Starting phenix.real_space_refine on Tue Jul 29 16:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mt6_48601/07_2025/9mt6_48601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mt6_48601/07_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_48601/07_2025/9mt6_48601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mt6_48601/07_2025/9mt6_48601.map" model { file = "/net/cci-nas-00/data/ceres_data/9mt6_48601/07_2025/9mt6_48601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mt6_48601/07_2025/9mt6_48601.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.81, per 1000 atoms: 0.78 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: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.01 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: 3.12 Time building geometry restraints manager: 3.19 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 485 or resid 501 or resid 503)) selection = (chain 'F' and (resid 269 through 485 or resid 501 or resid 503)) selection = (chain 'I' and (resid 269 through 485 or resid 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: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.050 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (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 TRP 0.031 0.002 TRP C 395 HIS 0.010 0.001 HIS H 86 PHE 0.019 0.002 PHE E 175 TYR 0.013 0.001 TYR I 358 ARG 0.005 0.000 ARG H 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 16) link_NAG-ASN : angle 3.32967 ( 48) link_BETA1-4 : bond 0.02748 ( 9) link_BETA1-4 : angle 4.35082 ( 27) hydrogen bonds : bond 0.15883 ( 529) hydrogen bonds : angle 6.03021 ( 1458) metal coordination : bond 0.01055 ( 24) metal coordination : angle 2.11974 ( 18) SS BOND : bond 0.00342 ( 18) SS BOND : angle 1.00842 ( 36) covalent geometry : bond 0.00413 (11534) covalent geometry : angle 0.68553 (15625) *********************** 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 : 1.177 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: 0.7922 (t) REVERT: E 107 SER cc_start: 0.8428 (p) cc_final: 0.8213 (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: 0.6215 (m-70) REVERT: H 100 TYR cc_start: 0.8224 (m-80) cc_final: 0.7761 (m-80) REVERT: H 196 MET cc_start: 0.8688 (mmm) cc_final: 0.8352 (mmm) REVERT: H 228 LEU cc_start: 0.8456 (tp) cc_final: 0.8160 (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: 0.7932 time to fit residues: 165.2833 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 : 1.237 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN I 313 ASN ** I 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3892 r_free = 0.3892 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126374 restraints weight = 14080.670| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.95 r_work: 0.3466 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11601 Z= 0.192 Angle : 0.647 10.337 15754 Z= 0.310 Chirality : 0.045 0.303 1775 Planarity : 0.004 0.049 1933 Dihedral : 7.276 59.664 1962 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.82 % Allowed : 6.12 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1323 helix: 2.07 (0.21), residues: 564 sheet: -0.66 (0.41), residues: 159 loop : -0.64 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 395 HIS 0.009 0.001 HIS E 128 PHE 0.031 0.002 PHE B 175 TYR 0.014 0.001 TYR I 270 ARG 0.004 0.000 ARG H 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 16) link_NAG-ASN : angle 2.91406 ( 48) link_BETA1-4 : bond 0.00568 ( 9) link_BETA1-4 : angle 2.42977 ( 27) hydrogen bonds : bond 0.04919 ( 529) hydrogen bonds : angle 4.74778 ( 1458) metal coordination : bond 0.00774 ( 24) metal coordination : angle 2.24994 ( 18) SS BOND : bond 0.00460 ( 18) SS BOND : angle 1.11563 ( 36) covalent geometry : bond 0.00446 (11534) covalent geometry : angle 0.61355 (15625) *********************** 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 204 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8170 (m) REVERT: B 94 LEU cc_start: 0.7783 (tt) cc_final: 0.7343 (mp) REVERT: B 102 LYS cc_start: 0.8399 (tttm) cc_final: 0.8135 (ttpp) REVERT: B 155 ASP cc_start: 0.8209 (t0) cc_final: 0.7977 (t0) REVERT: B 159 ASP cc_start: 0.8097 (m-30) cc_final: 0.7776 (m-30) REVERT: B 196 MET cc_start: 0.8551 (mmm) cc_final: 0.8347 (mmm) REVERT: B 208 LEU cc_start: 0.8008 (mp) cc_final: 0.7792 (mp) REVERT: B 236 PHE cc_start: 0.8467 (t80) cc_final: 0.8181 (t80) REVERT: D 8 MET cc_start: 0.7580 (mmm) cc_final: 0.7228 (mmm) REVERT: H 77 MET cc_start: 0.6872 (mmt) cc_final: 0.6376 (mtt) REVERT: H 196 MET cc_start: 0.8674 (mmm) cc_final: 0.8416 (mmm) REVERT: H 228 LEU cc_start: 0.8599 (tp) cc_final: 0.8220 (tt) REVERT: C 274 GLU cc_start: 0.6252 (mp0) cc_final: 0.6036 (mp0) REVERT: C 351 MET cc_start: 0.8318 (mtt) cc_final: 0.8020 (mtm) REVERT: F 272 LEU cc_start: 0.7777 (mt) cc_final: 0.7475 (mp) REVERT: F 282 MET cc_start: 0.6673 (tpt) cc_final: 0.6446 (tmm) REVERT: F 304 MET cc_start: 0.8502 (mmm) cc_final: 0.8057 (mmm) REVERT: F 368 LEU cc_start: 0.8611 (mp) cc_final: 0.8395 (mt) REVERT: F 381 LYS cc_start: 0.8211 (tptp) cc_final: 0.7975 (tptp) REVERT: F 417 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8412 (mtmt) REVERT: A 8 MET cc_start: 0.7950 (tpt) cc_final: 0.7592 (tpt) outliers start: 22 outliers final: 11 residues processed: 190 average time/residue: 0.8072 time to fit residues: 171.9973 Evaluate side-chains 174 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 E residue 212 LEU 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 92 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS H 146 GLN C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124531 restraints weight = 14103.429| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.95 r_work: 0.3425 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11601 Z= 0.286 Angle : 0.715 11.944 15754 Z= 0.341 Chirality : 0.048 0.347 1775 Planarity : 0.005 0.047 1933 Dihedral : 7.243 58.749 1959 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.15 % Allowed : 9.43 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1323 helix: 1.76 (0.21), residues: 561 sheet: -1.16 (0.37), residues: 189 loop : -0.54 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 395 HIS 0.007 0.001 HIS E 128 PHE 0.033 0.002 PHE E 175 TYR 0.016 0.002 TYR C 385 ARG 0.003 0.000 ARG I 448 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 16) link_NAG-ASN : angle 3.34497 ( 48) link_BETA1-4 : bond 0.00729 ( 9) link_BETA1-4 : angle 2.50566 ( 27) hydrogen bonds : bond 0.05029 ( 529) hydrogen bonds : angle 4.69143 ( 1458) metal coordination : bond 0.00936 ( 24) metal coordination : angle 2.68968 ( 18) SS BOND : bond 0.00681 ( 18) SS BOND : angle 1.35679 ( 36) covalent geometry : bond 0.00681 (11534) covalent geometry : angle 0.67696 (15625) *********************** 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 187 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (m) REVERT: B 102 LYS cc_start: 0.8420 (tttm) cc_final: 0.8149 (ttpp) REVERT: B 159 ASP cc_start: 0.8121 (m-30) cc_final: 0.7791 (m-30) REVERT: B 196 MET cc_start: 0.8600 (mmm) cc_final: 0.8214 (mmt) REVERT: B 208 LEU cc_start: 0.8085 (mp) cc_final: 0.7839 (mp) REVERT: B 236 PHE cc_start: 0.8556 (t80) cc_final: 0.8228 (t80) REVERT: D 8 MET cc_start: 0.7508 (mmm) cc_final: 0.7178 (mmm) REVERT: I 336 LEU cc_start: 0.7584 (mt) cc_final: 0.7361 (mp) REVERT: I 338 SER cc_start: 0.8541 (t) cc_final: 0.8270 (t) REVERT: E 83 ASN cc_start: 0.7806 (t0) cc_final: 0.7532 (t0) REVERT: E 107 SER cc_start: 0.8480 (p) cc_final: 0.8222 (p) REVERT: H 63 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8071 (mtpp) REVERT: H 77 MET cc_start: 0.7150 (mmt) cc_final: 0.6472 (mmt) REVERT: H 134 TRP cc_start: 0.8174 (m100) cc_final: 0.7856 (m100) REVERT: H 208 LEU cc_start: 0.8101 (mt) cc_final: 0.7850 (mp) REVERT: C 371 GLN cc_start: 0.8290 (mt0) cc_final: 0.8003 (mt0) REVERT: F 282 MET cc_start: 0.6625 (tpt) cc_final: 0.6239 (tmm) REVERT: F 368 LEU cc_start: 0.8558 (mp) cc_final: 0.8349 (mt) REVERT: A 8 MET cc_start: 0.7918 (tpt) cc_final: 0.7542 (tpt) outliers start: 26 outliers final: 19 residues processed: 175 average time/residue: 0.8357 time to fit residues: 163.7680 Evaluate side-chains 175 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR 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 305 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 206 SER Chi-restraints excluded: chain E residue 212 LEU 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 350 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 111 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 115 optimal weight: 0.1980 chunk 118 optimal weight: 0.0980 chunk 96 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 121 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 overall best weight: 0.1718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 HIS C 345 ASN C 371 GLN ** 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 = 0.151370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127549 restraints weight = 14090.802| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.94 r_work: 0.3468 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2034 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= 0.113 Angle : 0.578 9.668 15754 Z= 0.278 Chirality : 0.041 0.278 1775 Planarity : 0.004 0.045 1933 Dihedral : 6.873 58.265 1959 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.82 % Allowed : 11.00 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1323 helix: 2.13 (0.21), residues: 558 sheet: -0.85 (0.42), residues: 153 loop : -0.54 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 395 HIS 0.006 0.001 HIS E 128 PHE 0.025 0.001 PHE B 175 TYR 0.012 0.001 TYR I 270 ARG 0.003 0.000 ARG B 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 16) link_NAG-ASN : angle 2.29631 ( 48) link_BETA1-4 : bond 0.00392 ( 9) link_BETA1-4 : angle 1.91043 ( 27) hydrogen bonds : bond 0.04073 ( 529) hydrogen bonds : angle 4.40628 ( 1458) metal coordination : bond 0.01091 ( 24) metal coordination : angle 2.09275 ( 18) SS BOND : bond 0.00336 ( 18) SS BOND : angle 0.88553 ( 36) covalent geometry : bond 0.00246 (11534) covalent geometry : angle 0.55494 (15625) *********************** 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 183 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.8450 (tttm) cc_final: 0.8176 (ttpp) REVERT: B 159 ASP cc_start: 0.8107 (m-30) cc_final: 0.7807 (m-30) REVERT: B 196 MET cc_start: 0.8602 (mmm) cc_final: 0.8182 (mmt) REVERT: B 236 PHE cc_start: 0.8507 (t80) cc_final: 0.8206 (t80) REVERT: D 8 MET cc_start: 0.7413 (mmm) cc_final: 0.7111 (mmm) REVERT: E 107 SER cc_start: 0.8583 (p) cc_final: 0.8345 (p) REVERT: E 196 MET cc_start: 0.8583 (mmm) cc_final: 0.8246 (mmt) REVERT: H 77 MET cc_start: 0.7141 (mmt) cc_final: 0.6465 (mmt) REVERT: H 176 GLN cc_start: 0.8334 (tt0) cc_final: 0.8080 (tt0) REVERT: H 201 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7938 (mtm110) REVERT: H 208 LEU cc_start: 0.8011 (mt) cc_final: 0.7772 (mp) REVERT: C 368 LEU cc_start: 0.7727 (mp) cc_final: 0.7380 (mt) REVERT: A 8 MET cc_start: 0.7831 (tpt) cc_final: 0.7467 (tpt) outliers start: 22 outliers final: 13 residues processed: 172 average time/residue: 0.8505 time to fit residues: 163.0101 Evaluate side-chains 166 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 212 LEU 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 59 optimal weight: 0.2980 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS I 371 GLN C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127284 restraints weight = 14087.470| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.94 r_work: 0.3478 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.002 0.029 11601 Z= 0.106 Angle : 0.544 9.653 15754 Z= 0.262 Chirality : 0.040 0.270 1775 Planarity : 0.004 0.042 1933 Dihedral : 6.809 57.791 1959 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.56 % Allowed : 11.58 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1323 helix: 2.32 (0.21), residues: 567 sheet: -0.79 (0.41), residues: 153 loop : -0.54 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 395 HIS 0.009 0.001 HIS B 86 PHE 0.023 0.001 PHE B 175 TYR 0.011 0.001 TYR C 358 ARG 0.002 0.000 ARG F 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 16) link_NAG-ASN : angle 2.01588 ( 48) link_BETA1-4 : bond 0.00353 ( 9) link_BETA1-4 : angle 1.75312 ( 27) hydrogen bonds : bond 0.03808 ( 529) hydrogen bonds : angle 4.21443 ( 1458) metal coordination : bond 0.00997 ( 24) metal coordination : angle 1.94898 ( 18) SS BOND : bond 0.00269 ( 18) SS BOND : angle 0.74637 ( 36) covalent geometry : bond 0.00232 (11534) covalent geometry : angle 0.52399 (15625) *********************** 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 190 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LYS cc_start: 0.8451 (tttm) cc_final: 0.8215 (ttpp) REVERT: B 159 ASP cc_start: 0.8098 (m-30) cc_final: 0.7802 (m-30) REVERT: B 196 MET cc_start: 0.8599 (mmm) cc_final: 0.8185 (mmt) REVERT: B 236 PHE cc_start: 0.8478 (t80) cc_final: 0.8205 (t80) REVERT: D 8 MET cc_start: 0.7332 (mmm) cc_final: 0.7024 (mmm) REVERT: I 307 LEU cc_start: 0.8302 (tp) cc_final: 0.8089 (mt) REVERT: E 107 SER cc_start: 0.8553 (p) cc_final: 0.8320 (p) REVERT: E 196 MET cc_start: 0.8599 (mmm) cc_final: 0.8223 (mmt) REVERT: E 201 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6769 (ttp80) REVERT: H 77 MET cc_start: 0.7219 (mmt) cc_final: 0.6474 (mmt) REVERT: H 176 GLN cc_start: 0.8313 (tt0) cc_final: 0.8042 (tt0) REVERT: H 208 LEU cc_start: 0.8030 (mt) cc_final: 0.7791 (mp) REVERT: C 368 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7372 (mt) REVERT: A 8 MET cc_start: 0.7750 (tpt) cc_final: 0.7424 (tpt) outliers start: 31 outliers final: 15 residues processed: 172 average time/residue: 0.8943 time to fit residues: 172.2973 Evaluate side-chains 170 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 G residue 11 ILE Chi-restraints excluded: chain I residue 350 LEU 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 201 ARG 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.150682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126110 restraints weight = 14213.769| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.98 r_work: 0.3431 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11601 Z= 0.285 Angle : 0.687 10.311 15754 Z= 0.327 Chirality : 0.048 0.342 1775 Planarity : 0.004 0.042 1933 Dihedral : 7.107 59.377 1959 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 12.82 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1323 helix: 1.92 (0.21), residues: 561 sheet: -0.74 (0.43), residues: 153 loop : -0.58 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 395 HIS 0.006 0.001 HIS E 128 PHE 0.033 0.002 PHE H 175 TYR 0.016 0.002 TYR C 358 ARG 0.002 0.000 ARG I 448 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 16) link_NAG-ASN : angle 3.11648 ( 48) link_BETA1-4 : bond 0.00727 ( 9) link_BETA1-4 : angle 2.29837 ( 27) hydrogen bonds : bond 0.04737 ( 529) hydrogen bonds : angle 4.53059 ( 1458) metal coordination : bond 0.00916 ( 24) metal coordination : angle 2.47305 ( 18) SS BOND : bond 0.00607 ( 18) SS BOND : angle 1.35955 ( 36) covalent geometry : bond 0.00678 (11534) covalent geometry : angle 0.65239 (15625) *********************** 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 175 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7824 (tt) cc_final: 0.7359 (mp) REVERT: B 102 LYS cc_start: 0.8470 (tttm) cc_final: 0.8211 (ttpp) REVERT: B 196 MET cc_start: 0.8590 (mmm) cc_final: 0.8211 (mmt) REVERT: B 208 LEU cc_start: 0.7995 (mp) cc_final: 0.7740 (mp) REVERT: B 236 PHE cc_start: 0.8509 (t80) cc_final: 0.8189 (t80) REVERT: D 8 MET cc_start: 0.7494 (mmm) cc_final: 0.7190 (mmm) REVERT: I 336 LEU cc_start: 0.7724 (mt) cc_final: 0.7480 (mp) REVERT: E 107 SER cc_start: 0.8482 (p) cc_final: 0.8230 (p) REVERT: E 201 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6757 (ttp80) REVERT: H 77 MET cc_start: 0.7235 (mmt) cc_final: 0.6491 (mmt) REVERT: H 176 GLN cc_start: 0.8411 (tt0) cc_final: 0.8068 (tt0) REVERT: H 208 LEU cc_start: 0.8079 (mt) cc_final: 0.7839 (mp) REVERT: F 282 MET cc_start: 0.6591 (tmm) cc_final: 0.6174 (tmm) REVERT: A 8 MET cc_start: 0.7847 (tpt) cc_final: 0.7488 (tpt) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 0.8711 time to fit residues: 155.5817 Evaluate side-chains 161 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 201 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 133 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 0.0970 chunk 114 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.3186 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.152217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127790 restraints weight = 14212.328| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.98 r_work: 0.3463 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11601 Z= 0.140 Angle : 0.591 9.748 15754 Z= 0.282 Chirality : 0.042 0.294 1775 Planarity : 0.004 0.042 1933 Dihedral : 6.815 58.173 1959 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.81 % Allowed : 12.82 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1323 helix: 2.16 (0.21), residues: 567 sheet: -0.74 (0.42), residues: 153 loop : -0.55 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 395 HIS 0.005 0.001 HIS E 128 PHE 0.027 0.001 PHE B 175 TYR 0.012 0.001 TYR C 358 ARG 0.002 0.000 ARG F 448 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 16) link_NAG-ASN : angle 2.44862 ( 48) link_BETA1-4 : bond 0.00426 ( 9) link_BETA1-4 : angle 1.93713 ( 27) hydrogen bonds : bond 0.04099 ( 529) hydrogen bonds : angle 4.37461 ( 1458) metal coordination : bond 0.00900 ( 24) metal coordination : angle 2.02855 ( 18) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.03771 ( 36) covalent geometry : bond 0.00321 (11534) covalent geometry : angle 0.56524 (15625) *********************** 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 183 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7785 (tt) cc_final: 0.7355 (mp) REVERT: B 102 LYS cc_start: 0.8474 (tttm) cc_final: 0.8209 (ttpp) REVERT: B 159 ASP cc_start: 0.8197 (m-30) cc_final: 0.7875 (m-30) REVERT: B 196 MET cc_start: 0.8593 (mmm) cc_final: 0.8206 (mmt) REVERT: B 208 LEU cc_start: 0.7910 (mp) cc_final: 0.7630 (mp) REVERT: B 236 PHE cc_start: 0.8491 (t80) cc_final: 0.8183 (t80) REVERT: D 8 MET cc_start: 0.7436 (mmm) cc_final: 0.7128 (mmm) REVERT: I 282 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7100 (tmm) REVERT: E 107 SER cc_start: 0.8510 (p) cc_final: 0.8262 (p) REVERT: E 201 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.6759 (ttp80) REVERT: H 77 MET cc_start: 0.7227 (mmt) cc_final: 0.6501 (mmt) REVERT: H 176 GLN cc_start: 0.8350 (tt0) cc_final: 0.8019 (tt0) REVERT: H 208 LEU cc_start: 0.8007 (mt) cc_final: 0.7752 (mp) REVERT: C 368 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7454 (mt) REVERT: F 282 MET cc_start: 0.6614 (tmm) cc_final: 0.6255 (tmm) REVERT: A 8 MET cc_start: 0.7780 (tpt) cc_final: 0.7430 (tpt) outliers start: 34 outliers final: 19 residues processed: 168 average time/residue: 0.8583 time to fit residues: 161.7615 Evaluate side-chains 172 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 282 MET 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 111 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain C residue 336 LEU 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 C residue 399 SER 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 67 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 123 optimal weight: 0.0570 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 0.0060 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128345 restraints weight = 14236.474| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.98 r_work: 0.3472 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11601 Z= 0.130 Angle : 0.572 9.741 15754 Z= 0.273 Chirality : 0.041 0.284 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.740 58.133 1959 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.15 % Allowed : 14.06 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1323 helix: 2.28 (0.21), residues: 567 sheet: -0.64 (0.42), residues: 153 loop : -0.55 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 395 HIS 0.005 0.001 HIS E 128 PHE 0.025 0.001 PHE B 175 TYR 0.013 0.001 TYR C 358 ARG 0.002 0.000 ARG F 448 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 16) link_NAG-ASN : angle 2.23917 ( 48) link_BETA1-4 : bond 0.00385 ( 9) link_BETA1-4 : angle 1.82324 ( 27) hydrogen bonds : bond 0.03961 ( 529) hydrogen bonds : angle 4.27794 ( 1458) metal coordination : bond 0.00879 ( 24) metal coordination : angle 1.92518 ( 18) SS BOND : bond 0.00351 ( 18) SS BOND : angle 0.93736 ( 36) covalent geometry : bond 0.00296 (11534) covalent geometry : angle 0.55000 (15625) *********************** 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 174 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7783 (tt) cc_final: 0.7314 (mp) REVERT: B 102 LYS cc_start: 0.8469 (tttm) cc_final: 0.8202 (ttpp) REVERT: B 159 ASP cc_start: 0.8195 (m-30) cc_final: 0.7868 (m-30) REVERT: B 196 MET cc_start: 0.8593 (mmm) cc_final: 0.8201 (mmt) REVERT: B 208 LEU cc_start: 0.7903 (mp) cc_final: 0.7659 (mp) REVERT: B 236 PHE cc_start: 0.8490 (t80) cc_final: 0.8203 (t80) REVERT: D 8 MET cc_start: 0.7413 (mmm) cc_final: 0.7116 (mmm) REVERT: I 282 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7063 (tmm) REVERT: I 336 LEU cc_start: 0.7684 (mt) cc_final: 0.7473 (mp) REVERT: E 107 SER cc_start: 0.8506 (p) cc_final: 0.8271 (p) REVERT: E 132 MET cc_start: 0.8445 (mtp) cc_final: 0.8205 (mmt) REVERT: E 149 MET cc_start: 0.8074 (mmp) cc_final: 0.7851 (mmm) REVERT: E 196 MET cc_start: 0.8458 (mmm) cc_final: 0.8149 (mmt) REVERT: E 201 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6805 (ttp80) REVERT: H 77 MET cc_start: 0.7220 (mmt) cc_final: 0.6462 (mmt) REVERT: H 176 GLN cc_start: 0.8337 (tt0) cc_final: 0.8031 (tt0) REVERT: H 208 LEU cc_start: 0.8032 (mt) cc_final: 0.7783 (mp) REVERT: C 368 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7444 (mt) REVERT: F 272 LEU cc_start: 0.7663 (mt) cc_final: 0.7442 (mp) REVERT: F 282 MET cc_start: 0.6571 (tmm) cc_final: 0.6216 (tmm) REVERT: A 8 MET cc_start: 0.7764 (tpt) cc_final: 0.7414 (tpt) outliers start: 26 outliers final: 15 residues processed: 162 average time/residue: 1.0066 time to fit residues: 181.6650 Evaluate side-chains 165 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER 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 282 MET 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 215 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 102 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.151192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126719 restraints weight = 14222.206| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.98 r_work: 0.3448 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11601 Z= 0.223 Angle : 0.637 9.988 15754 Z= 0.303 Chirality : 0.045 0.330 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.890 59.448 1959 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.32 % Allowed : 13.98 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1323 helix: 2.01 (0.21), residues: 564 sheet: -0.63 (0.43), residues: 153 loop : -0.61 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 395 HIS 0.005 0.001 HIS E 128 PHE 0.029 0.002 PHE E 175 TYR 0.015 0.001 TYR C 358 ARG 0.003 0.000 ARG H 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 16) link_NAG-ASN : angle 2.68731 ( 48) link_BETA1-4 : bond 0.00627 ( 9) link_BETA1-4 : angle 2.07101 ( 27) hydrogen bonds : bond 0.04373 ( 529) hydrogen bonds : angle 4.38689 ( 1458) metal coordination : bond 0.00804 ( 24) metal coordination : angle 2.21766 ( 18) SS BOND : bond 0.00513 ( 18) SS BOND : angle 1.12642 ( 36) covalent geometry : bond 0.00530 (11534) covalent geometry : angle 0.60898 (15625) *********************** 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 163 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7778 (tt) cc_final: 0.7342 (mp) REVERT: B 196 MET cc_start: 0.8591 (mmm) cc_final: 0.8211 (mmt) REVERT: B 208 LEU cc_start: 0.7949 (mp) cc_final: 0.7693 (mp) REVERT: D 8 MET cc_start: 0.7451 (mmm) cc_final: 0.7159 (mmm) REVERT: I 282 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7127 (tmm) REVERT: I 336 LEU cc_start: 0.7754 (mt) cc_final: 0.7517 (mp) REVERT: E 94 LEU cc_start: 0.7430 (tt) cc_final: 0.7017 (mp) REVERT: E 107 SER cc_start: 0.8491 (p) cc_final: 0.8253 (p) REVERT: E 201 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6785 (ttp80) REVERT: H 77 MET cc_start: 0.7216 (mmt) cc_final: 0.6481 (mmt) REVERT: H 176 GLN cc_start: 0.8405 (tt0) cc_final: 0.8057 (tt0) REVERT: H 208 LEU cc_start: 0.8074 (mt) cc_final: 0.7838 (mp) REVERT: C 368 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7566 (mt) REVERT: F 282 MET cc_start: 0.6671 (tmm) cc_final: 0.6198 (tmm) REVERT: A 8 MET cc_start: 0.7768 (tpt) cc_final: 0.7416 (tpt) outliers start: 28 outliers final: 18 residues processed: 150 average time/residue: 1.5420 time to fit residues: 257.3146 Evaluate side-chains 155 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain I residue 282 MET 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 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 215 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 0.0370 chunk 72 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 100 optimal weight: 0.0980 chunk 97 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 overall best weight: 0.1658 ------------------------------------------------------------------------------- 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 H 86 HIS C 345 ASN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.153412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129059 restraints weight = 14210.371| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.98 r_work: 0.3483 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11601 Z= 0.107 Angle : 0.564 9.538 15754 Z= 0.270 Chirality : 0.040 0.272 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.708 57.271 1959 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.65 % Allowed : 14.89 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1323 helix: 2.31 (0.21), residues: 567 sheet: -0.63 (0.42), residues: 153 loop : -0.58 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 395 HIS 0.005 0.001 HIS E 128 PHE 0.023 0.001 PHE B 175 TYR 0.011 0.001 TYR C 358 ARG 0.002 0.000 ARG F 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 16) link_NAG-ASN : angle 2.05521 ( 48) link_BETA1-4 : bond 0.00388 ( 9) link_BETA1-4 : angle 1.74865 ( 27) hydrogen bonds : bond 0.03836 ( 529) hydrogen bonds : angle 4.21793 ( 1458) metal coordination : bond 0.01003 ( 24) metal coordination : angle 1.88345 ( 18) SS BOND : bond 0.00343 ( 18) SS BOND : angle 1.01505 ( 36) covalent geometry : bond 0.00237 (11534) covalent geometry : angle 0.54435 (15625) ********************** 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 164 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.7784 (tt) cc_final: 0.7378 (mp) REVERT: B 102 LYS cc_start: 0.8472 (tttm) cc_final: 0.8210 (ttpp) REVERT: B 196 MET cc_start: 0.8584 (mmm) cc_final: 0.8183 (mmt) REVERT: B 208 LEU cc_start: 0.7859 (mp) cc_final: 0.7592 (mp) REVERT: B 236 PHE cc_start: 0.8503 (t80) cc_final: 0.8212 (t80) REVERT: D 8 MET cc_start: 0.7385 (mmm) cc_final: 0.7087 (mmm) REVERT: E 94 LEU cc_start: 0.7422 (tt) cc_final: 0.7048 (mp) REVERT: E 107 SER cc_start: 0.8484 (p) cc_final: 0.8259 (p) REVERT: E 132 MET cc_start: 0.8441 (mtp) cc_final: 0.8186 (mmt) REVERT: E 201 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6756 (ttp80) REVERT: H 77 MET cc_start: 0.7191 (mmt) cc_final: 0.6554 (mmt) REVERT: H 176 GLN cc_start: 0.8325 (tt0) cc_final: 0.8031 (tt0) REVERT: H 208 LEU cc_start: 0.7989 (mt) cc_final: 0.7748 (mp) REVERT: C 368 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7214 (mt) REVERT: F 282 MET cc_start: 0.6576 (tmm) cc_final: 0.6202 (tmm) REVERT: A 8 MET cc_start: 0.7726 (tpt) cc_final: 0.7379 (tpt) outliers start: 20 outliers final: 13 residues processed: 154 average time/residue: 1.4043 time to fit residues: 239.2151 Evaluate side-chains 154 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 SER 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 352 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 215 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 43 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 chunk 2 optimal weight: 0.0170 chunk 95 optimal weight: 0.0270 chunk 6 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 overall best weight: 0.1474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS B 176 GLN E 86 HIS H 86 HIS ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.154132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129780 restraints weight = 14156.143| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.99 r_work: 0.3487 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11601 Z= 0.106 Angle : 0.559 9.592 15754 Z= 0.267 Chirality : 0.040 0.268 1775 Planarity : 0.004 0.041 1933 Dihedral : 6.750 57.341 1959 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.65 % Allowed : 14.97 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1323 helix: 2.40 (0.22), residues: 567 sheet: -0.57 (0.42), residues: 153 loop : -0.54 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 395 HIS 0.005 0.001 HIS E 128 PHE 0.025 0.001 PHE B 175 TYR 0.011 0.001 TYR C 358 ARG 0.002 0.000 ARG I 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 16) link_NAG-ASN : angle 2.00820 ( 48) link_BETA1-4 : bond 0.00359 ( 9) link_BETA1-4 : angle 1.67640 ( 27) hydrogen bonds : bond 0.03783 ( 529) hydrogen bonds : angle 4.17380 ( 1458) metal coordination : bond 0.00977 ( 24) metal coordination : angle 1.85991 ( 18) SS BOND : bond 0.00296 ( 18) SS BOND : angle 0.89431 ( 36) covalent geometry : bond 0.00234 (11534) covalent geometry : angle 0.54081 (15625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8624.67 seconds wall clock time: 155 minutes 48.37 seconds (9348.37 seconds total)