Starting phenix.real_space_refine on Sat Feb 17 03:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/02_2024/7smm_25202_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/02_2024/7smm_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/02_2024/7smm_25202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/02_2024/7smm_25202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/02_2024/7smm_25202_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smm_25202/02_2024/7smm_25202_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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 dihedrals: 21 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 15 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: 39 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: 49 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: 9.48, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 7.11 Conformation dependent library (CDL) restraints added in 3.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 50 helices and 22 sheets defined 40.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 213 through 234 removed outlier: 4.736A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.879A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 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 273 through 299 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 371 through 432 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) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.798A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 removed outlier: 3.829A pdb=" N GLN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 417 through 478 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 218 through 240 Proline residue: C 227 - end of helix removed outlier: 4.540A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 248 through 269 removed outlier: 4.425A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 399 through 459 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 213 through 234 removed outlier: 4.344A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.794A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 320 through 323 Processing helix chain 'D' and resid 371 through 432 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 3 through 12 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.718A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 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 282 through 308 Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 411 through 469 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 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) removed outlier: 6.363A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 77 through 81 Processing sheet with id= D, 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: 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= E, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.399A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 92 through 94 Processing sheet with id= G, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= H, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.799A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.497A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 58 through 61 Processing sheet with id= K, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= L, 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= M, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.799A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.005A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= P, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= Q, 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: 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= R, first strand: chain 'E' and resid 156 through 160 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) removed outlier: 6.478A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= T, first strand: chain 'E' and resid 77 through 81 Processing sheet with id= U, 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= V, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.917A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2316 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: 5.40 Time building geometry restraints manager: 7.67 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: 99.30 - 106.25: 510 106.25 - 113.20: 10236 113.20 - 120.15: 6024 120.15 - 127.10: 6997 127.10 - 134.05: 263 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: 10638 31.58 - 63.16: 296 63.16 - 94.74: 56 94.74 - 126.32: 18 126.32 - 157.90: 4 Dihedral angle restraints: 11012 sinusoidal: 4991 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 11009 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: 204 2.66 - 3.22: 16123 3.22 - 3.78: 27234 3.78 - 4.34: 39186 4.34 - 4.90: 63418 Nonbonded interactions: 146165 Sorted by model distance: nonbonded pdb=" O MET D 324 " pdb=" NH2 ARG D 331 " model vdw 2.099 2.520 nonbonded pdb=" NH1 ARG E 187 " pdb=" OE1 GLN E 216 " model vdw 2.187 2.520 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.213 2.520 nonbonded pdb=" OD1 ASP E 113 " pdb=" OG SER E 115 " model vdw 2.233 2.440 nonbonded pdb=" O LEU E 40 " pdb=" ND2 ASN E 181 " model vdw 2.237 2.520 ... (remaining 146160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.010 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: 4.430 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 48.180 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 17634 Z= 0.361 Angle : 0.776 12.568 24030 Z= 0.337 Chirality : 0.046 0.298 2842 Planarity : 0.003 0.044 2895 Dihedral : 16.089 157.898 7071 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (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 TRP 0.007 0.001 TRP B 176 HIS 0.006 0.001 HIS B 60 PHE 0.012 0.001 PHE E 422 TYR 0.009 0.001 TYR D 277 ARG 0.004 0.000 ARG C 168 *********************** 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 fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.973 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: 1.3878 time to fit residues: 227.9860 Evaluate side-chains 117 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 168 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 305 ASN B 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17634 Z= 0.184 Angle : 0.506 6.450 24030 Z= 0.261 Chirality : 0.043 0.184 2842 Planarity : 0.004 0.042 2895 Dihedral : 13.272 142.580 3140 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.75 % Allowed : 4.75 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.19), residues: 2010 helix: 2.98 (0.18), residues: 738 sheet: 0.43 (0.26), residues: 411 loop : -0.37 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 60 HIS 0.005 0.001 HIS B 313 PHE 0.013 0.001 PHE D 256 TYR 0.012 0.001 TYR E 117 ARG 0.008 0.000 ARG A 66 *********************** 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 144 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 2.090 Fit side-chains REVERT: A 397 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6600 (tm-30) REVERT: B 214 ASP cc_start: 0.8458 (t70) cc_final: 0.8091 (t70) REVERT: B 293 MET cc_start: 0.8069 (mmp) cc_final: 0.7733 (mmp) REVERT: E 116 MET cc_start: 0.8929 (mmm) cc_final: 0.8662 (mmm) outliers start: 14 outliers final: 3 residues processed: 137 average time/residue: 1.2754 time to fit residues: 196.9440 Evaluate side-chains 120 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ASP 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 100 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 0.0970 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN B 267 GLN B 328 GLN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17634 Z= 0.288 Angle : 0.529 8.186 24030 Z= 0.272 Chirality : 0.044 0.248 2842 Planarity : 0.004 0.049 2895 Dihedral : 12.438 132.997 3140 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.33 % Allowed : 6.41 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2010 helix: 2.97 (0.18), residues: 743 sheet: 0.45 (0.25), residues: 414 loop : -0.37 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS A 204 PHE 0.014 0.001 PHE B 473 TYR 0.010 0.001 TYR D 277 ARG 0.007 0.000 ARG A 66 *********************** 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 154 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: B 186 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: C 165 LYS cc_start: 0.8483 (ptmt) cc_final: 0.7691 (tptt) REVERT: C 200 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8002 (p0) outliers start: 25 outliers final: 8 residues processed: 139 average time/residue: 1.2959 time to fit residues: 203.0059 Evaluate side-chains 129 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 94 optimal weight: 0.0020 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 chunk 182 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 328 GLN B 437 ASN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17634 Z= 0.165 Angle : 0.473 6.584 24030 Z= 0.244 Chirality : 0.042 0.211 2842 Planarity : 0.003 0.048 2895 Dihedral : 11.569 121.547 3138 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 7.69 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.19), residues: 2010 helix: 3.14 (0.18), residues: 743 sheet: 0.49 (0.25), residues: 414 loop : -0.32 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.000 HIS B 313 PHE 0.012 0.001 PHE D 256 TYR 0.011 0.001 TYR D 277 ARG 0.003 0.000 ARG A 66 *********************** 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 148 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.914 Fit side-chains REVERT: A 278 MET cc_start: 0.7390 (ttt) cc_final: 0.7087 (ttt) REVERT: B 186 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: B 214 ASP cc_start: 0.8423 (t70) cc_final: 0.8047 (OUTLIER) REVERT: D 128 CYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6403 (t) outliers start: 27 outliers final: 11 residues processed: 137 average time/residue: 1.2533 time to fit residues: 193.8717 Evaluate side-chains 129 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.050 ------------------------------------------------------------------------------- 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 C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 274 ILE 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 161 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 328 GLN B 437 ASN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17634 Z= 0.277 Angle : 0.512 6.646 24030 Z= 0.263 Chirality : 0.043 0.219 2842 Planarity : 0.004 0.052 2895 Dihedral : 11.362 114.196 3138 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 8.60 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 2010 helix: 3.06 (0.18), residues: 744 sheet: 0.48 (0.25), residues: 414 loop : -0.33 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.004 0.001 HIS A 204 PHE 0.014 0.001 PHE B 473 TYR 0.010 0.001 TYR B 439 ARG 0.003 0.000 ARG A 66 *********************** 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 154 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 2.053 Fit side-chains REVERT: A 260 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8484 (mt) REVERT: B 186 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 214 ASP cc_start: 0.8457 (t70) cc_final: 0.8107 (t70) REVERT: B 293 MET cc_start: 0.8088 (mmp) cc_final: 0.7776 (mmp) REVERT: C 165 LYS cc_start: 0.8524 (ptmt) cc_final: 0.7762 (tptt) REVERT: C 200 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8011 (p0) REVERT: D 128 CYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6205 (t) REVERT: E 323 HIS cc_start: 0.7211 (m-70) cc_final: 0.6921 (m-70) REVERT: E 438 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7372 (mm-30) outliers start: 29 outliers final: 14 residues processed: 139 average time/residue: 1.3358 time to fit residues: 208.9476 Evaluate side-chains 137 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 454 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 128 CYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 328 GLN B 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17634 Z= 0.170 Angle : 0.467 6.531 24030 Z= 0.241 Chirality : 0.042 0.226 2842 Planarity : 0.003 0.055 2895 Dihedral : 10.865 105.943 3138 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.82 % Allowed : 9.24 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2010 helix: 3.22 (0.18), residues: 736 sheet: 0.50 (0.25), residues: 409 loop : -0.34 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 313 PHE 0.011 0.001 PHE B 473 TYR 0.011 0.001 TYR D 277 ARG 0.002 0.000 ARG D 301 *********************** 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 157 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.891 Fit side-chains REVERT: A 46 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8397 (t) REVERT: A 142 CYS cc_start: 0.4565 (OUTLIER) cc_final: 0.4146 (m) REVERT: A 260 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 278 MET cc_start: 0.7321 (ttt) cc_final: 0.6913 (ttt) REVERT: A 326 PHE cc_start: 0.7452 (m-10) cc_final: 0.6445 (p90) REVERT: B 186 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: B 214 ASP cc_start: 0.8342 (t70) cc_final: 0.8067 (t70) REVERT: C 165 LYS cc_start: 0.8478 (ptmt) cc_final: 0.7713 (tptt) REVERT: C 200 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (p0) REVERT: E 323 HIS cc_start: 0.7247 (m-70) cc_final: 0.6942 (m-70) REVERT: E 438 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7307 (mm-30) outliers start: 34 outliers final: 13 residues processed: 146 average time/residue: 1.1595 time to fit residues: 191.3359 Evaluate side-chains 133 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 162 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN B 267 GLN B 328 GLN B 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17634 Z= 0.161 Angle : 0.461 8.155 24030 Z= 0.236 Chirality : 0.041 0.223 2842 Planarity : 0.003 0.055 2895 Dihedral : 10.509 97.422 3138 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.55 % Allowed : 9.50 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 2010 helix: 3.26 (0.18), residues: 742 sheet: 0.54 (0.25), residues: 410 loop : -0.29 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.000 HIS B 313 PHE 0.011 0.001 PHE B 473 TYR 0.009 0.001 TYR B 439 ARG 0.003 0.000 ARG A 66 *********************** 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 147 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 2.223 Fit side-chains REVERT: A 46 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8433 (t) REVERT: A 260 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 278 MET cc_start: 0.7307 (ttt) cc_final: 0.6852 (ttt) REVERT: A 326 PHE cc_start: 0.7430 (m-10) cc_final: 0.6458 (p90) REVERT: B 186 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: B 214 ASP cc_start: 0.8300 (t70) cc_final: 0.8053 (t70) REVERT: C 165 LYS cc_start: 0.8470 (ptmt) cc_final: 0.7729 (tptt) REVERT: C 200 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7974 (p0) REVERT: E 438 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7308 (mm-30) outliers start: 29 outliers final: 12 residues processed: 137 average time/residue: 1.2092 time to fit residues: 188.0139 Evaluate side-chains 131 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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 C residue 200 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 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 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 119 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 175 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 328 GLN B 437 ASN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17634 Z= 0.236 Angle : 0.493 8.438 24030 Z= 0.253 Chirality : 0.042 0.221 2842 Planarity : 0.004 0.053 2895 Dihedral : 10.551 90.251 3138 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.49 % Allowed : 9.66 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2010 helix: 3.18 (0.18), residues: 742 sheet: 0.49 (0.25), residues: 415 loop : -0.30 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.003 0.001 HIS A 204 PHE 0.014 0.001 PHE B 473 TYR 0.010 0.001 TYR B 439 ARG 0.004 0.000 ARG A 66 *********************** 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 fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 2.188 Fit side-chains REVERT: A 46 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8357 (t) REVERT: B 186 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: B 214 ASP cc_start: 0.8307 (t70) cc_final: 0.8045 (t70) REVERT: C 165 LYS cc_start: 0.8489 (ptmt) cc_final: 0.7740 (tptt) REVERT: C 200 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (p0) REVERT: E 323 HIS cc_start: 0.7151 (m-70) cc_final: 0.6814 (m-70) REVERT: E 438 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7311 (mm-30) outliers start: 28 outliers final: 12 residues processed: 134 average time/residue: 1.2047 time to fit residues: 183.1487 Evaluate side-chains 130 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 328 GLN B 437 ASN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17634 Z= 0.157 Angle : 0.463 10.042 24030 Z= 0.237 Chirality : 0.041 0.223 2842 Planarity : 0.003 0.052 2895 Dihedral : 10.211 88.171 3138 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.07 % Allowed : 10.30 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 2010 helix: 3.26 (0.18), residues: 742 sheet: 0.52 (0.26), residues: 408 loop : -0.27 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.004 0.000 HIS B 313 PHE 0.011 0.001 PHE D 256 TYR 0.009 0.001 TYR B 439 ARG 0.004 0.000 ARG A 66 *********************** 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 136 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 2.138 Fit side-chains REVERT: A 46 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8368 (t) REVERT: B 186 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: B 214 ASP cc_start: 0.8263 (t70) cc_final: 0.8036 (t70) REVERT: C 165 LYS cc_start: 0.8467 (ptmt) cc_final: 0.7729 (tptt) REVERT: C 200 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7971 (p0) REVERT: E 438 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7308 (mm-30) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 1.2549 time to fit residues: 184.5620 Evaluate side-chains 131 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 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 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 115 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN B 328 GLN B 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17634 Z= 0.232 Angle : 0.495 10.918 24030 Z= 0.253 Chirality : 0.042 0.219 2842 Planarity : 0.004 0.054 2895 Dihedral : 10.224 83.896 3138 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.07 % Allowed : 10.36 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2010 helix: 3.18 (0.18), residues: 741 sheet: 0.51 (0.25), residues: 414 loop : -0.31 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.004 0.001 HIS A 204 PHE 0.014 0.001 PHE B 473 TYR 0.010 0.001 TYR D 277 ARG 0.005 0.000 ARG A 66 ********************** 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 135 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.947 Fit side-chains revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8348 (t) REVERT: B 186 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 214 ASP cc_start: 0.8294 (t70) cc_final: 0.8044 (t70) REVERT: C 165 LYS cc_start: 0.8487 (ptmt) cc_final: 0.7747 (tptt) REVERT: C 200 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7977 (p0) REVERT: E 438 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7312 (mm-30) outliers start: 20 outliers final: 12 residues processed: 127 average time/residue: 1.2646 time to fit residues: 181.1941 Evaluate side-chains 130 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 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 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 48 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN B 437 ASN E 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.092513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070632 restraints weight = 27425.923| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.17 r_work: 0.2763 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17634 Z= 0.168 Angle : 0.465 10.342 24030 Z= 0.238 Chirality : 0.041 0.224 2842 Planarity : 0.003 0.053 2895 Dihedral : 9.873 81.933 3138 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.12 % Allowed : 10.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2010 helix: 3.23 (0.18), residues: 742 sheet: 0.53 (0.26), residues: 408 loop : -0.28 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.000 HIS B 313 PHE 0.011 0.001 PHE B 473 TYR 0.009 0.001 TYR B 439 ARG 0.004 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4697.14 seconds wall clock time: 85 minutes 49.09 seconds (5149.09 seconds total)