Starting phenix.real_space_refine on Sat Jul 4 02:48:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.cif Found real_map, /net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.map" model { file = "/net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7smm_25202/07_2026/7smm_25202.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 86 5.16 5 C 11267 2.51 5 N 2659 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17256 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3451 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3315 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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 chiralities: 2 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'DD9': 1, 'NAG': 2, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {'NAG': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N POV A 501 " occ=0.75 ... (44 atoms not shown) pdb="C314 POV A 501 " occ=0.75 residue: pdb=" C1 CLR A 502 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 502 " occ=0.80 residue: pdb=" N POV B 603 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV B 603 " occ=0.75 residue: pdb=" N POV B 604 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 604 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 501 " occ=0.75 residue: pdb=" C1 CLR C 502 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 502 " occ=0.89 residue: pdb=" C1 CLR D 501 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 501 " occ=0.75 residue: pdb=" N POV D 502 " occ=0.75 ... (35 atoms not shown) pdb="C310 POV D 502 " occ=0.75 residue: pdb=" N POV E 502 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV E 502 " occ=0.75 residue: pdb=" N POV E 503 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 503 " occ=0.75 residue: pdb=" N POV E 504 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 504 " occ=0.75 Time building chain proxies: 3.06, per 1000 atoms: 0.18 Number of scatterers: 17256 At special positions: 0 Unit cell: (101.593, 165.757, 114.426, 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) S 86 16.00 P 8 15.00 O 3236 8.00 N 2659 7.00 C 11267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG B 602 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 648.4 milliseconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 43.3% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.764A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.095A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.879A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.892A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.743A pdb=" N MET A 324 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 433 removed outlier: 4.340A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 232 through 242 removed outlier: 3.504A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.043A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.829A pdb=" N GLN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.583A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.078A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.729A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 4.055A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 268 removed outlier: 4.425A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.940A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.524A pdb=" N ARG D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.241A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 232 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.571A pdb=" N MET D 324 " --> pdb=" O PRO D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 433 removed outlier: 3.770A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.938A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.169A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.537A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.885A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 411 through 470 removed outlier: 3.672A pdb=" N GLY E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.231A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.231A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.634A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.747A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.747A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 94 removed outlier: 6.799A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.876A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.876A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 161 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 35 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 161 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.258A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.258A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.853A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.853A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN D 53 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU D 40 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ARG D 55 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 38 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D 57 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN D 36 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLN D 59 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLY D 34 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N ILE D 61 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N THR D 32 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.528A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR D 196 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR D 190 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.956A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.956A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.361A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.361A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 946 hydrogen bonds defined for protein. 2739 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: 3.34 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2668 1.32 - 1.45: 4882 1.45 - 1.59: 9928 1.59 - 1.72: 16 1.72 - 1.86: 140 Bond restraints: 17634 Sorted by residual: bond pdb=" C VAL B 93 " pdb=" N LEU B 94 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.42e-02 4.96e+03 1.04e+01 bond pdb=" N POV E 503 " pdb=" C12 POV E 503 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" N POV E 502 " pdb=" C12 POV E 502 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" N POV E 504 " pdb=" C12 POV E 504 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" N POV A 501 " pdb=" C12 POV A 501 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.90e+00 ... (remaining 17629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 23570 2.51 - 5.03: 387 5.03 - 7.54: 49 7.54 - 10.05: 8 10.05 - 12.57: 16 Bond angle restraints: 24030 Sorted by residual: angle pdb=" O11 POV D 502 " pdb=" P POV D 502 " pdb=" O12 POV D 502 " ideal model delta sigma weight residual 97.67 110.24 -12.57 3.00e+00 1.11e-01 1.75e+01 angle pdb=" O11 POV C 501 " pdb=" P POV C 501 " pdb=" O12 POV C 501 " ideal model delta sigma weight residual 97.67 109.90 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O13 POV A 501 " pdb=" P POV A 501 " pdb=" O14 POV A 501 " ideal model delta sigma weight residual 121.11 109.18 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV B 604 " pdb=" P POV B 604 " pdb=" O12 POV B 604 " ideal model delta sigma weight residual 97.67 109.57 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV B 604 " pdb=" P POV B 604 " pdb=" O14 POV B 604 " ideal model delta sigma weight residual 121.11 109.32 11.79 3.00e+00 1.11e-01 1.54e+01 ... (remaining 24025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.58: 9961 31.58 - 63.16: 262 63.16 - 94.74: 28 94.74 - 126.32: 2 126.32 - 157.90: 4 Dihedral angle restraints: 10257 sinusoidal: 4236 harmonic: 6021 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS B 130 " pdb=" SG CYS B 130 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual 93.00 48.05 44.95 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 10254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2394 0.060 - 0.119: 398 0.119 - 0.179: 36 0.179 - 0.238: 9 0.238 - 0.298: 5 Chirality restraints: 2842 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2839 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 222 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL C 222 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL C 222 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 223 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 234 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 235 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ILE C 221 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE C 221 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 222 " -0.009 2.00e-02 2.50e+03 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 203 2.66 - 3.22: 16068 3.22 - 3.78: 27171 3.78 - 4.34: 39043 4.34 - 4.90: 63404 Nonbonded interactions: 145889 Sorted by model distance: nonbonded pdb=" O MET D 324 " pdb=" NH2 ARG D 331 " model vdw 2.099 3.120 nonbonded pdb=" NH1 ARG E 187 " pdb=" OE1 GLN E 216 " model vdw 2.187 3.120 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP E 113 " pdb=" OG SER E 115 " model vdw 2.233 3.040 nonbonded pdb=" O LEU E 40 " pdb=" ND2 ASN E 181 " model vdw 2.237 3.120 ... (remaining 145884 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' and resid 1 through 433) selection = (chain 'D' and resid 1 through 433) } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=0.99 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.480 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.006 0.058 17668 Z= 0.260 Angle : 0.788 12.568 24125 Z= 0.341 Chirality : 0.046 0.298 2842 Planarity : 0.003 0.044 2895 Dihedral : 14.738 157.898 6316 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 2010 helix: 2.72 (0.18), residues: 747 sheet: 0.26 (0.26), residues: 413 loop : -0.41 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.009 0.001 TYR D 277 PHE 0.012 0.001 PHE E 422 TRP 0.007 0.001 TRP B 176 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (17634) covalent geometry : angle 0.77649 / 0.34 (24030) SS BOND : bond 0.00972 / 0.48 ( 7) SS BOND : angle 2.68723 / 1.43 ( 14) hydrogen bonds : bond 0.11889 / 8.05 ( 860) hydrogen bonds : angle 6.13400 / 4.42 ( 2739) link_ALPHA1-3 : bond 0.00065 / 0.03 ( 4) link_ALPHA1-3 : angle 2.33025 / 1.37 ( 12) link_ALPHA1-6 : bond 0.00361 / 0.18 ( 6) link_ALPHA1-6 : angle 1.81505 / 1.14 ( 18) link_BETA1-4 : bond 0.00394 / 0.24 ( 9) link_BETA1-4 : angle 2.54203 / 1.56 ( 27) link_NAG-ASN : bond 0.00279 / 0.20 ( 8) link_NAG-ASN : angle 2.07120 / 1.24 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: E 198 GLN cc_start: 0.7937 (mp-120) cc_final: 0.7604 (mp10) outliers start: 0 outliers final: 1 residues processed: 147 average time/residue: 0.6040 time to fit residues: 98.8918 Evaluate side-chains 117 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN B 213 GLN B 305 ASN B 328 GLN E 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.068385 restraints weight = 27187.691| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.16 r_work: 0.2715 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17668 Z= 0.177 Angle : 0.563 7.613 24125 Z= 0.291 Chirality : 0.043 0.189 2842 Planarity : 0.004 0.046 2895 Dihedral : 11.429 146.954 2385 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.80 % Allowed : 4.97 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.19), residues: 2010 helix: 2.78 (0.18), residues: 752 sheet: 0.41 (0.25), residues: 410 loop : -0.31 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.011 0.001 TYR D 277 PHE 0.014 0.001 PHE D 256 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (17634) covalent geometry : angle 0.54600 / 0.29 (24030) SS BOND : bond 0.01103 / 0.57 ( 7) SS BOND : angle 3.97074 / 2.18 ( 14) hydrogen bonds : bond 0.05550 / 3.64 ( 860) hydrogen bonds : angle 4.72419 / 3.36 ( 2739) link_ALPHA1-3 : bond 0.00192 / 0.10 ( 4) link_ALPHA1-3 : angle 1.56758 / 0.91 ( 12) link_ALPHA1-6 : bond 0.00443 / 0.24 ( 6) link_ALPHA1-6 : angle 1.68015 / 1.16 ( 18) link_BETA1-4 : bond 0.00284 / 0.16 ( 9) link_BETA1-4 : angle 1.99664 / 1.28 ( 27) link_NAG-ASN : bond 0.00198 / 0.14 ( 8) link_NAG-ASN : angle 1.90146 / 1.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: E 198 GLN cc_start: 0.8520 (mp-120) cc_final: 0.8124 (mp10) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 0.5995 time to fit residues: 89.6731 Evaluate side-chains 117 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 287 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 GLN D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.069178 restraints weight = 27475.738| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.18 r_work: 0.2734 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17668 Z= 0.141 Angle : 0.522 8.561 24125 Z= 0.269 Chirality : 0.042 0.213 2842 Planarity : 0.004 0.050 2895 Dihedral : 10.536 126.370 2383 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.01 % Allowed : 6.51 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 2010 helix: 2.97 (0.18), residues: 749 sheet: 0.45 (0.25), residues: 407 loop : -0.31 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.011 0.001 TYR D 277 PHE 0.012 0.001 PHE D 256 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17634) covalent geometry : angle 0.50213 / 0.26 (24030) SS BOND : bond 0.00966 / 0.48 ( 7) SS BOND : angle 4.28299 / 2.39 ( 14) hydrogen bonds : bond 0.05058 / 3.30 ( 860) hydrogen bonds : angle 4.41175 / 3.13 ( 2739) link_ALPHA1-3 : bond 0.00271 / 0.14 ( 4) link_ALPHA1-3 : angle 1.48575 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00423 / 0.23 ( 6) link_ALPHA1-6 : angle 1.59584 / 1.08 ( 18) link_BETA1-4 : bond 0.00281 / 0.16 ( 9) link_BETA1-4 : angle 1.95942 / 1.26 ( 27) link_NAG-ASN : bond 0.00120 / 0.08 ( 8) link_NAG-ASN : angle 1.86623 / 1.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: B 186 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7830 (mm-30) REVERT: C 244 ASP cc_start: 0.8811 (m-30) cc_final: 0.8591 (m-30) REVERT: E 198 GLN cc_start: 0.8527 (mp-120) cc_final: 0.8142 (mp10) outliers start: 19 outliers final: 9 residues processed: 134 average time/residue: 0.5640 time to fit residues: 84.9703 Evaluate side-chains 125 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.069987 restraints weight = 27329.387| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.17 r_work: 0.2753 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17668 Z= 0.126 Angle : 0.503 8.333 24125 Z= 0.258 Chirality : 0.041 0.183 2842 Planarity : 0.004 0.053 2895 Dihedral : 9.872 112.084 2383 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.17 % Allowed : 7.79 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 2010 helix: 3.13 (0.18), residues: 747 sheet: 0.53 (0.26), residues: 401 loop : -0.31 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.012 0.001 TYR D 277 PHE 0.012 0.001 PHE B 473 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17634) covalent geometry : angle 0.48464 / 0.25 (24030) SS BOND : bond 0.00913 / 0.45 ( 7) SS BOND : angle 3.94779 / 2.12 ( 14) hydrogen bonds : bond 0.04749 / 3.09 ( 860) hydrogen bonds : angle 4.23024 / 3.00 ( 2739) link_ALPHA1-3 : bond 0.00288 / 0.14 ( 4) link_ALPHA1-3 : angle 1.48444 / 0.87 ( 12) link_ALPHA1-6 : bond 0.00428 / 0.24 ( 6) link_ALPHA1-6 : angle 1.55636 / 1.05 ( 18) link_BETA1-4 : bond 0.00302 / 0.17 ( 9) link_BETA1-4 : angle 1.85708 / 1.20 ( 27) link_NAG-ASN : bond 0.00133 / 0.07 ( 8) link_NAG-ASN : angle 1.79354 / 1.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8616 (tpp) REVERT: A 260 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 278 MET cc_start: 0.8168 (ttt) cc_final: 0.7713 (ttt) REVERT: A 404 MET cc_start: 0.8980 (tmm) cc_final: 0.8774 (tmt) REVERT: B 186 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: B 293 MET cc_start: 0.8558 (mmp) cc_final: 0.8302 (mmp) REVERT: C 244 ASP cc_start: 0.8814 (m-30) cc_final: 0.8603 (m-30) REVERT: E 198 GLN cc_start: 0.8515 (mp-120) cc_final: 0.8130 (mp10) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 0.5833 time to fit residues: 88.6328 Evaluate side-chains 128 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068550 restraints weight = 27164.977| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.16 r_work: 0.2728 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17668 Z= 0.171 Angle : 0.540 8.408 24125 Z= 0.274 Chirality : 0.043 0.190 2842 Planarity : 0.004 0.052 2895 Dihedral : 9.591 103.637 2383 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.55 % Allowed : 8.54 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.19), residues: 2010 helix: 3.09 (0.18), residues: 746 sheet: 0.47 (0.25), residues: 412 loop : -0.28 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.011 0.001 TYR D 277 PHE 0.014 0.001 PHE B 473 TRP 0.009 0.001 TRP A 187 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (17634) covalent geometry : angle 0.52037 / 0.27 (24030) SS BOND : bond 0.00948 / 0.47 ( 7) SS BOND : angle 4.08988 / 2.23 ( 14) hydrogen bonds : bond 0.05056 / 3.29 ( 860) hydrogen bonds : angle 4.32049 / 3.06 ( 2739) link_ALPHA1-3 : bond 0.00178 / 0.09 ( 4) link_ALPHA1-3 : angle 1.53872 / 0.90 ( 12) link_ALPHA1-6 : bond 0.00330 / 0.19 ( 6) link_ALPHA1-6 : angle 1.61646 / 1.09 ( 18) link_BETA1-4 : bond 0.00212 / 0.13 ( 9) link_BETA1-4 : angle 2.07927 / 1.35 ( 27) link_NAG-ASN : bond 0.00209 / 0.15 ( 8) link_NAG-ASN : angle 1.92900 / 1.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.8991 (tmm) cc_final: 0.8773 (tmt) REVERT: B 186 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: C 165 LYS cc_start: 0.8690 (ptmt) cc_final: 0.7753 (tptt) REVERT: C 244 ASP cc_start: 0.8831 (m-30) cc_final: 0.8629 (m-30) REVERT: E 198 GLN cc_start: 0.8518 (mp-120) cc_final: 0.8128 (mp10) REVERT: E 438 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7857 (mm-30) outliers start: 29 outliers final: 16 residues processed: 139 average time/residue: 0.5895 time to fit residues: 91.6146 Evaluate side-chains 134 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.068721 restraints weight = 27254.040| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.16 r_work: 0.2734 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17668 Z= 0.164 Angle : 0.532 8.368 24125 Z= 0.270 Chirality : 0.042 0.185 2842 Planarity : 0.004 0.053 2895 Dihedral : 9.344 96.838 2383 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.76 % Allowed : 8.97 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2010 helix: 3.07 (0.18), residues: 747 sheet: 0.46 (0.25), residues: 412 loop : -0.28 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.012 0.001 TYR D 277 PHE 0.013 0.001 PHE B 473 TRP 0.010 0.001 TRP A 187 HIS 0.005 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17634) covalent geometry : angle 0.51280 / 0.26 (24030) SS BOND : bond 0.00932 / 0.46 ( 7) SS BOND : angle 4.02318 / 2.18 ( 14) hydrogen bonds : bond 0.05002 / 3.26 ( 860) hydrogen bonds : angle 4.28759 / 3.04 ( 2739) link_ALPHA1-3 : bond 0.00189 / 0.09 ( 4) link_ALPHA1-3 : angle 1.51658 / 0.88 ( 12) link_ALPHA1-6 : bond 0.00357 / 0.20 ( 6) link_ALPHA1-6 : angle 1.59574 / 1.07 ( 18) link_BETA1-4 : bond 0.00224 / 0.13 ( 9) link_BETA1-4 : angle 2.02223 / 1.30 ( 27) link_NAG-ASN : bond 0.00173 / 0.12 ( 8) link_NAG-ASN : angle 1.91175 / 1.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (t) REVERT: A 142 CYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5756 (m) REVERT: A 260 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 278 MET cc_start: 0.8124 (ttt) cc_final: 0.7593 (ttt) REVERT: B 186 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: C 165 LYS cc_start: 0.8690 (ptmt) cc_final: 0.7750 (tptt) REVERT: C 244 ASP cc_start: 0.8828 (m-30) cc_final: 0.8623 (m-30) REVERT: E 198 GLN cc_start: 0.8519 (mp-120) cc_final: 0.8130 (mp10) REVERT: E 438 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7842 (mm-30) outliers start: 33 outliers final: 19 residues processed: 146 average time/residue: 0.5626 time to fit residues: 92.2020 Evaluate side-chains 144 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 192 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 GLN B 328 GLN C 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.070445 restraints weight = 27092.565| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.17 r_work: 0.2762 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17668 Z= 0.117 Angle : 0.499 8.364 24125 Z= 0.254 Chirality : 0.041 0.198 2842 Planarity : 0.004 0.052 2895 Dihedral : 8.963 88.364 2383 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.49 % Allowed : 9.61 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 2010 helix: 3.19 (0.18), residues: 747 sheet: 0.46 (0.25), residues: 406 loop : -0.24 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 301 TYR 0.010 0.001 TYR D 277 PHE 0.010 0.001 PHE B 473 TRP 0.012 0.001 TRP A 60 HIS 0.005 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17634) covalent geometry : angle 0.48181 / 0.25 (24030) SS BOND : bond 0.00894 / 0.44 ( 7) SS BOND : angle 3.84838 / 2.05 ( 14) hydrogen bonds : bond 0.04558 / 2.96 ( 860) hydrogen bonds : angle 4.13300 / 2.93 ( 2739) link_ALPHA1-3 : bond 0.00320 / 0.16 ( 4) link_ALPHA1-3 : angle 1.47324 / 0.86 ( 12) link_ALPHA1-6 : bond 0.00439 / 0.24 ( 6) link_ALPHA1-6 : angle 1.51772 / 1.02 ( 18) link_BETA1-4 : bond 0.00358 / 0.20 ( 9) link_BETA1-4 : angle 1.79488 / 1.15 ( 27) link_NAG-ASN : bond 0.00161 / 0.08 ( 8) link_NAG-ASN : angle 1.78981 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 260 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8255 (mt) REVERT: A 278 MET cc_start: 0.8157 (ttt) cc_final: 0.7704 (ttt) REVERT: A 404 MET cc_start: 0.8924 (tmm) cc_final: 0.8695 (tmt) REVERT: B 186 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 165 LYS cc_start: 0.8675 (ptmt) cc_final: 0.7739 (tptt) REVERT: E 198 GLN cc_start: 0.8507 (mp-120) cc_final: 0.8117 (mp10) REVERT: E 438 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7811 (mm-30) outliers start: 28 outliers final: 14 residues processed: 139 average time/residue: 0.5513 time to fit residues: 86.3019 Evaluate side-chains 136 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 33 optimal weight: 0.0170 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.070681 restraints weight = 27084.391| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.16 r_work: 0.2773 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17668 Z= 0.118 Angle : 0.497 8.330 24125 Z= 0.253 Chirality : 0.041 0.202 2842 Planarity : 0.004 0.051 2895 Dihedral : 8.717 85.041 2383 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.44 % Allowed : 10.04 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2010 helix: 3.24 (0.18), residues: 747 sheet: 0.49 (0.25), residues: 402 loop : -0.26 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.012 0.001 TYR D 277 PHE 0.011 0.001 PHE B 473 TRP 0.011 0.001 TRP A 60 HIS 0.006 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (17634) covalent geometry : angle 0.47935 / 0.25 (24030) SS BOND : bond 0.00910 / 0.45 ( 7) SS BOND : angle 3.83902 / 2.04 ( 14) hydrogen bonds : bond 0.04479 / 2.91 ( 860) hydrogen bonds : angle 4.08468 / 2.90 ( 2739) link_ALPHA1-3 : bond 0.00270 / 0.14 ( 4) link_ALPHA1-3 : angle 1.48614 / 0.87 ( 12) link_ALPHA1-6 : bond 0.00401 / 0.22 ( 6) link_ALPHA1-6 : angle 1.52638 / 1.02 ( 18) link_BETA1-4 : bond 0.00301 / 0.17 ( 9) link_BETA1-4 : angle 1.77373 / 1.15 ( 27) link_NAG-ASN : bond 0.00136 / 0.08 ( 8) link_NAG-ASN : angle 1.75879 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (t) REVERT: B 186 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: C 165 LYS cc_start: 0.8707 (ptmt) cc_final: 0.7799 (tptt) REVERT: C 331 TRP cc_start: 0.7833 (m-10) cc_final: 0.7542 (m-90) REVERT: E 198 GLN cc_start: 0.8518 (mp-120) cc_final: 0.8131 (mp10) REVERT: E 438 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7810 (mm-30) outliers start: 27 outliers final: 14 residues processed: 138 average time/residue: 0.5409 time to fit residues: 83.8313 Evaluate side-chains 131 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 110 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.069968 restraints weight = 27282.445| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.18 r_work: 0.2758 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17668 Z= 0.137 Angle : 0.515 8.565 24125 Z= 0.261 Chirality : 0.042 0.195 2842 Planarity : 0.004 0.050 2895 Dihedral : 8.647 86.814 2383 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.07 % Allowed : 10.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 2010 helix: 3.20 (0.18), residues: 747 sheet: 0.51 (0.25), residues: 406 loop : -0.27 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.010 0.001 TYR B 439 PHE 0.013 0.001 PHE B 473 TRP 0.010 0.001 TRP A 187 HIS 0.006 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17634) covalent geometry : angle 0.49683 / 0.26 (24030) SS BOND : bond 0.00920 / 0.45 ( 7) SS BOND : angle 3.95071 / 2.12 ( 14) hydrogen bonds : bond 0.04607 / 3.00 ( 860) hydrogen bonds : angle 4.13355 / 2.93 ( 2739) link_ALPHA1-3 : bond 0.00240 / 0.12 ( 4) link_ALPHA1-3 : angle 1.50500 / 0.88 ( 12) link_ALPHA1-6 : bond 0.00367 / 0.21 ( 6) link_ALPHA1-6 : angle 1.55440 / 1.04 ( 18) link_BETA1-4 : bond 0.00254 / 0.15 ( 9) link_BETA1-4 : angle 1.84771 / 1.19 ( 27) link_NAG-ASN : bond 0.00146 / 0.09 ( 8) link_NAG-ASN : angle 1.79786 / 1.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8495 (t) REVERT: B 186 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: C 165 LYS cc_start: 0.8673 (ptmt) cc_final: 0.7744 (tptt) REVERT: C 331 TRP cc_start: 0.7850 (m-10) cc_final: 0.7556 (m-90) REVERT: E 198 GLN cc_start: 0.8510 (mp-120) cc_final: 0.8121 (mp10) REVERT: E 438 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7818 (mm-30) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.5586 time to fit residues: 79.3048 Evaluate side-chains 133 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 179 optimal weight: 0.0070 chunk 122 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 HIS C 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071339 restraints weight = 26883.762| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.16 r_work: 0.2787 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17668 Z= 0.113 Angle : 0.493 8.369 24125 Z= 0.251 Chirality : 0.041 0.203 2842 Planarity : 0.003 0.051 2895 Dihedral : 8.327 88.766 2383 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.12 % Allowed : 10.52 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 2010 helix: 3.24 (0.18), residues: 748 sheet: 0.46 (0.25), residues: 411 loop : -0.21 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.010 0.001 TYR B 439 PHE 0.010 0.001 PHE B 473 TRP 0.013 0.001 TRP A 60 HIS 0.007 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17634) covalent geometry : angle 0.47617 / 0.25 (24030) SS BOND : bond 0.00907 / 0.44 ( 7) SS BOND : angle 3.83349 / 2.03 ( 14) hydrogen bonds : bond 0.04328 / 2.80 ( 860) hydrogen bonds : angle 4.03034 / 2.86 ( 2739) link_ALPHA1-3 : bond 0.00318 / 0.16 ( 4) link_ALPHA1-3 : angle 1.46368 / 0.85 ( 12) link_ALPHA1-6 : bond 0.00422 / 0.24 ( 6) link_ALPHA1-6 : angle 1.49979 / 0.99 ( 18) link_BETA1-4 : bond 0.00333 / 0.19 ( 9) link_BETA1-4 : angle 1.70309 / 1.10 ( 27) link_NAG-ASN : bond 0.00139 / 0.07 ( 8) link_NAG-ASN : angle 1.68587 / 0.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 186 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: C 165 LYS cc_start: 0.8702 (ptmt) cc_final: 0.7788 (tptt) REVERT: D 223 LEU cc_start: 0.9112 (mt) cc_final: 0.8858 (mm) REVERT: D 278 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7374 (tmt) REVERT: E 198 GLN cc_start: 0.8510 (mp-120) cc_final: 0.8121 (mp10) REVERT: E 438 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7805 (mm-30) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.5571 time to fit residues: 83.6421 Evaluate side-chains 133 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 438 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.071159 restraints weight = 27199.143| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.17 r_work: 0.2782 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17668 Z= 0.117 Angle : 0.501 8.340 24125 Z= 0.255 Chirality : 0.041 0.200 2842 Planarity : 0.004 0.050 2895 Dihedral : 8.216 89.568 2383 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.12 % Allowed : 10.57 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 2010 helix: 3.24 (0.18), residues: 748 sheet: 0.46 (0.25), residues: 411 loop : -0.21 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.010 0.001 TYR B 439 PHE 0.011 0.001 PHE B 473 TRP 0.011 0.001 TRP A 60 HIS 0.008 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17634) covalent geometry : angle 0.48366 / 0.25 (24030) SS BOND : bond 0.00905 / 0.44 ( 7) SS BOND : angle 3.82548 / 2.02 ( 14) hydrogen bonds : bond 0.04337 / 2.81 ( 860) hydrogen bonds : angle 4.03086 / 2.86 ( 2739) link_ALPHA1-3 : bond 0.00285 / 0.14 ( 4) link_ALPHA1-3 : angle 1.48097 / 0.87 ( 12) link_ALPHA1-6 : bond 0.00399 / 0.22 ( 6) link_ALPHA1-6 : angle 1.51617 / 1.00 ( 18) link_BETA1-4 : bond 0.00303 / 0.18 ( 9) link_BETA1-4 : angle 1.72656 / 1.12 ( 27) link_NAG-ASN : bond 0.00135 / 0.08 ( 8) link_NAG-ASN : angle 1.70631 / 1.00 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5337.03 seconds wall clock time: 91 minutes 49.69 seconds (5509.69 seconds total)