Starting phenix.real_space_refine on Wed Feb 4 22:28:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lm6_63217/02_2026/9lm6_63217.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lm6_63217/02_2026/9lm6_63217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lm6_63217/02_2026/9lm6_63217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lm6_63217/02_2026/9lm6_63217.map" model { file = "/net/cci-nas-00/data/ceres_data/9lm6_63217/02_2026/9lm6_63217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lm6_63217/02_2026/9lm6_63217.cif" } resolution = 3.26 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= 0.001 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 8349 2.51 5 N 2193 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13278 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3496 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 930 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, E, F Time building chain proxies: 2.86, per 1000 atoms: 0.22 Number of scatterers: 13278 At special positions: 0 Unit cell: (134.9, 138.7, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2640 8.00 N 2193 7.00 C 8349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 113 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.02 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS F 101 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 113 " distance=2.03 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 113 " 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: 0.94 Conformation dependent library (CDL) restraints added in 403.7 milliseconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 28.4% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 73 through 94 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.645A pdb=" N LYS A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.389A pdb=" N ASN A 208 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 240 removed outlier: 4.023A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.501A pdb=" N ASN A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.655A pdb=" N GLN A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.936A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.976A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 518 removed outlier: 3.589A pdb=" N GLY A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'B' and resid 73 through 94 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.645A pdb=" N LYS B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 4.389A pdb=" N ASN B 208 " --> pdb=" O PRO B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 240 removed outlier: 4.023A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.501A pdb=" N ASN B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.655A pdb=" N GLN B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.937A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.975A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 518 removed outlier: 3.588A pdb=" N GLY B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'C' and resid 73 through 94 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.645A pdb=" N LYS C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 4.390A pdb=" N ASN C 208 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 240 removed outlier: 4.023A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.501A pdb=" N ASN C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.655A pdb=" N GLN C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.936A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.976A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 518 removed outlier: 3.588A pdb=" N GLY C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 361 removed outlier: 8.080A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 361 removed outlier: 8.080A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 10.707A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 287 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.625A pdb=" N GLY A 411 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 434 removed outlier: 6.642A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 7 through 8 Processing sheet with id=AA8, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.445A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 98 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 118 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.079A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.079A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP E 112 " --> pdb=" O SER E 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.707A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 287 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB4, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.626A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 431 through 434 removed outlier: 6.640A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 46 through 50 removed outlier: 5.445A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR E 98 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 118 " --> pdb=" O THR E 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 359 through 361 removed outlier: 8.079A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 361 removed outlier: 8.079A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP F 112 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.706A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 287 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AC3, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.626A pdb=" N GLY C 411 " --> pdb=" O THR C 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 434 removed outlier: 6.641A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AC6, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.444A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR F 98 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 118 " --> pdb=" O THR F 98 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1557 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: 2.32 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4329 1.35 - 1.48: 3202 1.48 - 1.61: 5828 1.61 - 1.74: 0 1.74 - 1.87: 126 Bond restraints: 13485 Sorted by residual: bond pdb=" CB CYS D 108 " pdb=" SG CYS D 108 " ideal model delta sigma weight residual 1.808 1.872 -0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB CYS E 108 " pdb=" SG CYS E 108 " ideal model delta sigma weight residual 1.808 1.872 -0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB CYS F 108 " pdb=" SG CYS F 108 " ideal model delta sigma weight residual 1.808 1.872 -0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" N ASP E 112 " pdb=" CA ASP E 112 " ideal model delta sigma weight residual 1.462 1.487 -0.025 1.35e-02 5.49e+03 3.50e+00 bond pdb=" N ASP F 112 " pdb=" CA ASP F 112 " ideal model delta sigma weight residual 1.462 1.487 -0.025 1.35e-02 5.49e+03 3.49e+00 ... (remaining 13480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 17914 1.90 - 3.81: 308 3.81 - 5.71: 30 5.71 - 7.61: 12 7.61 - 9.52: 3 Bond angle restraints: 18267 Sorted by residual: angle pdb=" C GLN B 361 " pdb=" N SER B 362 " pdb=" CA SER B 362 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C GLN A 361 " pdb=" N SER A 362 " pdb=" CA SER A 362 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C GLN C 361 " pdb=" N SER C 362 " pdb=" CA SER C 362 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CB MET F 93 " pdb=" CG MET F 93 " pdb=" SD MET F 93 " ideal model delta sigma weight residual 112.70 122.22 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET E 93 " pdb=" CG MET E 93 " pdb=" SD MET E 93 " ideal model delta sigma weight residual 112.70 122.18 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 18262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7273 17.97 - 35.95: 746 35.95 - 53.92: 141 53.92 - 71.89: 57 71.89 - 89.87: 15 Dihedral angle restraints: 8232 sinusoidal: 3201 harmonic: 5031 Sorted by residual: dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS B 69 " pdb=" SG CYS B 69 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual 93.00 161.79 -68.79 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual 93.00 161.78 -68.78 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 8229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1581 0.047 - 0.094: 465 0.094 - 0.141: 84 0.141 - 0.188: 6 0.188 - 0.235: 3 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CA CYS D 113 " pdb=" N CYS D 113 " pdb=" C CYS D 113 " pdb=" CB CYS D 113 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA CYS E 113 " pdb=" N CYS E 113 " pdb=" C CYS E 113 " pdb=" CB CYS E 113 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA CYS F 113 " pdb=" N CYS F 113 " pdb=" C CYS F 113 " pdb=" CB CYS F 113 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2136 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 204 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO B 205 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO C 205 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.30e+00 pdb=" N PRO A 205 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " 0.035 5.00e-02 4.00e+02 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1761 2.74 - 3.28: 13339 3.28 - 3.82: 21962 3.82 - 4.36: 25990 4.36 - 4.90: 44368 Nonbonded interactions: 107420 Sorted by model distance: nonbonded pdb=" OE2 GLU C 30 " pdb=" OH TYR C 441 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU B 30 " pdb=" OH TYR B 441 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU A 30 " pdb=" OH TYR A 441 " model vdw 2.205 3.040 nonbonded pdb=" OE1 GLN B 284 " pdb=" OH TYR B 306 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLN C 284 " pdb=" OH TYR C 306 " model vdw 2.214 3.040 ... (remaining 107415 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 0.064 13518 Z= 0.255 Angle : 0.648 9.516 18333 Z= 0.358 Chirality : 0.044 0.235 2139 Planarity : 0.004 0.063 2325 Dihedral : 15.784 89.867 4905 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.17 % Allowed : 13.10 % Favored : 83.73 % 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: -3.60 (0.17), residues: 1713 helix: -1.52 (0.22), residues: 447 sheet: -2.04 (0.21), residues: 483 loop : -3.13 (0.18), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 507 TYR 0.012 0.001 TYR A 86 PHE 0.009 0.001 PHE C 483 TRP 0.010 0.001 TRP B 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00561 (13485) covalent geometry : angle 0.63735 (18267) SS BOND : bond 0.00333 ( 33) SS BOND : angle 2.06971 ( 66) hydrogen bonds : bond 0.21090 ( 582) hydrogen bonds : angle 8.71113 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 0.545 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: A 335 THR cc_start: 0.8530 (p) cc_final: 0.8230 (p) REVERT: D 4 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7842 (tp40) REVERT: D 6 VAL cc_start: 0.9185 (t) cc_final: 0.8881 (p) REVERT: D 33 TYR cc_start: 0.7810 (t80) cc_final: 0.7294 (t80) REVERT: D 35 MET cc_start: 0.8049 (mmt) cc_final: 0.7810 (mmm) REVERT: D 37 TRP cc_start: 0.7187 (m100) cc_final: 0.6539 (m100) REVERT: D 95 TYR cc_start: 0.7787 (m-80) cc_final: 0.7452 (m-10) REVERT: E 4 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8121 (tp40) REVERT: E 6 VAL cc_start: 0.9116 (t) cc_final: 0.8826 (p) REVERT: E 33 TYR cc_start: 0.7771 (t80) cc_final: 0.7128 (t80) REVERT: E 35 MET cc_start: 0.8197 (mmt) cc_final: 0.7976 (mmp) REVERT: E 95 TYR cc_start: 0.7887 (m-80) cc_final: 0.7545 (m-10) REVERT: C 227 ASN cc_start: 0.8254 (t0) cc_final: 0.7436 (t0) REVERT: F 4 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: F 6 VAL cc_start: 0.9212 (t) cc_final: 0.8966 (p) REVERT: F 37 TRP cc_start: 0.7165 (m100) cc_final: 0.6899 (m100) REVERT: F 95 TYR cc_start: 0.7829 (m-80) cc_final: 0.7296 (m-10) outliers start: 48 outliers final: 11 residues processed: 289 average time/residue: 0.1130 time to fit residues: 46.9228 Evaluate side-chains 202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain F residue 4 GLN Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 345 ASN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN B 34 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 227 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 345 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.041535 restraints weight = 50120.228| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.83 r_work: 0.2602 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13518 Z= 0.160 Angle : 0.695 9.653 18333 Z= 0.365 Chirality : 0.044 0.159 2139 Planarity : 0.005 0.055 2325 Dihedral : 6.574 57.027 1868 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.31 % Allowed : 17.92 % Favored : 79.76 % 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: -2.48 (0.18), residues: 1713 helix: -0.05 (0.25), residues: 435 sheet: -1.47 (0.23), residues: 450 loop : -2.67 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 20 TYR 0.016 0.002 TYR B 299 PHE 0.013 0.001 PHE C 237 TRP 0.016 0.001 TRP E 37 HIS 0.005 0.002 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00354 (13485) covalent geometry : angle 0.68623 (18267) SS BOND : bond 0.00506 ( 33) SS BOND : angle 1.93720 ( 66) hydrogen bonds : bond 0.03857 ( 582) hydrogen bonds : angle 6.04418 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.369 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: A 335 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 339 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8413 (ptp90) REVERT: A 370 MET cc_start: 0.8822 (tmm) cc_final: 0.8297 (tmm) REVERT: A 429 ARG cc_start: 0.9232 (mmm-85) cc_final: 0.8965 (mmm-85) REVERT: D 35 MET cc_start: 0.8862 (mmt) cc_final: 0.8515 (tpp) REVERT: D 68 PHE cc_start: 0.8488 (m-10) cc_final: 0.7744 (m-80) REVERT: D 105 ASP cc_start: 0.8777 (m-30) cc_final: 0.8499 (m-30) REVERT: B 339 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8432 (ptp90) REVERT: B 396 MET cc_start: 0.8775 (ppp) cc_final: 0.8543 (ppp) REVERT: E 1 MET cc_start: 0.5957 (pmm) cc_final: 0.5702 (ptm) REVERT: E 35 MET cc_start: 0.9121 (mmt) cc_final: 0.8772 (mmp) REVERT: E 68 PHE cc_start: 0.8392 (m-10) cc_final: 0.7569 (m-80) REVERT: E 105 ASP cc_start: 0.8731 (m-30) cc_final: 0.8474 (m-30) REVERT: C 429 ARG cc_start: 0.9191 (mmm-85) cc_final: 0.8957 (mmm-85) REVERT: F 1 MET cc_start: 0.5858 (pmm) cc_final: 0.5628 (ptp) REVERT: F 5 LEU cc_start: 0.7156 (tt) cc_final: 0.6829 (tt) REVERT: F 37 TRP cc_start: 0.8366 (m100) cc_final: 0.8122 (m100) REVERT: F 68 PHE cc_start: 0.8444 (m-10) cc_final: 0.7649 (m-80) REVERT: F 71 SER cc_start: 0.9657 (t) cc_final: 0.9425 (p) REVERT: F 83 MET cc_start: 0.9206 (ppp) cc_final: 0.8901 (ppp) REVERT: F 93 MET cc_start: 0.9341 (tpp) cc_final: 0.8424 (tpp) REVERT: F 95 TYR cc_start: 0.9395 (m-80) cc_final: 0.8957 (m-10) REVERT: F 105 ASP cc_start: 0.8708 (m-30) cc_final: 0.8500 (m-30) REVERT: F 121 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7806 (mm-40) outliers start: 35 outliers final: 16 residues processed: 216 average time/residue: 0.1210 time to fit residues: 35.9368 Evaluate side-chains 197 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain F residue 30 TYR Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 73 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.038365 restraints weight = 51481.231| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 4.70 r_work: 0.2503 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 13518 Z= 0.358 Angle : 0.746 10.238 18333 Z= 0.387 Chirality : 0.045 0.226 2139 Planarity : 0.004 0.045 2325 Dihedral : 5.371 51.289 1852 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.17 % Allowed : 19.84 % Favored : 76.98 % 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: -1.94 (0.20), residues: 1713 helix: 0.77 (0.26), residues: 432 sheet: -1.44 (0.22), residues: 498 loop : -2.38 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.020 0.002 TYR F 33 PHE 0.011 0.002 PHE B 237 TRP 0.014 0.002 TRP A 314 HIS 0.007 0.002 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00792 (13485) covalent geometry : angle 0.73292 (18267) SS BOND : bond 0.00933 ( 33) SS BOND : angle 2.39132 ( 66) hydrogen bonds : bond 0.03810 ( 582) hydrogen bonds : angle 5.85731 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.492 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: A 289 MET cc_start: 0.8844 (tmm) cc_final: 0.8515 (tmm) REVERT: A 339 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8196 (ptp-170) REVERT: A 370 MET cc_start: 0.9041 (tmm) cc_final: 0.8609 (tmm) REVERT: A 396 MET cc_start: 0.8718 (ppp) cc_final: 0.8067 (tmm) REVERT: D 2 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7589 (tp40) REVERT: D 30 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.7442 (m-10) REVERT: D 35 MET cc_start: 0.8951 (mmt) cc_final: 0.8417 (mmm) REVERT: D 40 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8618 (tp40) REVERT: D 45 GLU cc_start: 0.9098 (tp30) cc_final: 0.8892 (tp30) REVERT: D 46 ARG cc_start: 0.8752 (ttm170) cc_final: 0.8526 (ttm170) REVERT: D 60 TYR cc_start: 0.9098 (m-80) cc_final: 0.8628 (m-80) REVERT: D 72 GLN cc_start: 0.9009 (pp30) cc_final: 0.8415 (tm-30) REVERT: D 73 ASP cc_start: 0.8630 (t0) cc_final: 0.8396 (t0) REVERT: D 93 MET cc_start: 0.9435 (tpp) cc_final: 0.8521 (tpp) REVERT: D 95 TYR cc_start: 0.9489 (m-80) cc_final: 0.8909 (m-10) REVERT: D 105 ASP cc_start: 0.8586 (m-30) cc_final: 0.8328 (m-30) REVERT: D 112 ASP cc_start: 0.9152 (t0) cc_final: 0.8612 (p0) REVERT: B 396 MET cc_start: 0.8753 (ppp) cc_final: 0.8468 (ppp) REVERT: E 1 MET cc_start: 0.6451 (pmm) cc_final: 0.5585 (ptm) REVERT: E 60 TYR cc_start: 0.9077 (m-80) cc_final: 0.8617 (m-80) REVERT: E 80 TYR cc_start: 0.9284 (m-80) cc_final: 0.9048 (m-80) REVERT: E 93 MET cc_start: 0.9335 (tpp) cc_final: 0.8407 (tpp) REVERT: E 95 TYR cc_start: 0.9487 (m-10) cc_final: 0.8831 (m-10) REVERT: E 105 ASP cc_start: 0.8663 (m-30) cc_final: 0.8355 (m-30) REVERT: E 112 ASP cc_start: 0.9151 (t0) cc_final: 0.8601 (p0) REVERT: E 114 ARG cc_start: 0.8544 (ppt170) cc_final: 0.7920 (ppt170) REVERT: C 396 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8481 (tmm) REVERT: F 1 MET cc_start: 0.5791 (pmm) cc_final: 0.5085 (ptp) REVERT: F 21 LEU cc_start: 0.9357 (tp) cc_final: 0.9138 (tp) REVERT: F 37 TRP cc_start: 0.8355 (m100) cc_final: 0.7625 (m100) REVERT: F 60 TYR cc_start: 0.9096 (m-80) cc_final: 0.8626 (m-80) REVERT: F 105 ASP cc_start: 0.8614 (m-30) cc_final: 0.8295 (m-30) REVERT: F 112 ASP cc_start: 0.9063 (t0) cc_final: 0.8532 (p0) REVERT: F 114 ARG cc_start: 0.8545 (ppt170) cc_final: 0.8032 (ppt170) outliers start: 48 outliers final: 25 residues processed: 211 average time/residue: 0.1246 time to fit residues: 37.0637 Evaluate side-chains 188 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 TYR Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 167 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 82 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040829 restraints weight = 50379.393| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.82 r_work: 0.2590 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 13518 Z= 0.129 Angle : 0.645 11.452 18333 Z= 0.331 Chirality : 0.043 0.205 2139 Planarity : 0.004 0.057 2325 Dihedral : 4.772 36.811 1851 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.45 % Allowed : 20.90 % Favored : 76.65 % 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: -1.48 (0.20), residues: 1713 helix: 1.20 (0.26), residues: 435 sheet: -1.03 (0.24), residues: 429 loop : -2.19 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 20 TYR 0.027 0.001 TYR F 33 PHE 0.009 0.001 PHE E 68 TRP 0.014 0.001 TRP E 37 HIS 0.009 0.002 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00304 (13485) covalent geometry : angle 0.63033 (18267) SS BOND : bond 0.00556 ( 33) SS BOND : angle 2.36830 ( 66) hydrogen bonds : bond 0.03035 ( 582) hydrogen bonds : angle 5.31080 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.477 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: A 339 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8101 (ptp-170) REVERT: A 370 MET cc_start: 0.9002 (tmm) cc_final: 0.8277 (tmm) REVERT: D 2 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7669 (tp40) REVERT: D 4 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8237 (tm-30) REVERT: D 5 LEU cc_start: 0.8589 (mm) cc_final: 0.7638 (tt) REVERT: D 38 TYR cc_start: 0.9077 (m-80) cc_final: 0.8821 (m-80) REVERT: D 40 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8503 (tp-100) REVERT: D 45 GLU cc_start: 0.8967 (tp30) cc_final: 0.8740 (tp30) REVERT: D 60 TYR cc_start: 0.9247 (m-80) cc_final: 0.8808 (m-80) REVERT: D 68 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: D 72 GLN cc_start: 0.9102 (pp30) cc_final: 0.8830 (pp30) REVERT: D 83 MET cc_start: 0.9332 (pmm) cc_final: 0.8653 (ppp) REVERT: D 93 MET cc_start: 0.9525 (tpp) cc_final: 0.8763 (tpp) REVERT: D 95 TYR cc_start: 0.9531 (m-80) cc_final: 0.8916 (m-10) REVERT: D 105 ASP cc_start: 0.8640 (m-30) cc_final: 0.8341 (m-30) REVERT: D 112 ASP cc_start: 0.9178 (t0) cc_final: 0.8610 (p0) REVERT: B 264 MET cc_start: 0.8460 (mmm) cc_final: 0.8031 (mmm) REVERT: B 339 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8043 (ptp-170) REVERT: B 396 MET cc_start: 0.8686 (ppp) cc_final: 0.8451 (ppp) REVERT: B 429 ARG cc_start: 0.9259 (mmm-85) cc_final: 0.9045 (mmm-85) REVERT: E 5 LEU cc_start: 0.8357 (mm) cc_final: 0.7201 (tt) REVERT: E 32 PHE cc_start: 0.8906 (m-10) cc_final: 0.8535 (m-10) REVERT: E 46 ARG cc_start: 0.8772 (ttm170) cc_final: 0.8529 (ttm170) REVERT: E 60 TYR cc_start: 0.9183 (m-80) cc_final: 0.8707 (m-80) REVERT: E 74 ASN cc_start: 0.8892 (m-40) cc_final: 0.8613 (p0) REVERT: E 98 THR cc_start: 0.9288 (p) cc_final: 0.8764 (t) REVERT: E 105 ASP cc_start: 0.8633 (m-30) cc_final: 0.8227 (m-30) REVERT: E 112 ASP cc_start: 0.9171 (t0) cc_final: 0.8629 (p0) REVERT: E 114 ARG cc_start: 0.8623 (ppt170) cc_final: 0.8009 (ppt170) REVERT: C 396 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8530 (tmm) REVERT: F 4 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7997 (tm-30) REVERT: F 21 LEU cc_start: 0.9335 (tp) cc_final: 0.8797 (pp) REVERT: F 37 TRP cc_start: 0.8191 (m100) cc_final: 0.7843 (m100) REVERT: F 53 ASP cc_start: 0.7950 (t0) cc_final: 0.7553 (t0) REVERT: F 60 TYR cc_start: 0.9172 (m-80) cc_final: 0.8768 (m-80) REVERT: F 81 LEU cc_start: 0.9747 (mt) cc_final: 0.9212 (mt) REVERT: F 83 MET cc_start: 0.9507 (pmm) cc_final: 0.8794 (ppp) REVERT: F 93 MET cc_start: 0.9467 (tpp) cc_final: 0.8446 (tpp) REVERT: F 95 TYR cc_start: 0.9439 (m-80) cc_final: 0.9053 (m-10) REVERT: F 105 ASP cc_start: 0.8606 (m-30) cc_final: 0.8298 (m-30) REVERT: F 112 ASP cc_start: 0.9115 (t0) cc_final: 0.8498 (p0) REVERT: F 114 ARG cc_start: 0.8640 (ppt170) cc_final: 0.8192 (ppt170) REVERT: F 121 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8195 (mm-40) outliers start: 37 outliers final: 18 residues processed: 208 average time/residue: 0.1436 time to fit residues: 40.6131 Evaluate side-chains 188 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 TYR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 139 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 93 optimal weight: 0.0070 chunk 107 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 74 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.3287 r_free = 0.3287 target = 0.060737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.039702 restraints weight = 51137.893| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.80 r_work: 0.2563 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 13518 Z= 0.196 Angle : 0.662 12.411 18333 Z= 0.339 Chirality : 0.042 0.229 2139 Planarity : 0.004 0.040 2325 Dihedral : 4.564 27.589 1848 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.11 % Allowed : 21.69 % Favored : 75.20 % 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: -1.29 (0.20), residues: 1713 helix: 1.44 (0.26), residues: 435 sheet: -1.08 (0.22), residues: 489 loop : -2.05 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 20 TYR 0.015 0.001 TYR F 30 PHE 0.008 0.001 PHE C 237 TRP 0.013 0.002 TRP D 37 HIS 0.009 0.002 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00458 (13485) covalent geometry : angle 0.64254 (18267) SS BOND : bond 0.00654 ( 33) SS BOND : angle 2.76183 ( 66) hydrogen bonds : bond 0.03062 ( 582) hydrogen bonds : angle 5.19184 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.513 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: A 339 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8107 (ptp-170) REVERT: A 370 MET cc_start: 0.9046 (tmm) cc_final: 0.8281 (tmm) REVERT: D 2 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7209 (tp40) REVERT: D 4 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8330 (mm-40) REVERT: D 5 LEU cc_start: 0.8436 (mm) cc_final: 0.7023 (tt) REVERT: D 35 MET cc_start: 0.8594 (mmt) cc_final: 0.8031 (mmm) REVERT: D 36 SER cc_start: 0.9125 (t) cc_final: 0.8908 (t) REVERT: D 38 TYR cc_start: 0.9039 (m-80) cc_final: 0.8776 (m-80) REVERT: D 40 GLN cc_start: 0.8932 (mm110) cc_final: 0.8614 (tp-100) REVERT: D 45 GLU cc_start: 0.8950 (tp30) cc_final: 0.8681 (tp30) REVERT: D 60 TYR cc_start: 0.9257 (m-80) cc_final: 0.8854 (m-80) REVERT: D 68 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: D 72 GLN cc_start: 0.9073 (pp30) cc_final: 0.8617 (pp30) REVERT: D 83 MET cc_start: 0.9312 (pmm) cc_final: 0.8592 (ppp) REVERT: D 93 MET cc_start: 0.9541 (tpp) cc_final: 0.8797 (tpp) REVERT: D 95 TYR cc_start: 0.9520 (m-80) cc_final: 0.8773 (m-10) REVERT: D 105 ASP cc_start: 0.8613 (m-30) cc_final: 0.8298 (m-30) REVERT: D 112 ASP cc_start: 0.9250 (t0) cc_final: 0.8680 (p0) REVERT: B 254 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8923 (m-40) REVERT: B 339 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8115 (ptp-170) REVERT: B 396 MET cc_start: 0.8713 (ppp) cc_final: 0.8449 (ppp) REVERT: E 5 LEU cc_start: 0.8254 (mm) cc_final: 0.7167 (tt) REVERT: E 32 PHE cc_start: 0.8999 (m-10) cc_final: 0.8664 (m-10) REVERT: E 36 SER cc_start: 0.9291 (t) cc_final: 0.9089 (t) REVERT: E 46 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8184 (tpp80) REVERT: E 60 TYR cc_start: 0.9170 (m-80) cc_final: 0.8741 (m-80) REVERT: E 68 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: E 74 ASN cc_start: 0.8907 (m110) cc_final: 0.8603 (p0) REVERT: E 93 MET cc_start: 0.9325 (tpp) cc_final: 0.8305 (tpp) REVERT: E 95 TYR cc_start: 0.9506 (m-80) cc_final: 0.8672 (m-10) REVERT: E 98 THR cc_start: 0.9362 (p) cc_final: 0.8932 (t) REVERT: E 105 ASP cc_start: 0.8574 (m-30) cc_final: 0.8258 (m-30) REVERT: E 112 ASP cc_start: 0.9203 (t0) cc_final: 0.8660 (p0) REVERT: E 114 ARG cc_start: 0.8679 (ppt170) cc_final: 0.8243 (ppt170) REVERT: C 396 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8492 (tmm) REVERT: C 429 ARG cc_start: 0.9327 (mmm-85) cc_final: 0.9123 (mmm-85) REVERT: F 4 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8047 (tm-30) REVERT: F 21 LEU cc_start: 0.9073 (tp) cc_final: 0.8643 (pp) REVERT: F 37 TRP cc_start: 0.8049 (m100) cc_final: 0.7787 (m100) REVERT: F 60 TYR cc_start: 0.9139 (m-80) cc_final: 0.8756 (m-80) REVERT: F 81 LEU cc_start: 0.9671 (mt) cc_final: 0.9452 (mt) REVERT: F 83 MET cc_start: 0.9525 (pmm) cc_final: 0.9057 (ppp) REVERT: F 105 ASP cc_start: 0.8586 (m-30) cc_final: 0.8262 (m-30) REVERT: F 112 ASP cc_start: 0.9198 (t0) cc_final: 0.8586 (p0) REVERT: F 114 ARG cc_start: 0.8644 (ppt170) cc_final: 0.8272 (ppt170) REVERT: F 121 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9052 (mm-40) outliers start: 47 outliers final: 19 residues processed: 206 average time/residue: 0.1302 time to fit residues: 36.9004 Evaluate side-chains 189 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 TYR Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 163 optimal weight: 6.9990 chunk 14 optimal weight: 0.0980 chunk 161 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.3301 r_free = 0.3301 target = 0.061262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.040200 restraints weight = 50848.032| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 4.83 r_work: 0.2580 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 13518 Z= 0.165 Angle : 0.646 12.585 18333 Z= 0.331 Chirality : 0.042 0.218 2139 Planarity : 0.004 0.040 2325 Dihedral : 4.450 26.936 1848 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.17 % Allowed : 21.63 % Favored : 75.20 % 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: -1.10 (0.20), residues: 1713 helix: 1.66 (0.26), residues: 435 sheet: -1.02 (0.23), residues: 459 loop : -1.91 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 20 TYR 0.022 0.001 TYR F 38 PHE 0.009 0.001 PHE C 237 TRP 0.012 0.001 TRP D 37 HIS 0.009 0.002 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00396 (13485) covalent geometry : angle 0.62637 (18267) SS BOND : bond 0.00709 ( 33) SS BOND : angle 2.71472 ( 66) hydrogen bonds : bond 0.02968 ( 582) hydrogen bonds : angle 5.00116 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.411 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: A 311 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 339 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8099 (ptp-170) REVERT: A 370 MET cc_start: 0.9065 (tmm) cc_final: 0.8281 (tmm) REVERT: D 2 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7202 (tp40) REVERT: D 4 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8734 (mm-40) REVERT: D 35 MET cc_start: 0.8607 (mmt) cc_final: 0.8089 (mmm) REVERT: D 38 TYR cc_start: 0.9037 (m-80) cc_final: 0.8810 (m-80) REVERT: D 40 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8461 (mm110) REVERT: D 45 GLU cc_start: 0.8926 (tp30) cc_final: 0.8718 (tp30) REVERT: D 46 ARG cc_start: 0.8683 (ttm170) cc_final: 0.8257 (ttm170) REVERT: D 60 TYR cc_start: 0.9222 (m-80) cc_final: 0.8864 (m-80) REVERT: D 68 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: D 72 GLN cc_start: 0.9019 (pp30) cc_final: 0.8349 (pp30) REVERT: D 83 MET cc_start: 0.9407 (pmm) cc_final: 0.8727 (ppp) REVERT: D 93 MET cc_start: 0.9555 (tpp) cc_final: 0.8829 (tpp) REVERT: D 95 TYR cc_start: 0.9518 (m-80) cc_final: 0.8731 (m-80) REVERT: D 105 ASP cc_start: 0.8623 (m-30) cc_final: 0.8326 (m-30) REVERT: D 112 ASP cc_start: 0.9297 (t0) cc_final: 0.8734 (p0) REVERT: B 264 MET cc_start: 0.8201 (mmt) cc_final: 0.7829 (mmt) REVERT: B 311 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8827 (p) REVERT: B 339 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8103 (ptp-170) REVERT: B 396 MET cc_start: 0.8709 (ppp) cc_final: 0.8433 (ppp) REVERT: E 4 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8069 (tm-30) REVERT: E 5 LEU cc_start: 0.8186 (mm) cc_final: 0.7630 (tt) REVERT: E 32 PHE cc_start: 0.9041 (m-10) cc_final: 0.8709 (m-10) REVERT: E 36 SER cc_start: 0.9261 (t) cc_final: 0.8968 (t) REVERT: E 38 TYR cc_start: 0.9054 (m-80) cc_final: 0.8598 (m-80) REVERT: E 46 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8206 (tpp80) REVERT: E 60 TYR cc_start: 0.9181 (m-80) cc_final: 0.8768 (m-80) REVERT: E 68 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: E 93 MET cc_start: 0.9449 (tpp) cc_final: 0.9213 (tpp) REVERT: E 95 TYR cc_start: 0.9518 (m-80) cc_final: 0.9269 (m-10) REVERT: E 98 THR cc_start: 0.9374 (p) cc_final: 0.8972 (t) REVERT: E 105 ASP cc_start: 0.8598 (m-30) cc_final: 0.8319 (m-30) REVERT: E 112 ASP cc_start: 0.9230 (t0) cc_final: 0.8717 (p0) REVERT: E 114 ARG cc_start: 0.8673 (ppt170) cc_final: 0.8243 (ppt170) REVERT: C 311 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8772 (p) REVERT: C 396 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8477 (tmm) REVERT: F 21 LEU cc_start: 0.9011 (tp) cc_final: 0.8803 (pp) REVERT: F 60 TYR cc_start: 0.9126 (m-80) cc_final: 0.8746 (m-80) REVERT: F 68 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: F 83 MET cc_start: 0.9559 (pmm) cc_final: 0.8988 (ppp) REVERT: F 103 GLU cc_start: 0.8958 (tt0) cc_final: 0.8466 (tt0) REVERT: F 105 ASP cc_start: 0.8625 (m-30) cc_final: 0.8334 (m-30) REVERT: F 112 ASP cc_start: 0.9197 (t0) cc_final: 0.8674 (p0) REVERT: F 114 ARG cc_start: 0.8697 (ppt170) cc_final: 0.8338 (ppt170) REVERT: F 121 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8978 (mm-40) outliers start: 48 outliers final: 28 residues processed: 206 average time/residue: 0.1161 time to fit residues: 33.7082 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 TYR Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.3323 r_free = 0.3323 target = 0.062085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.041097 restraints weight = 50955.430| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 4.87 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 13518 Z= 0.142 Angle : 0.669 12.778 18333 Z= 0.337 Chirality : 0.043 0.247 2139 Planarity : 0.004 0.040 2325 Dihedral : 4.336 26.725 1848 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.91 % Allowed : 22.49 % Favored : 74.60 % 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: -0.95 (0.20), residues: 1713 helix: 1.70 (0.26), residues: 435 sheet: -0.91 (0.23), residues: 426 loop : -1.77 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 429 TYR 0.017 0.001 TYR F 30 PHE 0.011 0.001 PHE C 237 TRP 0.030 0.002 TRP F 37 HIS 0.009 0.002 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00359 (13485) covalent geometry : angle 0.64870 (18267) SS BOND : bond 0.00651 ( 33) SS BOND : angle 2.81486 ( 66) hydrogen bonds : bond 0.02849 ( 582) hydrogen bonds : angle 4.84162 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.568 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: A 311 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8738 (p) REVERT: A 339 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8046 (ptp-170) REVERT: A 370 MET cc_start: 0.8741 (tmm) cc_final: 0.7927 (tmm) REVERT: D 2 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7252 (tp40) REVERT: D 4 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8687 (mm-40) REVERT: D 21 LEU cc_start: 0.9575 (mm) cc_final: 0.9297 (mm) REVERT: D 35 MET cc_start: 0.8508 (mmt) cc_final: 0.7906 (mmm) REVERT: D 45 GLU cc_start: 0.8934 (tp30) cc_final: 0.8601 (tp30) REVERT: D 46 ARG cc_start: 0.8470 (ttm170) cc_final: 0.7994 (ttm170) REVERT: D 60 TYR cc_start: 0.9252 (m-80) cc_final: 0.8869 (m-80) REVERT: D 64 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8565 (p) REVERT: D 68 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: D 83 MET cc_start: 0.9285 (pmm) cc_final: 0.8409 (ppp) REVERT: D 93 MET cc_start: 0.9543 (tpp) cc_final: 0.9268 (tpp) REVERT: D 95 TYR cc_start: 0.9460 (m-80) cc_final: 0.9073 (m-10) REVERT: D 105 ASP cc_start: 0.8443 (m-30) cc_final: 0.8074 (m-30) REVERT: D 112 ASP cc_start: 0.9406 (t0) cc_final: 0.8846 (p0) REVERT: D 121 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8769 (mm-40) REVERT: B 264 MET cc_start: 0.7909 (mmt) cc_final: 0.7653 (mmt) REVERT: B 311 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8749 (p) REVERT: B 339 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7930 (ptp-170) REVERT: B 396 MET cc_start: 0.8657 (ppp) cc_final: 0.8367 (ppp) REVERT: B 429 ARG cc_start: 0.9051 (mmm-85) cc_final: 0.8712 (mmm-85) REVERT: E 4 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8194 (tm-30) REVERT: E 5 LEU cc_start: 0.8314 (mm) cc_final: 0.7783 (tt) REVERT: E 32 PHE cc_start: 0.8996 (m-10) cc_final: 0.8697 (m-10) REVERT: E 35 MET cc_start: 0.9149 (mmt) cc_final: 0.8803 (mmm) REVERT: E 36 SER cc_start: 0.9187 (t) cc_final: 0.8969 (t) REVERT: E 38 TYR cc_start: 0.9011 (m-80) cc_final: 0.8587 (m-80) REVERT: E 46 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7990 (tpp80) REVERT: E 60 TYR cc_start: 0.9275 (m-80) cc_final: 0.8907 (m-80) REVERT: E 68 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: E 86 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8371 (mp) REVERT: E 93 MET cc_start: 0.9460 (tpp) cc_final: 0.9183 (tpp) REVERT: E 95 TYR cc_start: 0.9452 (m-80) cc_final: 0.9181 (m-10) REVERT: E 98 THR cc_start: 0.9349 (p) cc_final: 0.8706 (t) REVERT: E 105 ASP cc_start: 0.8460 (m-30) cc_final: 0.8119 (m-30) REVERT: E 112 ASP cc_start: 0.9314 (t0) cc_final: 0.8846 (p0) REVERT: E 114 ARG cc_start: 0.8542 (ppt170) cc_final: 0.8195 (ppt170) REVERT: C 311 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8698 (p) REVERT: F 20 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8256 (tmm160) REVERT: F 21 LEU cc_start: 0.9035 (tp) cc_final: 0.8691 (pp) REVERT: F 60 TYR cc_start: 0.9237 (m-80) cc_final: 0.8870 (m-80) REVERT: F 83 MET cc_start: 0.9576 (pmm) cc_final: 0.9278 (ppp) REVERT: F 99 ARG cc_start: 0.8886 (mtm110) cc_final: 0.8604 (mtp-110) REVERT: F 103 GLU cc_start: 0.8746 (tt0) cc_final: 0.8101 (tp30) REVERT: F 105 ASP cc_start: 0.8450 (m-30) cc_final: 0.7909 (m-30) REVERT: F 112 ASP cc_start: 0.9300 (t0) cc_final: 0.8755 (p0) REVERT: F 114 ARG cc_start: 0.8548 (ppt170) cc_final: 0.8268 (ppt170) REVERT: F 121 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8885 (mm-40) outliers start: 44 outliers final: 25 residues processed: 200 average time/residue: 0.1336 time to fit residues: 36.5701 Evaluate side-chains 198 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 126 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 150 optimal weight: 0.0000 chunk 128 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.3313 r_free = 0.3313 target = 0.061573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.040552 restraints weight = 50633.154| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.84 r_work: 0.2594 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 13518 Z= 0.165 Angle : 0.681 13.189 18333 Z= 0.343 Chirality : 0.043 0.267 2139 Planarity : 0.004 0.040 2325 Dihedral : 4.325 27.297 1848 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.58 % Allowed : 22.42 % Favored : 75.00 % 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: -0.88 (0.20), residues: 1713 helix: 1.82 (0.26), residues: 435 sheet: -0.92 (0.23), residues: 459 loop : -1.74 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 59 TYR 0.015 0.001 TYR A 250 PHE 0.010 0.001 PHE C 237 TRP 0.027 0.002 TRP F 37 HIS 0.009 0.002 HIS F 28 Details of bonding type rmsd covalent geometry : bond 0.00399 (13485) covalent geometry : angle 0.66190 (18267) SS BOND : bond 0.00721 ( 33) SS BOND : angle 2.72554 ( 66) hydrogen bonds : bond 0.02886 ( 582) hydrogen bonds : angle 4.81875 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8301 (mmm) cc_final: 0.7920 (mmm) REVERT: A 311 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 339 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8135 (ptp-170) REVERT: A 370 MET cc_start: 0.9070 (tmm) cc_final: 0.8286 (tmm) REVERT: A 429 ARG cc_start: 0.9215 (mmm-85) cc_final: 0.8901 (mmm-85) REVERT: D 2 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7193 (tp40) REVERT: D 4 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8729 (mm-40) REVERT: D 19 LEU cc_start: 0.8858 (pt) cc_final: 0.8644 (pp) REVERT: D 35 MET cc_start: 0.8583 (mmt) cc_final: 0.7938 (mmm) REVERT: D 45 GLU cc_start: 0.8734 (tp30) cc_final: 0.8414 (tp30) REVERT: D 60 TYR cc_start: 0.9226 (m-80) cc_final: 0.8924 (m-80) REVERT: D 83 MET cc_start: 0.9314 (pmm) cc_final: 0.8652 (ppp) REVERT: D 93 MET cc_start: 0.9577 (tpp) cc_final: 0.9188 (tpp) REVERT: D 95 TYR cc_start: 0.9553 (m-80) cc_final: 0.9278 (m-10) REVERT: D 105 ASP cc_start: 0.8613 (m-30) cc_final: 0.8262 (m-30) REVERT: D 112 ASP cc_start: 0.9468 (t0) cc_final: 0.8920 (p0) REVERT: D 121 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8710 (mm-40) REVERT: B 264 MET cc_start: 0.8230 (mmt) cc_final: 0.7868 (mmt) REVERT: B 311 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 339 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8112 (ptp-170) REVERT: B 396 MET cc_start: 0.8717 (ppp) cc_final: 0.8432 (ppp) REVERT: B 429 ARG cc_start: 0.9256 (mmm-85) cc_final: 0.8990 (mmm-85) REVERT: E 4 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8108 (tm-30) REVERT: E 5 LEU cc_start: 0.8231 (mm) cc_final: 0.7719 (tt) REVERT: E 32 PHE cc_start: 0.9101 (m-10) cc_final: 0.8818 (m-10) REVERT: E 46 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8184 (tpp80) REVERT: E 60 TYR cc_start: 0.9237 (m-80) cc_final: 0.8888 (m-80) REVERT: E 86 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8450 (mp) REVERT: E 93 MET cc_start: 0.9507 (tpp) cc_final: 0.9228 (tpp) REVERT: E 95 TYR cc_start: 0.9511 (m-80) cc_final: 0.9282 (m-10) REVERT: E 98 THR cc_start: 0.9397 (p) cc_final: 0.9005 (t) REVERT: E 105 ASP cc_start: 0.8637 (m-30) cc_final: 0.8305 (m-30) REVERT: E 112 ASP cc_start: 0.9362 (t0) cc_final: 0.8903 (p0) REVERT: E 114 ARG cc_start: 0.8702 (ppt170) cc_final: 0.8378 (ppt170) REVERT: C 311 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8758 (p) REVERT: C 429 ARG cc_start: 0.9353 (mmm-85) cc_final: 0.9124 (mmm-85) REVERT: F 21 LEU cc_start: 0.9196 (tp) cc_final: 0.8948 (pp) REVERT: F 60 TYR cc_start: 0.9248 (m-80) cc_final: 0.8909 (m-80) REVERT: F 83 MET cc_start: 0.9545 (pmm) cc_final: 0.9222 (ppp) REVERT: F 95 TYR cc_start: 0.9444 (m-10) cc_final: 0.8955 (m-10) REVERT: F 103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8382 (tp30) REVERT: F 105 ASP cc_start: 0.8649 (m-30) cc_final: 0.8157 (m-30) REVERT: F 112 ASP cc_start: 0.9451 (t0) cc_final: 0.8997 (p0) REVERT: F 114 ARG cc_start: 0.8703 (ppt170) cc_final: 0.8450 (ppt170) REVERT: F 121 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8596 (mm-40) outliers start: 39 outliers final: 30 residues processed: 198 average time/residue: 0.1501 time to fit residues: 40.9303 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 166 optimal weight: 0.0870 chunk 45 optimal weight: 0.0030 chunk 156 optimal weight: 3.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN C 317 HIS C 454 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.042264 restraints weight = 50797.687| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 4.95 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 13518 Z= 0.127 Angle : 0.692 15.221 18333 Z= 0.345 Chirality : 0.043 0.251 2139 Planarity : 0.004 0.040 2325 Dihedral : 4.325 25.625 1848 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.51 % Allowed : 22.29 % Favored : 75.20 % 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: -0.76 (0.20), residues: 1713 helix: 1.86 (0.26), residues: 435 sheet: -0.81 (0.23), residues: 426 loop : -1.64 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 20 TYR 0.026 0.001 TYR A 250 PHE 0.009 0.001 PHE C 237 TRP 0.018 0.002 TRP F 37 HIS 0.008 0.002 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00315 (13485) covalent geometry : angle 0.67572 (18267) SS BOND : bond 0.00751 ( 33) SS BOND : angle 2.59680 ( 66) hydrogen bonds : bond 0.02810 ( 582) hydrogen bonds : angle 4.61863 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7983 (mmm) cc_final: 0.7777 (mmm) REVERT: A 311 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8763 (p) REVERT: A 339 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7945 (ptp-170) REVERT: A 370 MET cc_start: 0.8708 (tmm) cc_final: 0.7917 (tmm) REVERT: A 429 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8458 (mmm-85) REVERT: D 2 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7339 (tp40) REVERT: D 4 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8681 (mm-40) REVERT: D 21 LEU cc_start: 0.9496 (mm) cc_final: 0.9139 (mm) REVERT: D 60 TYR cc_start: 0.9296 (m-80) cc_final: 0.9045 (m-80) REVERT: D 83 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8522 (ppp) REVERT: D 93 MET cc_start: 0.9566 (tpp) cc_final: 0.9210 (tpp) REVERT: D 95 TYR cc_start: 0.9537 (m-80) cc_final: 0.9305 (m-10) REVERT: D 105 ASP cc_start: 0.8438 (m-30) cc_final: 0.8053 (m-30) REVERT: D 121 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8682 (mm-40) REVERT: B 311 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8727 (p) REVERT: B 339 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7980 (ptp-170) REVERT: B 396 MET cc_start: 0.8599 (ppp) cc_final: 0.8299 (ppp) REVERT: B 429 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.7577 (mmm-85) REVERT: E 4 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8193 (tm-30) REVERT: E 5 LEU cc_start: 0.8258 (mm) cc_final: 0.7748 (tt) REVERT: E 32 PHE cc_start: 0.9031 (m-10) cc_final: 0.8723 (m-10) REVERT: E 35 MET cc_start: 0.9087 (mmt) cc_final: 0.8803 (mmm) REVERT: E 38 TYR cc_start: 0.8911 (m-80) cc_final: 0.8519 (m-80) REVERT: E 60 TYR cc_start: 0.9293 (m-80) cc_final: 0.9060 (m-80) REVERT: E 93 MET cc_start: 0.9498 (tpp) cc_final: 0.9203 (tpp) REVERT: E 95 TYR cc_start: 0.9451 (m-80) cc_final: 0.9132 (m-10) REVERT: E 98 THR cc_start: 0.9304 (p) cc_final: 0.8813 (t) REVERT: E 105 ASP cc_start: 0.8492 (m-30) cc_final: 0.8183 (m-30) REVERT: E 112 ASP cc_start: 0.9497 (t0) cc_final: 0.9083 (p0) REVERT: E 114 ARG cc_start: 0.8551 (ppt170) cc_final: 0.8187 (ppt170) REVERT: C 311 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8713 (p) REVERT: C 429 ARG cc_start: 0.9021 (mmm-85) cc_final: 0.8716 (mmm-85) REVERT: F 60 TYR cc_start: 0.9332 (m-80) cc_final: 0.9029 (m-80) REVERT: F 83 MET cc_start: 0.9573 (pmm) cc_final: 0.9137 (ppp) REVERT: F 95 TYR cc_start: 0.9410 (m-10) cc_final: 0.8997 (m-10) REVERT: F 103 GLU cc_start: 0.8766 (tt0) cc_final: 0.8538 (tt0) REVERT: F 105 ASP cc_start: 0.8360 (m-30) cc_final: 0.7999 (m-30) REVERT: F 112 ASP cc_start: 0.9520 (t0) cc_final: 0.9085 (p0) REVERT: F 121 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8501 (mm-40) outliers start: 38 outliers final: 29 residues processed: 201 average time/residue: 0.1318 time to fit residues: 36.6088 Evaluate side-chains 195 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.062462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.041388 restraints weight = 50984.383| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.90 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 13518 Z= 0.151 Angle : 0.711 14.253 18333 Z= 0.354 Chirality : 0.043 0.215 2139 Planarity : 0.004 0.046 2325 Dihedral : 4.353 25.000 1848 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.31 % Allowed : 22.95 % Favored : 74.74 % 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: -0.65 (0.20), residues: 1713 helix: 1.98 (0.26), residues: 435 sheet: -0.77 (0.23), residues: 456 loop : -1.59 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 20 TYR 0.030 0.001 TYR A 250 PHE 0.010 0.001 PHE C 237 TRP 0.019 0.002 TRP F 37 HIS 0.008 0.002 HIS F 28 Details of bonding type rmsd covalent geometry : bond 0.00360 (13485) covalent geometry : angle 0.69785 (18267) SS BOND : bond 0.00767 ( 33) SS BOND : angle 2.35706 ( 66) hydrogen bonds : bond 0.02914 ( 582) hydrogen bonds : angle 4.68879 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8089 (mmm) cc_final: 0.7780 (mmm) REVERT: A 311 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8749 (p) REVERT: A 339 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8082 (ptp-170) REVERT: A 370 MET cc_start: 0.8769 (tmm) cc_final: 0.7956 (tmm) REVERT: A 429 ARG cc_start: 0.8803 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: D 1 MET cc_start: 0.4632 (ptp) cc_final: 0.4278 (ptt) REVERT: D 2 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7481 (tp40) REVERT: D 4 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8681 (mm-40) REVERT: D 21 LEU cc_start: 0.9456 (mm) cc_final: 0.9175 (mm) REVERT: D 35 MET cc_start: 0.8636 (mmm) cc_final: 0.7585 (mmm) REVERT: D 44 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8298 (mmmm) REVERT: D 60 TYR cc_start: 0.9280 (m-80) cc_final: 0.9035 (m-80) REVERT: D 83 MET cc_start: 0.9117 (pmm) cc_final: 0.8393 (ppp) REVERT: D 105 ASP cc_start: 0.8399 (m-30) cc_final: 0.8038 (m-30) REVERT: D 121 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8639 (mm-40) REVERT: B 311 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8765 (p) REVERT: B 339 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8039 (ptp-170) REVERT: B 396 MET cc_start: 0.8646 (ppp) cc_final: 0.8315 (ppp) REVERT: B 429 ARG cc_start: 0.9048 (mmm-85) cc_final: 0.8740 (mmm-85) REVERT: E 4 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8200 (tm-30) REVERT: E 5 LEU cc_start: 0.8399 (mm) cc_final: 0.7845 (tt) REVERT: E 32 PHE cc_start: 0.9110 (m-10) cc_final: 0.8847 (m-10) REVERT: E 38 TYR cc_start: 0.8973 (m-80) cc_final: 0.8709 (m-80) REVERT: E 60 TYR cc_start: 0.9366 (m-80) cc_final: 0.9055 (m-80) REVERT: E 86 LEU cc_start: 0.8809 (tt) cc_final: 0.8420 (mt) REVERT: E 93 MET cc_start: 0.9501 (tpp) cc_final: 0.9271 (tpp) REVERT: E 98 THR cc_start: 0.9262 (p) cc_final: 0.8915 (t) REVERT: E 105 ASP cc_start: 0.8487 (m-30) cc_final: 0.8133 (m-30) REVERT: E 107 TYR cc_start: 0.9015 (m-80) cc_final: 0.8334 (m-10) REVERT: E 112 ASP cc_start: 0.9532 (t0) cc_final: 0.9166 (p0) REVERT: E 114 ARG cc_start: 0.8607 (ppt170) cc_final: 0.8149 (ppt170) REVERT: C 311 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8702 (p) REVERT: C 429 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8678 (mmm-85) REVERT: F 5 LEU cc_start: 0.8270 (pt) cc_final: 0.8048 (pt) REVERT: F 34 ASP cc_start: 0.8611 (t0) cc_final: 0.8326 (t70) REVERT: F 60 TYR cc_start: 0.9349 (m-80) cc_final: 0.9038 (m-80) REVERT: F 83 MET cc_start: 0.9540 (pmm) cc_final: 0.8990 (ppp) REVERT: F 95 TYR cc_start: 0.9404 (m-10) cc_final: 0.9029 (m-10) REVERT: F 103 GLU cc_start: 0.8793 (tt0) cc_final: 0.8209 (tp30) REVERT: F 105 ASP cc_start: 0.8342 (m-30) cc_final: 0.7990 (m-30) REVERT: F 112 ASP cc_start: 0.9581 (t0) cc_final: 0.9142 (p0) REVERT: F 121 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8432 (mm-40) outliers start: 35 outliers final: 28 residues processed: 193 average time/residue: 0.1351 time to fit residues: 36.4482 Evaluate side-chains 194 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.060796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.039523 restraints weight = 51470.203| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.84 r_work: 0.2561 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 13518 Z= 0.240 Angle : 0.731 12.937 18333 Z= 0.368 Chirality : 0.043 0.195 2139 Planarity : 0.004 0.038 2325 Dihedral : 4.491 27.115 1848 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.45 % Allowed : 23.02 % Favored : 74.54 % 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: -0.65 (0.20), residues: 1713 helix: 2.00 (0.26), residues: 435 sheet: -0.76 (0.23), residues: 459 loop : -1.62 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 20 TYR 0.035 0.002 TYR A 250 PHE 0.012 0.001 PHE B 237 TRP 0.020 0.002 TRP F 37 HIS 0.009 0.002 HIS F 28 Details of bonding type rmsd covalent geometry : bond 0.00542 (13485) covalent geometry : angle 0.71937 (18267) SS BOND : bond 0.00729 ( 33) SS BOND : angle 2.26787 ( 66) hydrogen bonds : bond 0.03106 ( 582) hydrogen bonds : angle 4.98926 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.40 seconds wall clock time: 49 minutes 20.20 seconds (2960.20 seconds total)