc_final: 0.7647 (t0) REVERT: A 8 MET cc_start: 0.7859 (tpt) cc_final: 0.7499 (tpt) outliers start: 18 outliers final: 13 residues processed: 171 average time/residue: 0.4258 time to fit residues: 81.1248 Evaluate side-chains 170 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 118 optimal weight: 0.0980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 459 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.151029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127083 restraints weight = 14218.472| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.95 r_work: 0.3471 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11601 Z= 0.151 Angle : 0.579 9.867 15754 Z= 0.277 Chirality : 0.042 0.299 1775 Planarity : 0.004 0.042 1933 Dihedral : 6.909 59.946 1959 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.15 % Allowed : 10.92 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.04 (0.24), residues: 1323 helix: 2.32 (0.21), residues: 567 sheet: -0.65 (0.42), residues: 153 loop : -0.52 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 448 TYR 0.014 0.001 TYR I 270 PHE 0.026 0.002 PHE E 175 TRP 0.031 0.002 TRP I 395 HIS 0.006 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00352 (11534) covalent geometry : angle 0.55444 (15625) SS BOND : bond 0.00377 ( 18) SS BOND : angle 0.89026 ( 36) hydrogen bonds : bond 0.04067 ( 529) hydrogen bonds : angle 4.25105 ( 1458) metal coordination : bond 0.00771 ( 24) metal coordination : angle 2.03860 ( 18) link_BETA1-4 : bond 0.00446 ( 9) link_BETA1-4 : angle 1.96054 ( 27) link_NAG-ASN : bond 0.00354 ( 16) link_NAG-ASN : angle 2.38789 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.8474 (tttm) cc_final: 0.8250 (ttpp) REVERT: B 155 ASP cc_start: 0.8209 (t0) cc_final: 0.7957 (t0) REVERT: B 159 ASP cc_start: 0.8094 (m-30) cc_final: 0.7788 (m-30) REVERT: B 208 LEU cc_start: 0.8013 (mp) cc_final: 0.7764 (mp) REVERT: B 236 PHE cc_start: 0.8497 (t80) cc_final: 0.8212 (t80) REVERT: D 8 MET cc_start: 0.7373 (mmm) cc_final: 0.7056 (mmm) REVERT: I 271 CYS cc_start: 0.6434 (m) cc_final: 0.6055 (m) REVERT: E 107 SER cc_start: 0.8519 (p) cc_final: 0.8255 (p) REVERT: H 77 MET cc_start: 0.7134 (mmt) cc_final: 0.6427 (mmt) REVERT: H 134 TRP cc_start: 0.8170 (m100) cc_final: 0.7849 (m100) REVERT: H 196 MET cc_start: 0.8673 (mmm) cc_final: 0.8445 (mmm) REVERT: H 201 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8044 (ttp80) REVERT: H 208 LEU cc_start: 0.8076 (mt) cc_final: 0.7843 (mp) REVERT: C 299 SER cc_start: 0.8187 (t) cc_final: 0.7951 (t) REVERT: C 368 LEU cc_start: 0.7732 (mp) cc_final: 0.7414 (mt) REVERT: F 272 LEU cc_start: 0.7860 (mp) cc_final: 0.7587 (mt) REVERT: F 299 SER cc_start: 0.8452 (t) cc_final: 0.8201 (t) REVERT: F 368 LEU cc_start: 0.8566 (mp) cc_final: 0.8356 (mt) REVERT: F 383 ASN cc_start: 0.7881 (t0) cc_final: 0.7674 (t0) REVERT: A 8 MET cc_start: 0.7839 (tpt) cc_final: 0.7495 (tpt) outliers start: 26 outliers final: 19 residues processed: 168 average time/residue: 0.4202 time to fit residues: 78.8741 Evaluate side-chains 171 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 43 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS E 86 HIS C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127382 restraints weight = 14227.695| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.10 r_work: 0.3462 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11601 Z= 0.142 Angle : 0.565 9.769 15754 Z= 0.271 Chirality : 0.042 0.295 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.885 58.227 1959 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.56 % Allowed : 11.91 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.04 (0.24), residues: 1323 helix: 2.31 (0.21), residues: 567 sheet: -0.63 (0.42), residues: 153 loop : -0.52 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 482 TYR 0.012 0.001 TYR C 358 PHE 0.026 0.001 PHE B 175 TRP 0.029 0.002 TRP I 395 HIS 0.008 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00330 (11534) covalent geometry : angle 0.54250 (15625) SS BOND : bond 0.00363 ( 18) SS BOND : angle 0.80005 ( 36) hydrogen bonds : bond 0.03970 ( 529) hydrogen bonds : angle 4.18328 ( 1458) metal coordination : bond 0.00806 ( 24) metal coordination : angle 1.93140 ( 18) link_BETA1-4 : bond 0.00365 ( 9) link_BETA1-4 : angle 1.91059 ( 27) link_NAG-ASN : bond 0.00324 ( 16) link_NAG-ASN : angle 2.27164 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.8498 (tttm) cc_final: 0.8242 (ttpp) REVERT: B 155 ASP cc_start: 0.8206 (t0) cc_final: 0.7949 (t0) REVERT: B 159 ASP cc_start: 0.8131 (m-30) cc_final: 0.7808 (m-30) REVERT: B 208 LEU cc_start: 0.7932 (mp) cc_final: 0.7688 (mp) REVERT: B 236 PHE cc_start: 0.8464 (t80) cc_final: 0.8180 (t80) REVERT: D 8 MET cc_start: 0.7462 (mmm) cc_final: 0.7142 (mmm) REVERT: I 271 CYS cc_start: 0.6610 (m) cc_final: 0.6225 (m) REVERT: I 307 LEU cc_start: 0.8277 (tp) cc_final: 0.7921 (mp) REVERT: E 107 SER cc_start: 0.8494 (p) cc_final: 0.8234 (p) REVERT: E 196 MET cc_start: 0.8553 (mmm) cc_final: 0.8254 (mmt) REVERT: H 77 MET cc_start: 0.7209 (mmt) cc_final: 0.6447 (mmt) REVERT: H 196 MET cc_start: 0.8643 (mmm) cc_final: 0.8415 (mmm) REVERT: H 208 LEU cc_start: 0.8019 (mt) cc_final: 0.7762 (mp) REVERT: C 299 SER cc_start: 0.8199 (t) cc_final: 0.7928 (t) REVERT: C 368 LEU cc_start: 0.7664 (mp) cc_final: 0.7368 (mt) REVERT: C 371 GLN cc_start: 0.8325 (mt0) cc_final: 0.8096 (mt0) REVERT: F 272 LEU cc_start: 0.7775 (mp) cc_final: 0.7503 (mt) REVERT: F 299 SER cc_start: 0.8388 (t) cc_final: 0.8149 (t) REVERT: F 383 ASN cc_start: 0.7919 (t0) cc_final: 0.7664 (t0) REVERT: A 8 MET cc_start: 0.7809 (tpt) cc_final: 0.7458 (tpt) outliers start: 31 outliers final: 20 residues processed: 170 average time/residue: 0.4162 time to fit residues: 79.0458 Evaluate side-chains 168 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 0.0070 chunk 104 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS E 86 HIS ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126574 restraints weight = 14209.318| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.12 r_work: 0.3451 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11601 Z= 0.168 Angle : 0.588 9.949 15754 Z= 0.281 Chirality : 0.043 0.306 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.929 58.723 1959 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.23 % Allowed : 12.32 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.02 (0.24), residues: 1323 helix: 2.28 (0.21), residues: 567 sheet: -0.62 (0.42), residues: 153 loop : -0.53 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 448 TYR 0.012 0.001 TYR C 358 PHE 0.026 0.002 PHE E 175 TRP 0.033 0.002 TRP I 395 HIS 0.005 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00394 (11534) covalent geometry : angle 0.56214 (15625) SS BOND : bond 0.00432 ( 18) SS BOND : angle 1.07312 ( 36) hydrogen bonds : bond 0.04111 ( 529) hydrogen bonds : angle 4.20786 ( 1458) metal coordination : bond 0.00759 ( 24) metal coordination : angle 2.04867 ( 18) link_BETA1-4 : bond 0.00456 ( 9) link_BETA1-4 : angle 1.96790 ( 27) link_NAG-ASN : bond 0.00348 ( 16) link_NAG-ASN : angle 2.43035 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.8508 (tttm) cc_final: 0.8261 (ttpp) REVERT: B 159 ASP cc_start: 0.8171 (m-30) cc_final: 0.7838 (m-30) REVERT: B 208 LEU cc_start: 0.7963 (mp) cc_final: 0.7725 (mp) REVERT: B 236 PHE cc_start: 0.8516 (t80) cc_final: 0.8242 (t80) REVERT: D 8 MET cc_start: 0.7476 (mmm) cc_final: 0.7166 (mmm) REVERT: I 271 CYS cc_start: 0.6606 (m) cc_final: 0.6227 (m) REVERT: E 107 SER cc_start: 0.8481 (p) cc_final: 0.8228 (p) REVERT: H 77 MET cc_start: 0.7209 (mmt) cc_final: 0.6429 (mmt) REVERT: H 196 MET cc_start: 0.8655 (mmm) cc_final: 0.8369 (mmm) REVERT: H 208 LEU cc_start: 0.8050 (mt) cc_final: 0.7802 (mp) REVERT: C 299 SER cc_start: 0.8217 (t) cc_final: 0.7946 (t) REVERT: C 368 LEU cc_start: 0.7818 (mp) cc_final: 0.7527 (mt) REVERT: C 415 GLN cc_start: 0.8591 (mt0) cc_final: 0.8314 (mt0) REVERT: F 272 LEU cc_start: 0.7771 (mp) cc_final: 0.7500 (mt) REVERT: F 383 ASN cc_start: 0.7916 (t0) cc_final: 0.7663 (t0) REVERT: A 8 MET cc_start: 0.7835 (tpt) cc_final: 0.7494 (tpt) outliers start: 27 outliers final: 19 residues processed: 169 average time/residue: 0.4279 time to fit residues: 80.4862 Evaluate side-chains 171 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS ** I 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS H 86 HIS ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126773 restraints weight = 14215.678| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.08 r_work: 0.3443 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11601 Z= 0.201 Angle : 0.620 9.940 15754 Z= 0.295 Chirality : 0.044 0.324 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.955 59.299 1959 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.81 % Allowed : 12.41 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.89 (0.24), residues: 1323 helix: 2.11 (0.21), residues: 564 sheet: -0.52 (0.41), residues: 159 loop : -0.55 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 448 TYR 0.013 0.001 TYR C 358 PHE 0.028 0.002 PHE E 175 TRP 0.036 0.002 TRP C 395 HIS 0.005 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00477 (11534) covalent geometry : angle 0.59238 (15625) SS BOND : bond 0.00498 ( 18) SS BOND : angle 1.13787 ( 36) hydrogen bonds : bond 0.04304 ( 529) hydrogen bonds : angle 4.30439 ( 1458) metal coordination : bond 0.00770 ( 24) metal coordination : angle 2.11681 ( 18) link_BETA1-4 : bond 0.00533 ( 9) link_BETA1-4 : angle 2.05321 ( 27) link_NAG-ASN : bond 0.00381 ( 16) link_NAG-ASN : angle 2.62351 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7800 (tt) cc_final: 0.7346 (mp) REVERT: B 102 LYS cc_start: 0.8494 (tttm) cc_final: 0.8245 (ttpp) REVERT: B 159 ASP cc_start: 0.8169 (m-30) cc_final: 0.7855 (m-30) REVERT: B 208 LEU cc_start: 0.7978 (mp) cc_final: 0.7721 (mp) REVERT: B 236 PHE cc_start: 0.8531 (t80) cc_final: 0.8235 (t80) REVERT: D 8 MET cc_start: 0.7499 (mmm) cc_final: 0.7184 (mmm) REVERT: I 271 CYS cc_start: 0.6589 (m) cc_final: 0.6253 (m) REVERT: I 336 LEU cc_start: 0.7740 (mt) cc_final: 0.7524 (mp) REVERT: E 94 LEU cc_start: 0.7373 (tt) cc_final: 0.7001 (mt) REVERT: E 107 SER cc_start: 0.8465 (p) cc_final: 0.8193 (p) REVERT: E 149 MET cc_start: 0.8119 (mmm) cc_final: 0.7915 (mmp) REVERT: E 207 CYS cc_start: 0.7057 (m) cc_final: 0.6560 (m) REVERT: H 77 MET cc_start: 0.7227 (mmt) cc_final: 0.6489 (mmt) REVERT: H 196 MET cc_start: 0.8648 (mmm) cc_final: 0.8381 (mmm) REVERT: H 208 LEU cc_start: 0.8045 (mt) cc_final: 0.7791 (mp) REVERT: C 299 SER cc_start: 0.8203 (t) cc_final: 0.7925 (t) REVERT: C 368 LEU cc_start: 0.7923 (mp) cc_final: 0.7638 (mt) REVERT: C 371 GLN cc_start: 0.8337 (mt0) cc_final: 0.7937 (mt0) REVERT: F 272 LEU cc_start: 0.7755 (mp) cc_final: 0.7508 (mt) REVERT: F 282 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6162 (tmm) REVERT: F 368 LEU cc_start: 0.8522 (mp) cc_final: 0.8319 (mp) REVERT: F 383 ASN cc_start: 0.7921 (t0) cc_final: 0.7644 (t0) REVERT: A 8 MET cc_start: 0.7833 (tpt) cc_final: 0.7479 (tpt) outliers start: 34 outliers final: 20 residues processed: 170 average time/residue: 0.4088 time to fit residues: 77.8596 Evaluate side-chains 167 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 27 optimal weight: 0.0370 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS ** I 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS H 86 HIS C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127852 restraints weight = 14056.268| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.96 r_work: 0.3469 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11601 Z= 0.152 Angle : 0.586 9.743 15754 Z= 0.279 Chirality : 0.042 0.297 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.850 58.405 1959 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.15 % Allowed : 13.32 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.99 (0.24), residues: 1323 helix: 2.23 (0.21), residues: 567 sheet: -0.57 (0.43), residues: 153 loop : -0.53 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 167 TYR 0.012 0.001 TYR C 358 PHE 0.027 0.001 PHE B 175 TRP 0.030 0.002 TRP I 395 HIS 0.005 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00354 (11534) covalent geometry : angle 0.56229 (15625) SS BOND : bond 0.00420 ( 18) SS BOND : angle 0.97158 ( 36) hydrogen bonds : bond 0.04047 ( 529) hydrogen bonds : angle 4.22746 ( 1458) metal coordination : bond 0.00835 ( 24) metal coordination : angle 1.97712 ( 18) link_BETA1-4 : bond 0.00464 ( 9) link_BETA1-4 : angle 1.87285 ( 27) link_NAG-ASN : bond 0.00296 ( 16) link_NAG-ASN : angle 2.33951 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7780 (tt) cc_final: 0.7340 (mp) REVERT: B 102 LYS cc_start: 0.8463 (tttm) cc_final: 0.8201 (ttpp) REVERT: B 159 ASP cc_start: 0.8169 (m-30) cc_final: 0.7853 (m-30) REVERT: B 208 LEU cc_start: 0.7927 (mp) cc_final: 0.7647 (mp) REVERT: D 8 MET cc_start: 0.7417 (mmm) cc_final: 0.7107 (mmm) REVERT: I 271 CYS cc_start: 0.6539 (m) cc_final: 0.6211 (m) REVERT: I 336 LEU cc_start: 0.7730 (mt) cc_final: 0.7499 (mp) REVERT: E 94 LEU cc_start: 0.7342 (tt) cc_final: 0.6992 (mt) REVERT: E 107 SER cc_start: 0.8453 (p) cc_final: 0.8183 (p) REVERT: E 132 MET cc_start: 0.8442 (mtp) cc_final: 0.8194 (mmt) REVERT: E 196 MET cc_start: 0.8464 (mmm) cc_final: 0.8166 (mmt) REVERT: E 207 CYS cc_start: 0.6981 (m) cc_final: 0.6455 (m) REVERT: H 77 MET cc_start: 0.7223 (mmt) cc_final: 0.6480 (mmt) REVERT: H 196 MET cc_start: 0.8605 (mmm) cc_final: 0.8356 (mmm) REVERT: H 208 LEU cc_start: 0.7999 (mt) cc_final: 0.7734 (mp) REVERT: C 299 SER cc_start: 0.8196 (t) cc_final: 0.7919 (t) REVERT: C 368 LEU cc_start: 0.7820 (mp) cc_final: 0.7550 (mt) REVERT: C 371 GLN cc_start: 0.8287 (mt0) cc_final: 0.7879 (mt0) REVERT: C 415 GLN cc_start: 0.8562 (mt0) cc_final: 0.8279 (mt0) REVERT: F 272 LEU cc_start: 0.7727 (mp) cc_final: 0.7460 (mt) REVERT: F 282 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6158 (tmm) REVERT: F 383 ASN cc_start: 0.7880 (t0) cc_final: 0.7598 (t0) REVERT: A 8 MET cc_start: 0.7769 (tpt) cc_final: 0.7415 (tpt) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.4280 time to fit residues: 76.3723 Evaluate side-chains 164 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.0870 chunk 45 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS ** I 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS ** C 459 HIS ** 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 = 0.3903 r_free = 0.3903 target = 0.152232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127782 restraints weight = 14189.250| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.99 r_work: 0.3459 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11601 Z= 0.162 Angle : 0.591 9.802 15754 Z= 0.282 Chirality : 0.042 0.305 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.873 58.744 1959 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.99 % Allowed : 13.48 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.97 (0.24), residues: 1323 helix: 2.21 (0.21), residues: 567 sheet: -0.55 (0.43), residues: 153 loop : -0.55 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 167 TYR 0.012 0.001 TYR C 358 PHE 0.027 0.002 PHE B 175 TRP 0.032 0.002 TRP I 395 HIS 0.005 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00379 (11534) covalent geometry : angle 0.56774 (15625) SS BOND : bond 0.00430 ( 18) SS BOND : angle 1.00064 ( 36) hydrogen bonds : bond 0.04088 ( 529) hydrogen bonds : angle 4.22165 ( 1458) metal coordination : bond 0.00789 ( 24) metal coordination : angle 1.96378 ( 18) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.89681 ( 27) link_NAG-ASN : bond 0.00305 ( 16) link_NAG-ASN : angle 2.37116 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7779 (tt) cc_final: 0.7353 (mp) REVERT: B 102 LYS cc_start: 0.8461 (tttm) cc_final: 0.8199 (ttpp) REVERT: B 208 LEU cc_start: 0.7949 (mp) cc_final: 0.7674 (mp) REVERT: D 8 MET cc_start: 0.7414 (mmm) cc_final: 0.7125 (mmm) REVERT: I 271 CYS cc_start: 0.6510 (m) cc_final: 0.6215 (m) REVERT: I 307 LEU cc_start: 0.8235 (mt) cc_final: 0.7998 (mp) REVERT: I 404 SER cc_start: 0.8370 (t) cc_final: 0.8119 (m) REVERT: E 94 LEU cc_start: 0.7368 (tt) cc_final: 0.7026 (mt) REVERT: E 107 SER cc_start: 0.8440 (p) cc_final: 0.8175 (p) REVERT: E 132 MET cc_start: 0.8443 (mtp) cc_final: 0.8192 (mmt) REVERT: E 149 MET cc_start: 0.8105 (mmp) cc_final: 0.7898 (mmm) REVERT: E 201 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6743 (ttp80) REVERT: E 207 CYS cc_start: 0.6983 (m) cc_final: 0.6460 (m) REVERT: H 77 MET cc_start: 0.7256 (mmt) cc_final: 0.6480 (mmt) REVERT: H 196 MET cc_start: 0.8621 (mmm) cc_final: 0.8369 (mmm) REVERT: H 208 LEU cc_start: 0.8024 (mt) cc_final: 0.7762 (mp) REVERT: C 299 SER cc_start: 0.8182 (t) cc_final: 0.7887 (t) REVERT: C 368 LEU cc_start: 0.7858 (mp) cc_final: 0.7584 (mt) REVERT: C 415 GLN cc_start: 0.8564 (mt0) cc_final: 0.8277 (mt0) REVERT: F 272 LEU cc_start: 0.7723 (mp) cc_final: 0.7449 (mt) REVERT: F 282 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6160 (tmm) REVERT: A 8 MET cc_start: 0.7747 (tpt) cc_final: 0.7401 (tpt) outliers start: 24 outliers final: 20 residues processed: 158 average time/residue: 0.4249 time to fit residues: 74.6546 Evaluate side-chains 165 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 399 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS ** I 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS H 86 HIS ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127682 restraints weight = 14274.542| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.00 r_work: 0.3465 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11601 Z= 0.156 Angle : 0.590 9.766 15754 Z= 0.280 Chirality : 0.042 0.301 1775 Planarity : 0.004 0.040 1933 Dihedral : 6.860 58.531 1959 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.23 % Allowed : 13.73 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.96 (0.24), residues: 1323 helix: 2.21 (0.21), residues: 564 sheet: -0.55 (0.42), residues: 153 loop : -0.54 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 167 TYR 0.012 0.001 TYR C 358 PHE 0.027 0.001 PHE B 175 TRP 0.032 0.002 TRP I 395 HIS 0.005 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00364 (11534) covalent geometry : angle 0.56686 (15625) SS BOND : bond 0.00415 ( 18) SS BOND : angle 0.96186 ( 36) hydrogen bonds : bond 0.04063 ( 529) hydrogen bonds : angle 4.23522 ( 1458) metal coordination : bond 0.00802 ( 24) metal coordination : angle 1.95273 ( 18) link_BETA1-4 : bond 0.00444 ( 9) link_BETA1-4 : angle 1.87186 ( 27) link_NAG-ASN : bond 0.00296 ( 16) link_NAG-ASN : angle 2.33519 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3887.26 seconds wall clock time: 67 minutes 12.77 seconds (4032.77 seconds total)