Starting phenix.real_space_refine on Fri Mar 6 14:00:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5b_10693/03_2026/6y5b_10693.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5b_10693/03_2026/6y5b_10693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5b_10693/03_2026/6y5b_10693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5b_10693/03_2026/6y5b_10693.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5b_10693/03_2026/6y5b_10693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5b_10693/03_2026/6y5b_10693.cif" } resolution = 3.1 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= 0.002 sd= 0.017 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 S 45 5.16 5 C 10311 2.51 5 N 2541 2.21 5 O 2738 1.98 5 H 15794 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31429 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6299 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 2 Chain: "B" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6243 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Chain: "C" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6293 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 2 Chain: "D" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6281 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 2 Chain: "E" Number of atoms: 6313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6313 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain breaks: 2 Time building chain proxies: 5.63, per 1000 atoms: 0.18 Number of scatterers: 31429 At special positions: 0 Unit cell: (100.672, 95.68, 155.584, 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 45 16.00 O 2738 8.00 N 2541 7.00 C 10311 6.00 H 15794 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 944.2 milliseconds 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3674 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 19 sheets defined 46.4% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.830A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.569A pdb=" N LEU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 Processing helix chain 'A' and resid 281 through 310 removed outlier: 3.627A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 405 through 422 removed outlier: 4.497A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.283A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 244 removed outlier: 4.422A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.669A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.676A pdb=" N HIS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.979A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'B' and resid 414 through 460 removed outlier: 5.263A pdb=" N VAL B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.719A pdb=" N ASP C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 244 removed outlier: 3.593A pdb=" N SER C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 249 through 273 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.631A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 419 through 462 removed outlier: 3.865A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.577A pdb=" N ALA D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.101A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.882A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 273 Processing helix chain 'D' and resid 282 through 309 removed outlier: 4.714A pdb=" N HIS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 419 through 462 removed outlier: 3.938A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 20 removed outlier: 3.944A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.872A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 220 through 243 removed outlier: 3.694A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 248 through 273 removed outlier: 3.926A pdb=" N VAL E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.611A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 405 through 418 Processing helix chain 'E' and resid 422 through 462 removed outlier: 3.672A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 52 removed outlier: 6.862A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 4.514A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 149 removed outlier: 4.090A pdb=" N GLN A 147 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.145A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.145A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.536A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.270A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.886A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 148 removed outlier: 5.851A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 52 removed outlier: 7.710A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 85 through 89 removed outlier: 4.202A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 98 through 99 Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.705A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 201 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 195 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 52 removed outlier: 7.448A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 85 through 89 removed outlier: 4.323A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 removed outlier: 4.499A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 4.499A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2397 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: 6.07 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15784 1.03 - 1.23: 83 1.23 - 1.42: 6764 1.42 - 1.62: 9161 1.62 - 1.82: 70 Bond restraints: 31862 Sorted by residual: bond pdb=" C LYS B 24 " pdb=" N LYS B 25 " ideal model delta sigma weight residual 1.335 1.430 -0.095 1.31e-02 5.83e+03 5.25e+01 bond pdb=" C ARG B 420 " pdb=" O ARG B 420 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.17e-02 7.31e+03 3.54e+01 bond pdb=" C ILE E 268 " pdb=" O ILE E 268 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.93e+01 bond pdb=" N THR E 280 " pdb=" CA THR E 280 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" C GLU B 421 " pdb=" O GLU B 421 " ideal model delta sigma weight residual 1.236 1.281 -0.044 1.15e-02 7.56e+03 1.47e+01 ... (remaining 31857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 51667 1.78 - 3.55: 5542 3.55 - 5.33: 408 5.33 - 7.10: 79 7.10 - 8.88: 10 Bond angle restraints: 57706 Sorted by residual: angle pdb=" C LEU A 436 " pdb=" N LEU A 437 " pdb=" CA LEU A 437 " ideal model delta sigma weight residual 120.44 127.74 -7.30 1.36e+00 5.41e-01 2.88e+01 angle pdb=" N ILE E 268 " pdb=" CA ILE E 268 " pdb=" CB ILE E 268 " ideal model delta sigma weight residual 110.54 117.83 -7.29 1.36e+00 5.41e-01 2.88e+01 angle pdb=" CA ILE E 268 " pdb=" C ILE E 268 " pdb=" O ILE E 268 " ideal model delta sigma weight residual 120.95 115.41 5.54 1.04e+00 9.25e-01 2.84e+01 angle pdb=" C LEU E 282 " pdb=" N ILE E 283 " pdb=" CA ILE E 283 " ideal model delta sigma weight residual 120.70 127.35 -6.65 1.25e+00 6.40e-01 2.83e+01 angle pdb=" CA ARG B 420 " pdb=" C ARG B 420 " pdb=" O ARG B 420 " ideal model delta sigma weight residual 120.55 114.94 5.61 1.06e+00 8.90e-01 2.80e+01 ... (remaining 57701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13724 17.95 - 35.90: 892 35.90 - 53.85: 249 53.85 - 71.80: 64 71.80 - 89.74: 19 Dihedral angle restraints: 14948 sinusoidal: 7973 harmonic: 6975 Sorted by residual: dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLN E 130 " pdb=" C GLN E 130 " pdb=" N LEU E 131 " pdb=" CA LEU E 131 " ideal model delta harmonic sigma weight residual 180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA VAL D 308 " pdb=" C VAL D 308 " pdb=" N HIS D 309 " pdb=" CA HIS D 309 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 14945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2066 0.058 - 0.117: 370 0.117 - 0.175: 95 0.175 - 0.233: 11 0.233 - 0.291: 4 Chirality restraints: 2546 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE E 268 " pdb=" CA ILE E 268 " pdb=" CG1 ILE E 268 " pdb=" CG2 ILE E 268 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2543 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 242 " -0.010 2.00e-02 2.50e+03 2.49e-02 1.86e+01 pdb=" CG PHE A 242 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 242 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 242 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 242 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 242 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 242 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE A 242 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 242 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 PHE A 242 " -0.049 2.00e-02 2.50e+03 pdb=" HZ PHE A 242 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 142 " -0.022 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C PHE B 142 " 0.074 2.00e-02 2.50e+03 pdb=" O PHE B 142 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO B 143 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 269 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C VAL E 269 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL E 269 " 0.027 2.00e-02 2.50e+03 pdb=" N SER E 270 " 0.025 2.00e-02 2.50e+03 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1781 2.21 - 2.81: 67441 2.81 - 3.40: 87888 3.40 - 4.00: 113862 4.00 - 4.60: 176401 Nonbonded interactions: 447373 Sorted by model distance: nonbonded pdb=" HG1 THR B 154 " pdb=" O ALA B 208 " model vdw 1.610 2.450 nonbonded pdb=" OE1 GLN C 56 " pdb=" H LEU C 137 " model vdw 1.611 2.450 nonbonded pdb=" HG3 GLU A 188 " pdb=" H LEU A 189 " model vdw 1.619 2.270 nonbonded pdb=" H THR C 90 " pdb=" O PRO C 113 " model vdw 1.632 2.450 nonbonded pdb="HD23 LEU E 15 " pdb="HD22 LEU E 86 " model vdw 1.637 2.440 ... (remaining 447368 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 8 through 309 or resid 318 through 328 or resid 404 throug \ h 462)) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or (resid 404 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name \ HE22)) or resid 405 through 462)) selection = (chain 'C' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or resid 404 through 462)) selection = (chain 'D' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or (resid 404 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name \ HE22)) or resid 405 through 462)) selection = (chain 'E' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 15 through 309 or resid 318 through 328 or resid 404 through 462)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.170 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.750 Find NCS groups from input model: 0.510 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 0.095 16073 Z= 0.352 Angle : 0.867 8.565 21955 Z= 0.556 Chirality : 0.051 0.291 2546 Planarity : 0.006 0.056 2685 Dihedral : 13.310 89.745 5769 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.18), residues: 1857 helix: -1.20 (0.16), residues: 796 sheet: -3.68 (0.18), residues: 448 loop : -1.49 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 424 TYR 0.023 0.002 TYR A 441 PHE 0.034 0.002 PHE A 103 TRP 0.018 0.001 TRP B 68 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00588 (16068) covalent geometry : angle 0.86728 (21945) SS BOND : bond 0.00131 ( 5) SS BOND : angle 1.03999 ( 10) hydrogen bonds : bond 0.16820 ( 806) hydrogen bonds : angle 7.28156 ( 2397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9102 (m-30) cc_final: 0.8502 (t0) REVERT: B 235 MET cc_start: 0.9232 (mtt) cc_final: 0.9016 (mtp) REVERT: D 210 MET cc_start: 0.7951 (tpt) cc_final: 0.7618 (tpt) REVERT: E 415 LYS cc_start: 0.9621 (tttt) cc_final: 0.9041 (tptt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.4409 time to fit residues: 87.7361 Evaluate side-chains 88 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN C 125 ASN C 184 GLN E 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.040765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.032622 restraints weight = 354539.595| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.58 r_work: 0.2944 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16073 Z= 0.210 Angle : 0.615 7.869 21955 Z= 0.337 Chirality : 0.043 0.161 2546 Planarity : 0.005 0.057 2685 Dihedral : 5.124 25.614 2067 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.02 % Allowed : 5.37 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.19), residues: 1857 helix: -0.09 (0.17), residues: 799 sheet: -3.11 (0.21), residues: 447 loop : -1.12 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.017 0.001 TYR A 441 PHE 0.025 0.001 PHE A 242 TRP 0.010 0.001 TRP E 68 HIS 0.004 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00433 (16068) covalent geometry : angle 0.61530 (21945) SS BOND : bond 0.00098 ( 5) SS BOND : angle 0.39245 ( 10) hydrogen bonds : bond 0.05073 ( 806) hydrogen bonds : angle 5.66286 ( 2397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9091 (m-30) cc_final: 0.8530 (t0) REVERT: B 235 MET cc_start: 0.9315 (mtt) cc_final: 0.9110 (mtp) REVERT: D 210 MET cc_start: 0.8419 (tpt) cc_final: 0.7938 (tpt) REVERT: D 419 MET cc_start: 0.7759 (tpt) cc_final: 0.7418 (tpt) REVERT: D 435 ARG cc_start: 0.9185 (mmp-170) cc_final: 0.8863 (mmp-170) outliers start: 18 outliers final: 15 residues processed: 97 average time/residue: 0.4334 time to fit residues: 56.3460 Evaluate side-chains 94 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.039894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.031783 restraints weight = 356327.394| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.51 r_work: 0.2905 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16073 Z= 0.240 Angle : 0.595 6.252 21955 Z= 0.326 Chirality : 0.043 0.153 2546 Planarity : 0.005 0.091 2685 Dihedral : 4.963 24.046 2067 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.96 % Allowed : 7.30 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1857 helix: 0.42 (0.17), residues: 794 sheet: -2.84 (0.22), residues: 452 loop : -0.96 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.017 0.001 TYR A 441 PHE 0.022 0.002 PHE A 242 TRP 0.012 0.001 TRP E 426 HIS 0.019 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00495 (16068) covalent geometry : angle 0.59504 (21945) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.33928 ( 10) hydrogen bonds : bond 0.04776 ( 806) hydrogen bonds : angle 5.40693 ( 2397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9092 (m-30) cc_final: 0.8551 (t0) REVERT: D 210 MET cc_start: 0.8595 (tpt) cc_final: 0.8221 (tpt) REVERT: D 435 ARG cc_start: 0.9220 (mmp-170) cc_final: 0.8901 (mmp-170) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.4193 time to fit residues: 52.2844 Evaluate side-chains 90 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 overall best weight: 2.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.031951 restraints weight = 350290.226| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.51 r_work: 0.2908 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16073 Z= 0.165 Angle : 0.550 6.642 21955 Z= 0.296 Chirality : 0.042 0.149 2546 Planarity : 0.004 0.068 2685 Dihedral : 4.750 22.162 2067 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.13 % Allowed : 8.26 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1857 helix: 0.82 (0.17), residues: 794 sheet: -2.61 (0.22), residues: 448 loop : -0.87 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 420 TYR 0.017 0.001 TYR A 441 PHE 0.023 0.001 PHE A 242 TRP 0.013 0.001 TRP E 426 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00347 (16068) covalent geometry : angle 0.55003 (21945) SS BOND : bond 0.00070 ( 5) SS BOND : angle 0.27178 ( 10) hydrogen bonds : bond 0.04270 ( 806) hydrogen bonds : angle 5.09083 ( 2397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9099 (m-30) cc_final: 0.8526 (t0) REVERT: D 210 MET cc_start: 0.8694 (tpt) cc_final: 0.8372 (tpt) REVERT: D 435 ARG cc_start: 0.9219 (mmp-170) cc_final: 0.8909 (mmp-170) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.4123 time to fit residues: 53.4213 Evaluate side-chains 94 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.039586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031473 restraints weight = 354723.972| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.49 r_work: 0.2894 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16073 Z= 0.188 Angle : 0.542 6.253 21955 Z= 0.293 Chirality : 0.042 0.145 2546 Planarity : 0.004 0.065 2685 Dihedral : 4.653 21.558 2067 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.07 % Allowed : 8.65 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1857 helix: 0.95 (0.17), residues: 799 sheet: -2.53 (0.23), residues: 445 loop : -0.73 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 416 TYR 0.016 0.001 TYR A 441 PHE 0.020 0.001 PHE A 242 TRP 0.015 0.001 TRP E 426 HIS 0.008 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00394 (16068) covalent geometry : angle 0.54249 (21945) SS BOND : bond 0.00101 ( 5) SS BOND : angle 0.26472 ( 10) hydrogen bonds : bond 0.04141 ( 806) hydrogen bonds : angle 5.02592 ( 2397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9105 (m-30) cc_final: 0.8533 (t0) REVERT: D 435 ARG cc_start: 0.9224 (mmp-170) cc_final: 0.8916 (mmp-170) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.4051 time to fit residues: 52.2786 Evaluate side-chains 96 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 127 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031367 restraints weight = 350989.509| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.45 r_work: 0.2889 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16073 Z= 0.163 Angle : 0.526 6.650 21955 Z= 0.283 Chirality : 0.042 0.143 2546 Planarity : 0.004 0.089 2685 Dihedral : 4.557 20.866 2067 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.07 % Allowed : 8.82 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1857 helix: 1.21 (0.17), residues: 794 sheet: -2.38 (0.23), residues: 448 loop : -0.74 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 120 TYR 0.016 0.001 TYR A 441 PHE 0.021 0.001 PHE A 242 TRP 0.013 0.001 TRP E 426 HIS 0.008 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00345 (16068) covalent geometry : angle 0.52641 (21945) SS BOND : bond 0.00091 ( 5) SS BOND : angle 0.23600 ( 10) hydrogen bonds : bond 0.03971 ( 806) hydrogen bonds : angle 4.87650 ( 2397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9094 (m-30) cc_final: 0.8523 (t0) REVERT: D 141 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (m-40) REVERT: D 435 ARG cc_start: 0.9230 (mmp-170) cc_final: 0.8931 (mmp-170) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.3824 time to fit residues: 51.2400 Evaluate side-chains 98 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.039643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.031584 restraints weight = 350983.060| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.47 r_work: 0.2896 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16073 Z= 0.123 Angle : 0.508 7.603 21955 Z= 0.270 Chirality : 0.041 0.156 2546 Planarity : 0.004 0.099 2685 Dihedral : 4.411 20.022 2067 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.19 % Allowed : 8.82 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1857 helix: 1.46 (0.18), residues: 794 sheet: -2.27 (0.23), residues: 450 loop : -0.61 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG E 120 TYR 0.015 0.001 TYR A 441 PHE 0.020 0.001 PHE A 242 TRP 0.011 0.001 TRP E 426 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00266 (16068) covalent geometry : angle 0.50826 (21945) SS BOND : bond 0.00054 ( 5) SS BOND : angle 0.21609 ( 10) hydrogen bonds : bond 0.03746 ( 806) hydrogen bonds : angle 4.77005 ( 2397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9132 (m-30) cc_final: 0.8583 (t0) REVERT: B 210 MET cc_start: 0.8697 (tpp) cc_final: 0.8495 (tpp) REVERT: D 141 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (m-40) REVERT: D 435 ARG cc_start: 0.9230 (mmp-170) cc_final: 0.8938 (mmp-170) outliers start: 21 outliers final: 18 residues processed: 98 average time/residue: 0.3639 time to fit residues: 50.1297 Evaluate side-chains 103 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.039514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.031455 restraints weight = 350360.494| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.46 r_work: 0.2891 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16073 Z= 0.142 Angle : 0.508 7.012 21955 Z= 0.271 Chirality : 0.041 0.141 2546 Planarity : 0.004 0.076 2685 Dihedral : 4.334 19.445 2067 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.07 % Allowed : 8.99 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1857 helix: 1.59 (0.18), residues: 794 sheet: -2.18 (0.23), residues: 454 loop : -0.58 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 120 TYR 0.015 0.001 TYR A 441 PHE 0.020 0.001 PHE A 242 TRP 0.012 0.001 TRP E 426 HIS 0.008 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00305 (16068) covalent geometry : angle 0.50820 (21945) SS BOND : bond 0.00096 ( 5) SS BOND : angle 0.21147 ( 10) hydrogen bonds : bond 0.03697 ( 806) hydrogen bonds : angle 4.71713 ( 2397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9105 (m-30) cc_final: 0.8535 (t0) REVERT: D 141 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: D 435 ARG cc_start: 0.9267 (mmp-170) cc_final: 0.8987 (mmp-170) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.3593 time to fit residues: 48.6487 Evaluate side-chains 99 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 177 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 167 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 100 optimal weight: 0.0270 chunk 104 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN C 125 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.039672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.031437 restraints weight = 352052.136| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.51 r_work: 0.2891 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16073 Z= 0.125 Angle : 0.500 7.456 21955 Z= 0.265 Chirality : 0.041 0.140 2546 Planarity : 0.004 0.072 2685 Dihedral : 4.268 18.781 2067 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.24 % Allowed : 8.99 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1857 helix: 1.70 (0.18), residues: 794 sheet: -2.12 (0.23), residues: 454 loop : -0.52 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 120 TYR 0.014 0.001 TYR A 441 PHE 0.019 0.001 PHE A 242 TRP 0.011 0.001 TRP E 426 HIS 0.008 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00270 (16068) covalent geometry : angle 0.49987 (21945) SS BOND : bond 0.00077 ( 5) SS BOND : angle 0.19671 ( 10) hydrogen bonds : bond 0.03595 ( 806) hydrogen bonds : angle 4.64390 ( 2397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9097 (m-30) cc_final: 0.8529 (t0) REVERT: B 210 MET cc_start: 0.8791 (tpp) cc_final: 0.8506 (tpp) REVERT: D 210 MET cc_start: 0.8803 (tpt) cc_final: 0.8509 (tpt) REVERT: D 435 ARG cc_start: 0.9267 (mmp-170) cc_final: 0.8988 (mmp-170) outliers start: 22 outliers final: 19 residues processed: 100 average time/residue: 0.3932 time to fit residues: 54.4881 Evaluate side-chains 102 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 118 optimal weight: 0.8980 chunk 101 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.040054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.031994 restraints weight = 345318.552| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.47 r_work: 0.2910 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16073 Z= 0.095 Angle : 0.492 7.919 21955 Z= 0.258 Chirality : 0.041 0.141 2546 Planarity : 0.004 0.068 2685 Dihedral : 4.175 18.161 2067 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.07 % Allowed : 9.33 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1857 helix: 1.88 (0.18), residues: 794 sheet: -2.05 (0.23), residues: 454 loop : -0.44 (0.28), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 120 TYR 0.015 0.001 TYR E 140 PHE 0.020 0.001 PHE A 242 TRP 0.010 0.001 TRP C 68 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00214 (16068) covalent geometry : angle 0.49218 (21945) SS BOND : bond 0.00040 ( 5) SS BOND : angle 0.19341 ( 10) hydrogen bonds : bond 0.03469 ( 806) hydrogen bonds : angle 4.54838 ( 2397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASP cc_start: 0.9092 (m-30) cc_final: 0.8518 (t0) REVERT: D 319 ASP cc_start: 0.9285 (m-30) cc_final: 0.8876 (t0) REVERT: D 435 ARG cc_start: 0.9261 (mmp-170) cc_final: 0.8991 (mmp-170) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.4020 time to fit residues: 54.2461 Evaluate side-chains 100 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 431 TYR Chi-restraints excluded: chain E residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 126 optimal weight: 0.0870 chunk 151 optimal weight: 0.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.039945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.031887 restraints weight = 349738.225| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.50 r_work: 0.2903 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16073 Z= 0.106 Angle : 0.492 7.889 21955 Z= 0.259 Chirality : 0.041 0.140 2546 Planarity : 0.004 0.063 2685 Dihedral : 4.113 18.054 2067 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.90 % Allowed : 9.50 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1857 helix: 1.91 (0.18), residues: 796 sheet: -2.01 (0.23), residues: 454 loop : -0.44 (0.28), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 120 TYR 0.013 0.001 TYR A 441 PHE 0.019 0.001 PHE A 242 TRP 0.009 0.001 TRP E 426 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00235 (16068) covalent geometry : angle 0.49252 (21945) SS BOND : bond 0.00063 ( 5) SS BOND : angle 0.16932 ( 10) hydrogen bonds : bond 0.03457 ( 806) hydrogen bonds : angle 4.52058 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6253.12 seconds wall clock time: 106 minutes 50.19 seconds (6410.19 seconds total)