Starting phenix.real_space_refine on Sun Aug 24 00:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz3_37945/08_2025/8wz3_37945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz3_37945/08_2025/8wz3_37945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz3_37945/08_2025/8wz3_37945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz3_37945/08_2025/8wz3_37945.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz3_37945/08_2025/8wz3_37945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz3_37945/08_2025/8wz3_37945.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 90 5.16 5 C 9987 2.51 5 N 2577 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15741 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 925 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, G, H, K, B, C Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 15741 At special positions: 0 Unit cell: (138.484, 150.154, 123.702, 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 90 16.00 O 3087 8.00 N 2577 7.00 C 9987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 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=2.33 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=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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=2.33 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.33 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=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 500 " " NAG B 601 " - " ASN B 500 " " NAG C 601 " - " ASN C 500 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 733.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 36 sheets defined 25.4% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR D 91 " --> pdb=" O ASN D 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 98 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 209 Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'E' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR E 91 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 98 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 209 Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER B 372 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.184A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.859A pdb=" N LEU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 142' Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 209 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.805A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.750A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL D 18 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.634A pdb=" N THR D 113 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 94 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.634A pdb=" N THR D 113 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 94 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 98 " --> pdb=" O TYR D 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.794A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.663A pdb=" N TRP A 341 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG A 49 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 307 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 301 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.894A pdb=" N SER A 398 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL E 18 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 94 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 94 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 98 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.793A pdb=" N GLN H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AC1, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.663A pdb=" N TRP B 341 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG B 49 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 307 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 301 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 333 through 336 removed outlier: 3.895A pdb=" N SER B 398 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 431 through 434 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.509A pdb=" N VAL G 18 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR G 113 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 110 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR G 94 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.633A pdb=" N THR G 113 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 110 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR G 94 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG G 98 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.794A pdb=" N GLN K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'C' and resid 373 through 375 removed outlier: 3.662A pdb=" N TRP C 341 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ARG C 49 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.336A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 333 through 336 removed outlier: 3.894A pdb=" N SER C 398 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.536A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 431 through 434 684 hydrogen bonds defined for protein. 1764 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: 2.13 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2607 1.30 - 1.43: 4050 1.43 - 1.56: 9258 1.56 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 16035 Sorted by residual: bond pdb=" C PHE B 190 " pdb=" O PHE B 190 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.29e-02 6.01e+03 2.89e+01 bond pdb=" C PHE A 190 " pdb=" O PHE A 190 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.29e-02 6.01e+03 2.87e+01 bond pdb=" C PHE C 190 " pdb=" O PHE C 190 " ideal model delta sigma weight residual 1.234 1.166 0.069 1.29e-02 6.01e+03 2.85e+01 bond pdb=" C PHE C 190 " pdb=" N LYS C 191 " ideal model delta sigma weight residual 1.331 1.290 0.040 1.29e-02 6.01e+03 9.82e+00 bond pdb=" C PHE B 190 " pdb=" N LYS B 191 " ideal model delta sigma weight residual 1.331 1.290 0.040 1.29e-02 6.01e+03 9.77e+00 ... (remaining 16030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 20891 1.39 - 2.78: 693 2.78 - 4.16: 115 4.16 - 5.55: 24 5.55 - 6.94: 6 Bond angle restraints: 21729 Sorted by residual: angle pdb=" CA PHE A 190 " pdb=" C PHE A 190 " pdb=" O PHE A 190 " ideal model delta sigma weight residual 120.75 116.12 4.63 1.12e+00 7.97e-01 1.71e+01 angle pdb=" CA PHE B 190 " pdb=" C PHE B 190 " pdb=" O PHE B 190 " ideal model delta sigma weight residual 120.75 116.13 4.62 1.12e+00 7.97e-01 1.70e+01 angle pdb=" CA PHE C 190 " pdb=" C PHE C 190 " pdb=" O PHE C 190 " ideal model delta sigma weight residual 120.75 116.15 4.60 1.12e+00 7.97e-01 1.69e+01 angle pdb=" N GLN C 501 " pdb=" CA GLN C 501 " pdb=" C GLN C 501 " ideal model delta sigma weight residual 111.33 106.91 4.42 1.21e+00 6.83e-01 1.33e+01 angle pdb=" N GLN B 501 " pdb=" CA GLN B 501 " pdb=" C GLN B 501 " ideal model delta sigma weight residual 111.33 106.93 4.40 1.21e+00 6.83e-01 1.32e+01 ... (remaining 21724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 9073 23.41 - 46.83: 551 46.83 - 70.24: 60 70.24 - 93.66: 3 93.66 - 117.07: 51 Dihedral angle restraints: 9738 sinusoidal: 3879 harmonic: 5859 Sorted by residual: dihedral pdb=" CB CYS A 37 " pdb=" SG CYS A 37 " pdb=" SG CYS A 439 " pdb=" CB CYS A 439 " ideal model delta sinusoidal sigma weight residual 93.00 158.36 -65.36 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CB CYS B 37 " pdb=" SG CYS B 37 " pdb=" SG CYS B 439 " pdb=" CB CYS B 439 " ideal model delta sinusoidal sigma weight residual 93.00 158.34 -65.34 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CB CYS C 37 " pdb=" SG CYS C 37 " pdb=" SG CYS C 439 " pdb=" CB CYS C 439 " ideal model delta sinusoidal sigma weight residual 93.00 158.34 -65.34 1 1.00e+01 1.00e-02 5.59e+01 ... (remaining 9735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2501 0.128 - 0.256: 13 0.256 - 0.385: 3 0.385 - 0.513: 0 0.513 - 0.641: 3 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 500 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 500 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 2517 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 200 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASP B 200 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP B 200 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS B 201 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 200 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C ASP C 200 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP C 200 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 201 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 200 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ASP A 200 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP A 200 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 201 " -0.011 2.00e-02 2.50e+03 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 378 2.69 - 3.24: 15005 3.24 - 3.79: 23054 3.79 - 4.35: 32573 4.35 - 4.90: 55851 Nonbonded interactions: 126861 Sorted by model distance: nonbonded pdb=" OH TYR D 99 " pdb=" OH TYR F 96 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OH TYR H 96 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR G 99 " pdb=" OH TYR K 96 " model vdw 2.134 3.040 nonbonded pdb=" O ARG B 49 " pdb=" OG1 THR B 369 " model vdw 2.159 3.040 nonbonded pdb=" O ARG C 49 " pdb=" OG1 THR C 369 " model vdw 2.159 3.040 ... (remaining 126856 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 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 0.299 16068 Z= 0.276 Angle : 0.729 33.613 21798 Z= 0.400 Chirality : 0.049 0.641 2520 Planarity : 0.004 0.046 2736 Dihedral : 16.998 117.069 5886 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -4.35 (0.15), residues: 1992 helix: -0.87 (0.22), residues: 432 sheet: -3.45 (0.15), residues: 711 loop : -3.33 (0.16), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 282 TYR 0.015 0.001 TYR B 342 PHE 0.011 0.001 PHE K 91 TRP 0.008 0.001 TRP C 52 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00369 (16035) covalent geometry : angle 0.60405 (21729) SS BOND : bond 0.09458 ( 30) SS BOND : angle 7.76178 ( 60) hydrogen bonds : bond 0.21612 ( 657) hydrogen bonds : angle 8.67161 ( 1764) link_NAG-ASN : bond 0.00673 ( 3) link_NAG-ASN : angle 2.46183 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7515 (mtpp) REVERT: F 42 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7771 (mtmt) REVERT: F 79 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: H 42 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7768 (mtmt) REVERT: H 79 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: B 274 MET cc_start: 0.8146 (mtp) cc_final: 0.7945 (mtt) REVERT: B 289 MET cc_start: 0.8512 (tpt) cc_final: 0.7838 (tpt) REVERT: K 37 GLN cc_start: 0.8382 (pt0) cc_final: 0.8119 (pt0) REVERT: K 79 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: C 289 MET cc_start: 0.8488 (tpt) cc_final: 0.8070 (tpt) outliers start: 3 outliers final: 0 residues processed: 277 average time/residue: 0.1352 time to fit residues: 53.8130 Evaluate side-chains 178 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain K residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 79 GLN A 254 ASN A 501 GLN H 31 ASN H 79 GLN B 254 ASN B 501 GLN K 3 GLN K 79 GLN C 254 ASN C 501 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110107 restraints weight = 22248.145| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.11 r_work: 0.3234 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16068 Z= 0.169 Angle : 0.641 8.326 21798 Z= 0.331 Chirality : 0.047 0.255 2520 Planarity : 0.004 0.039 2736 Dihedral : 13.927 106.651 2214 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.78 % Allowed : 11.20 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -3.18 (0.17), residues: 1992 helix: 0.64 (0.24), residues: 432 sheet: -2.91 (0.16), residues: 687 loop : -2.78 (0.17), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 67 TYR 0.016 0.002 TYR E 60 PHE 0.023 0.002 PHE E 70 TRP 0.011 0.002 TRP C 314 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00391 (16035) covalent geometry : angle 0.63948 (21729) SS BOND : bond 0.00355 ( 30) SS BOND : angle 0.90281 ( 60) hydrogen bonds : bond 0.04209 ( 657) hydrogen bonds : angle 5.84913 ( 1764) link_NAG-ASN : bond 0.00434 ( 3) link_NAG-ASN : angle 1.55188 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7496 (mtpp) REVERT: F 42 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7538 (mtmt) REVERT: H 42 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7521 (mtmt) REVERT: B 274 MET cc_start: 0.8448 (mtp) cc_final: 0.8164 (mtt) REVERT: G 82 GLN cc_start: 0.8317 (tt0) cc_final: 0.8084 (tt0) REVERT: C 289 MET cc_start: 0.8989 (tpt) cc_final: 0.8602 (tpt) outliers start: 32 outliers final: 22 residues processed: 201 average time/residue: 0.1401 time to fit residues: 41.0349 Evaluate side-chains 182 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 290 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 152 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN A 63 ASN H 3 GLN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107598 restraints weight = 22505.038| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.16 r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16068 Z= 0.225 Angle : 0.674 9.430 21798 Z= 0.344 Chirality : 0.047 0.316 2520 Planarity : 0.004 0.040 2736 Dihedral : 10.296 101.005 2205 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.56 % Allowed : 15.22 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -2.68 (0.17), residues: 1992 helix: 0.94 (0.25), residues: 432 sheet: -2.50 (0.17), residues: 672 loop : -2.52 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 67 TYR 0.021 0.002 TYR C 86 PHE 0.014 0.002 PHE K 91 TRP 0.013 0.002 TRP C 314 HIS 0.006 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00527 (16035) covalent geometry : angle 0.67271 (21729) SS BOND : bond 0.00307 ( 30) SS BOND : angle 0.99940 ( 60) hydrogen bonds : bond 0.04445 ( 657) hydrogen bonds : angle 5.47969 ( 1764) link_NAG-ASN : bond 0.00532 ( 3) link_NAG-ASN : angle 1.43205 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7539 (mtpp) REVERT: F 42 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7523 (mtmt) REVERT: F 54 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8586 (tt) REVERT: H 42 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7439 (mtmt) REVERT: H 54 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 274 MET cc_start: 0.8466 (mtp) cc_final: 0.8210 (mtt) REVERT: K 54 LEU cc_start: 0.8844 (pp) cc_final: 0.8512 (tt) REVERT: C 289 MET cc_start: 0.9080 (tpt) cc_final: 0.8342 (tpt) outliers start: 46 outliers final: 34 residues processed: 198 average time/residue: 0.1370 time to fit residues: 39.7433 Evaluate side-chains 197 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 80 TYR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 81 optimal weight: 0.0770 chunk 149 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 31 ASN H 3 GLN B 501 GLN K 3 GLN K 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112515 restraints weight = 22242.428| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.13 r_work: 0.3269 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16068 Z= 0.108 Angle : 0.550 7.652 21798 Z= 0.285 Chirality : 0.043 0.179 2520 Planarity : 0.004 0.042 2736 Dihedral : 7.822 85.780 2205 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.78 % Allowed : 16.00 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -2.02 (0.18), residues: 1992 helix: 1.62 (0.25), residues: 432 sheet: -2.04 (0.18), residues: 651 loop : -2.26 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.027 0.001 TYR C 86 PHE 0.011 0.001 PHE G 70 TRP 0.012 0.002 TRP A 314 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00245 (16035) covalent geometry : angle 0.54614 (21729) SS BOND : bond 0.00257 ( 30) SS BOND : angle 0.75567 ( 60) hydrogen bonds : bond 0.03295 ( 657) hydrogen bonds : angle 5.00178 ( 1764) link_NAG-ASN : bond 0.00502 ( 3) link_NAG-ASN : angle 3.06242 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7477 (mtpp) REVERT: D 81 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7917 (tp) REVERT: F 42 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7512 (mtmt) REVERT: F 54 LEU cc_start: 0.8852 (pp) cc_final: 0.8631 (tt) REVERT: A 251 MET cc_start: 0.9033 (mmp) cc_final: 0.8761 (mmp) REVERT: A 486 ASP cc_start: 0.7758 (p0) cc_final: 0.7142 (p0) REVERT: H 42 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7479 (mtmt) REVERT: K 54 LEU cc_start: 0.8794 (pp) cc_final: 0.8463 (tt) REVERT: C 251 MET cc_start: 0.8972 (mmp) cc_final: 0.8705 (mmp) REVERT: C 289 MET cc_start: 0.9130 (tpt) cc_final: 0.8267 (tpt) outliers start: 32 outliers final: 23 residues processed: 212 average time/residue: 0.1422 time to fit residues: 44.0060 Evaluate side-chains 198 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 290 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108084 restraints weight = 22437.672| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.15 r_work: 0.3208 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16068 Z= 0.219 Angle : 0.636 9.525 21798 Z= 0.327 Chirality : 0.046 0.198 2520 Planarity : 0.004 0.040 2736 Dihedral : 7.879 81.406 2205 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.29 % Allowed : 16.22 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -2.00 (0.18), residues: 1992 helix: 1.46 (0.25), residues: 432 sheet: -1.93 (0.18), residues: 654 loop : -2.23 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.024 0.002 TYR B 86 PHE 0.015 0.002 PHE F 91 TRP 0.012 0.002 TRP C 314 HIS 0.007 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00513 (16035) covalent geometry : angle 0.63193 (21729) SS BOND : bond 0.00317 ( 30) SS BOND : angle 0.94013 ( 60) hydrogen bonds : bond 0.04118 ( 657) hydrogen bonds : angle 5.15747 ( 1764) link_NAG-ASN : bond 0.00135 ( 3) link_NAG-ASN : angle 3.22470 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 0.664 Fit side-chains REVERT: D 13 LYS cc_start: 0.8263 (mtpp) cc_final: 0.8037 (mtpp) REVERT: D 81 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7687 (tp) REVERT: F 42 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7518 (mtmt) REVERT: F 54 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8597 (tt) REVERT: E 13 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7830 (mtpp) REVERT: H 42 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7491 (mtmt) REVERT: C 95 LEU cc_start: 0.8784 (mm) cc_final: 0.8488 (mm) REVERT: C 289 MET cc_start: 0.9175 (tpt) cc_final: 0.8318 (tpt) outliers start: 59 outliers final: 48 residues processed: 206 average time/residue: 0.1465 time to fit residues: 44.1793 Evaluate side-chains 207 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 89 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN H 6 GLN B 501 GLN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110857 restraints weight = 22153.136| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.14 r_work: 0.3246 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16068 Z= 0.136 Angle : 0.570 8.467 21798 Z= 0.293 Chirality : 0.043 0.165 2520 Planarity : 0.004 0.043 2736 Dihedral : 7.589 79.033 2205 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.18 % Allowed : 17.17 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.69 (0.18), residues: 1992 helix: 1.76 (0.25), residues: 432 sheet: -1.73 (0.18), residues: 660 loop : -2.06 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.027 0.002 TYR C 86 PHE 0.010 0.001 PHE G 70 TRP 0.012 0.002 TRP E 47 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00318 (16035) covalent geometry : angle 0.56557 (21729) SS BOND : bond 0.00262 ( 30) SS BOND : angle 0.76390 ( 60) hydrogen bonds : bond 0.03459 ( 657) hydrogen bonds : angle 4.89929 ( 1764) link_NAG-ASN : bond 0.00208 ( 3) link_NAG-ASN : angle 3.23512 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8251 (mtpp) cc_final: 0.8019 (mtpp) REVERT: F 42 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7542 (mtmt) REVERT: F 54 LEU cc_start: 0.8823 (pp) cc_final: 0.8606 (tt) REVERT: A 486 ASP cc_start: 0.7752 (p0) cc_final: 0.7115 (p0) REVERT: H 42 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7481 (mtmt) REVERT: G 82 GLN cc_start: 0.8060 (tp40) cc_final: 0.7828 (mm110) REVERT: K 54 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8464 (tt) REVERT: C 95 LEU cc_start: 0.8770 (mm) cc_final: 0.8440 (mm) REVERT: C 200 ASP cc_start: 0.6714 (m-30) cc_final: 0.6464 (m-30) REVERT: C 289 MET cc_start: 0.9168 (tpt) cc_final: 0.8296 (tpt) outliers start: 57 outliers final: 46 residues processed: 211 average time/residue: 0.1421 time to fit residues: 43.9955 Evaluate side-chains 208 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 80 TYR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 96 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN H 6 GLN B 225 GLN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110549 restraints weight = 22108.920| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.11 r_work: 0.3246 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16068 Z= 0.147 Angle : 0.577 8.640 21798 Z= 0.296 Chirality : 0.043 0.160 2520 Planarity : 0.003 0.042 2736 Dihedral : 7.477 76.643 2205 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.62 % Allowed : 16.61 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.53 (0.18), residues: 1992 helix: 1.80 (0.25), residues: 432 sheet: -1.56 (0.18), residues: 660 loop : -1.98 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 507 TYR 0.030 0.002 TYR B 86 PHE 0.011 0.001 PHE F 91 TRP 0.011 0.001 TRP E 47 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00344 (16035) covalent geometry : angle 0.57238 (21729) SS BOND : bond 0.00198 ( 30) SS BOND : angle 0.76629 ( 60) hydrogen bonds : bond 0.03506 ( 657) hydrogen bonds : angle 4.85004 ( 1764) link_NAG-ASN : bond 0.00155 ( 3) link_NAG-ASN : angle 3.36160 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: F 42 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7467 (mtmt) REVERT: F 54 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 486 ASP cc_start: 0.7742 (p0) cc_final: 0.7094 (p0) REVERT: E 13 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7852 (mtpp) REVERT: E 81 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7628 (tp) REVERT: H 42 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7448 (mtmt) REVERT: B 158 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8517 (mp) REVERT: K 54 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8474 (tt) REVERT: C 95 LEU cc_start: 0.8774 (mm) cc_final: 0.8447 (mm) REVERT: C 289 MET cc_start: 0.9165 (tpt) cc_final: 0.8258 (tpt) outliers start: 65 outliers final: 46 residues processed: 215 average time/residue: 0.1325 time to fit residues: 42.4643 Evaluate side-chains 216 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 chunk 185 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN B 225 GLN B 240 ASN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106735 restraints weight = 22470.938| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.13 r_work: 0.3191 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16068 Z= 0.276 Angle : 0.689 11.529 21798 Z= 0.353 Chirality : 0.047 0.193 2520 Planarity : 0.004 0.040 2736 Dihedral : 7.783 75.404 2205 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.12 % Allowed : 18.00 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.83 (0.18), residues: 1992 helix: 1.23 (0.24), residues: 438 sheet: -1.59 (0.19), residues: 654 loop : -2.14 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 98 TYR 0.034 0.002 TYR B 86 PHE 0.017 0.002 PHE F 91 TRP 0.011 0.002 TRP A 314 HIS 0.009 0.002 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00651 (16035) covalent geometry : angle 0.68392 (21729) SS BOND : bond 0.00444 ( 30) SS BOND : angle 1.04416 ( 60) hydrogen bonds : bond 0.04447 ( 657) hydrogen bonds : angle 5.16492 ( 1764) link_NAG-ASN : bond 0.00020 ( 3) link_NAG-ASN : angle 3.61599 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 0.656 Fit side-chains REVERT: D 13 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7604 (mtpp) REVERT: F 42 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7496 (mtmt) REVERT: F 54 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8627 (tt) REVERT: E 13 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7944 (mtpp) REVERT: H 42 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7485 (mtmt) REVERT: B 158 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8623 (mp) REVERT: C 95 LEU cc_start: 0.8765 (mm) cc_final: 0.8476 (mm) REVERT: C 200 ASP cc_start: 0.6855 (m-30) cc_final: 0.6604 (m-30) REVERT: C 289 MET cc_start: 0.9188 (tpt) cc_final: 0.8279 (tpt) outliers start: 56 outliers final: 49 residues processed: 202 average time/residue: 0.1446 time to fit residues: 42.8460 Evaluate side-chains 207 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 467 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 6 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110070 restraints weight = 22301.183| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.16 r_work: 0.3237 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16068 Z= 0.149 Angle : 0.598 9.749 21798 Z= 0.304 Chirality : 0.044 0.236 2520 Planarity : 0.004 0.042 2736 Dihedral : 7.531 74.287 2205 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.01 % Allowed : 18.34 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.52 (0.19), residues: 1992 helix: 1.61 (0.25), residues: 432 sheet: -1.46 (0.19), residues: 651 loop : -1.94 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 507 TYR 0.033 0.002 TYR B 86 PHE 0.010 0.001 PHE F 91 TRP 0.013 0.002 TRP E 47 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00352 (16035) covalent geometry : angle 0.59330 (21729) SS BOND : bond 0.00218 ( 30) SS BOND : angle 0.79243 ( 60) hydrogen bonds : bond 0.03602 ( 657) hydrogen bonds : angle 4.93027 ( 1764) link_NAG-ASN : bond 0.00128 ( 3) link_NAG-ASN : angle 3.47492 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7528 (mtpp) REVERT: F 42 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7507 (mtmt) REVERT: F 54 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 486 ASP cc_start: 0.7782 (p0) cc_final: 0.7130 (p0) REVERT: E 13 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7962 (mtpp) REVERT: H 42 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7432 (mtmt) REVERT: B 158 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8506 (mp) REVERT: K 54 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8475 (tt) REVERT: C 95 LEU cc_start: 0.8739 (mm) cc_final: 0.8436 (mm) REVERT: C 289 MET cc_start: 0.9165 (tpt) cc_final: 0.8303 (tpt) outliers start: 54 outliers final: 45 residues processed: 208 average time/residue: 0.1413 time to fit residues: 43.1221 Evaluate side-chains 217 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 126 optimal weight: 0.3980 chunk 182 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 6 GLN H 3 GLN H 6 GLN K 3 GLN K 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112841 restraints weight = 22024.179| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.10 r_work: 0.3259 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16068 Z= 0.131 Angle : 0.578 8.178 21798 Z= 0.295 Chirality : 0.043 0.208 2520 Planarity : 0.004 0.043 2736 Dihedral : 7.275 71.307 2205 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.79 % Allowed : 18.62 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.30 (0.19), residues: 1992 helix: 1.84 (0.25), residues: 432 sheet: -1.31 (0.19), residues: 651 loop : -1.86 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 507 TYR 0.029 0.002 TYR B 86 PHE 0.010 0.001 PHE G 70 TRP 0.014 0.002 TRP G 47 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00307 (16035) covalent geometry : angle 0.57331 (21729) SS BOND : bond 0.00164 ( 30) SS BOND : angle 0.72689 ( 60) hydrogen bonds : bond 0.03380 ( 657) hydrogen bonds : angle 4.79614 ( 1764) link_NAG-ASN : bond 0.00153 ( 3) link_NAG-ASN : angle 3.54180 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7515 (mtpp) REVERT: D 82 GLN cc_start: 0.8161 (tp40) cc_final: 0.7837 (mm110) REVERT: F 42 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7448 (mtmt) REVERT: F 52 LYS cc_start: 0.8753 (mttt) cc_final: 0.8262 (mmtt) REVERT: A 486 ASP cc_start: 0.7691 (p0) cc_final: 0.7022 (p0) REVERT: E 13 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7885 (mtpp) REVERT: H 42 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7437 (mtmt) REVERT: B 158 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8452 (mp) REVERT: K 52 LYS cc_start: 0.8840 (mttt) cc_final: 0.8512 (mtmm) REVERT: K 54 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (tt) REVERT: C 95 LEU cc_start: 0.8744 (mm) cc_final: 0.8416 (mm) REVERT: C 289 MET cc_start: 0.9146 (tpt) cc_final: 0.8212 (tpt) outliers start: 50 outliers final: 44 residues processed: 212 average time/residue: 0.1442 time to fit residues: 44.9923 Evaluate side-chains 217 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 190 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN K 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114327 restraints weight = 21933.918| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.10 r_work: 0.3281 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16068 Z= 0.112 Angle : 0.559 7.850 21798 Z= 0.284 Chirality : 0.043 0.204 2520 Planarity : 0.003 0.043 2736 Dihedral : 7.019 69.223 2205 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.45 % Allowed : 19.12 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.13 (0.19), residues: 1992 helix: 2.00 (0.25), residues: 432 sheet: -1.18 (0.19), residues: 651 loop : -1.78 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 507 TYR 0.027 0.001 TYR B 86 PHE 0.009 0.001 PHE G 70 TRP 0.015 0.001 TRP G 47 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00260 (16035) covalent geometry : angle 0.55398 (21729) SS BOND : bond 0.00133 ( 30) SS BOND : angle 0.69085 ( 60) hydrogen bonds : bond 0.03188 ( 657) hydrogen bonds : angle 4.67900 ( 1764) link_NAG-ASN : bond 0.00161 ( 3) link_NAG-ASN : angle 3.61869 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4345.69 seconds wall clock time: 75 minutes 24.04 seconds (4524.04 seconds total)