Starting phenix.real_space_refine on Thu Aug 6 14:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vwf_65395/08_2026/9vwf_65395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vwf_65395/08_2026/9vwf_65395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vwf_65395/08_2026/9vwf_65395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vwf_65395/08_2026/9vwf_65395.map" model { file = "/net/cci-nas-00/data/ceres_data/9vwf_65395/08_2026/9vwf_65395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vwf_65395/08_2026/9vwf_65395.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 9588 2.51 5 N 2583 2.21 5 O 2991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15258 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3394 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 762 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Restraints were copied for chains: B, C, D, E, F, G Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASP H 54 " occ=0.63 ... (6 atoms not shown) pdb=" OD2 ASP H 54 " occ=0.63 residue: pdb=" N SER H 56 " occ=0.83 ... (4 atoms not shown) pdb=" OG SER H 56 " occ=0.83 residue: pdb=" N ASP D 54 " occ=0.63 ... (6 atoms not shown) pdb=" OD2 ASP D 54 " occ=0.63 residue: pdb=" N SER D 56 " occ=0.83 ... (4 atoms not shown) pdb=" OG SER D 56 " occ=0.83 residue: pdb=" N ASP E 54 " occ=0.63 ... (6 atoms not shown) pdb=" OD2 ASP E 54 " occ=0.63 residue: pdb=" N SER E 56 " occ=0.83 ... (4 atoms not shown) pdb=" OG SER E 56 " occ=0.83 Time building chain proxies: 3.57, per 1000 atoms: 0.23 Number of scatterers: 15258 At special positions: 0 Unit cell: (135.2, 129.35, 122.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2991 8.00 N 2583 7.00 C 9588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.36 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS B 458 " distance=2.29 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=2.02 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS C 149 " distance=2.29 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=1.96 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=1.62 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.36 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.36 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 149 " - pdb=" SG CYS C 458 " distance=2.29 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=2.02 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=1.96 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=1.96 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=1.62 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=1.62 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 686.1 milliseconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3690 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 36 sheets defined 21.7% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 73 through 97 removed outlier: 3.527A pdb=" N LYS A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.557A pdb=" N HIS A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 216 through 241 removed outlier: 4.125A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.760A pdb=" N ARG A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.294A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.574A pdb=" N PHE A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.610A pdb=" N LYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 97 removed outlier: 3.527A pdb=" N LYS B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.557A pdb=" N HIS B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 241 removed outlier: 4.125A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.760A pdb=" N ARG B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.294A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.574A pdb=" N PHE B 477 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.611A pdb=" N LYS B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 97 removed outlier: 3.527A pdb=" N LYS C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.557A pdb=" N HIS C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 216 through 241 removed outlier: 4.125A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.760A pdb=" N ARG C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.293A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.574A pdb=" N PHE C 477 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.611A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 361 removed outlier: 7.129A pdb=" N LEU A 48 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE A 309 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 removed outlier: 7.129A pdb=" N LEU A 48 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE A 309 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 11.621A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.791A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.159A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN H 39 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.159A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN H 39 " --> pdb=" O ILE H 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 17 through 20 Processing sheet with id=AB2, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.601A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 91 through 94 removed outlier: 3.600A pdb=" N ASP L 94 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY L 99 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 358 through 361 removed outlier: 7.129A pdb=" N LEU B 48 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 309 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 361 removed outlier: 7.129A pdb=" N LEU B 48 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 309 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.621A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AB8, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.791A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.158A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 39 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS D 96 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP D 112 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG D 98 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.158A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 39 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 17 through 20 Processing sheet with id=AC5, first strand: chain 'F' and resid 55 through 56 removed outlier: 6.601A pdb=" N TRP F 37 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.600A pdb=" N ASP F 94 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY F 99 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 358 through 361 removed outlier: 7.130A pdb=" N LEU C 48 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 309 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 361 removed outlier: 7.130A pdb=" N LEU C 48 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 309 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.621A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 333 through 336 Processing sheet with id=AD2, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AD3, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.791A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.159A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN E 39 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS E 96 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP E 112 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG E 98 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.159A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN E 39 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AD8, first strand: chain 'G' and resid 55 through 56 removed outlier: 6.601A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.600A pdb=" N ASP G 94 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY G 99 " --> pdb=" O ASP G 94 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1881 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: 2.79 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4974 1.34 - 1.46: 3154 1.46 - 1.58: 7259 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 15513 Sorted by residual: bond pdb=" C GLU B 218 " pdb=" N THR B 219 " ideal model delta sigma weight residual 1.335 1.271 0.063 1.31e-02 5.83e+03 2.35e+01 bond pdb=" C GLU C 218 " pdb=" N THR C 219 " ideal model delta sigma weight residual 1.335 1.271 0.063 1.31e-02 5.83e+03 2.35e+01 bond pdb=" C GLU A 218 " pdb=" N THR A 219 " ideal model delta sigma weight residual 1.335 1.272 0.063 1.31e-02 5.83e+03 2.33e+01 bond pdb=" C SER H 71 " pdb=" N ARG H 72 " ideal model delta sigma weight residual 1.332 1.272 0.060 1.26e-02 6.30e+03 2.24e+01 bond pdb=" C SER E 71 " pdb=" N ARG E 72 " ideal model delta sigma weight residual 1.332 1.272 0.060 1.26e-02 6.30e+03 2.24e+01 ... (remaining 15508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 20231 1.43 - 2.86: 646 2.86 - 4.28: 103 4.28 - 5.71: 29 5.71 - 7.14: 15 Bond angle restraints: 21024 Sorted by residual: angle pdb=" C ILE B 292 " pdb=" N LYS B 293 " pdb=" CA LYS B 293 " ideal model delta sigma weight residual 122.07 115.12 6.95 2.01e+00 2.48e-01 1.19e+01 angle pdb=" C ILE A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta sigma weight residual 122.07 115.13 6.94 2.01e+00 2.48e-01 1.19e+01 angle pdb=" C ILE C 292 " pdb=" N LYS C 293 " pdb=" CA LYS C 293 " ideal model delta sigma weight residual 122.07 115.14 6.93 2.01e+00 2.48e-01 1.19e+01 angle pdb=" C THR G 52 " pdb=" N ASN G 53 " pdb=" CA ASN G 53 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C THR F 52 " pdb=" N ASN F 53 " pdb=" CA ASN F 53 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.60e+00 ... (remaining 21019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 8134 16.47 - 32.93: 974 32.93 - 49.40: 237 49.40 - 65.86: 72 65.86 - 82.33: 33 Dihedral angle restraints: 9450 sinusoidal: 3711 harmonic: 5739 Sorted by residual: dihedral pdb=" CB CYS B 69 " pdb=" SG CYS B 69 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -158.63 72.63 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -158.62 72.62 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -158.60 72.60 1 1.00e+01 1.00e-02 6.73e+01 ... (remaining 9447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1672 0.040 - 0.079: 561 0.079 - 0.119: 187 0.119 - 0.159: 28 0.159 - 0.198: 6 Chirality restraints: 2454 Sorted by residual: chirality pdb=" CB THR B 245 " pdb=" CA THR B 245 " pdb=" OG1 THR B 245 " pdb=" CG2 THR B 245 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CB THR C 245 " pdb=" CA THR C 245 " pdb=" OG1 THR C 245 " pdb=" CG2 THR C 245 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CB THR A 245 " pdb=" CA THR A 245 " pdb=" OG1 THR A 245 " pdb=" CG2 THR A 245 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 2451 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 72 " -0.824 9.50e-02 1.11e+02 3.70e-01 8.30e+01 pdb=" NE ARG D 72 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG D 72 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 72 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 72 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 72 " -0.824 9.50e-02 1.11e+02 3.69e-01 8.30e+01 pdb=" NE ARG E 72 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG E 72 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 72 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 72 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 72 " -0.824 9.50e-02 1.11e+02 3.69e-01 8.29e+01 pdb=" NE ARG H 72 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG H 72 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 72 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 72 " -0.024 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3381 2.78 - 3.31: 13877 3.31 - 3.84: 23848 3.84 - 4.37: 28727 4.37 - 4.90: 50493 Nonbonded interactions: 120326 Sorted by model distance: nonbonded pdb=" OE1 GLN A 284 " pdb=" OH TYR A 306 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLN B 284 " pdb=" OH TYR B 306 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLN C 284 " pdb=" OH TYR C 306 " model vdw 2.253 3.040 nonbonded pdb=" NE2 GLN E 82 " pdb=" O MET E 83 " model vdw 2.289 3.120 nonbonded pdb=" NE2 GLN H 82 " pdb=" O MET H 83 " model vdw 2.289 3.120 ... (remaining 120321 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'L' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.810 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.010 0.411 15546 Z= 0.525 Angle : 0.976 39.338 21090 Z= 0.493 Chirality : 0.045 0.198 2454 Planarity : 0.015 0.370 2676 Dihedral : 15.930 82.328 5661 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.17 % Allowed : 18.10 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.19), residues: 1965 helix: -0.69 (0.26), residues: 405 sheet: -1.16 (0.22), residues: 594 loop : -1.59 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 56 TYR 0.021 0.002 TYR A 417 PHE 0.007 0.001 PHE B 435 TRP 0.035 0.002 TRP G 37 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.26 (15513) covalent geometry : angle 0.63721 / 0.35 (21024) SS BOND : bond 0.19938 / 12.84 ( 33) SS BOND : angle 13.22604 / 10.40 ( 66) hydrogen bonds : bond 0.25103 / 16.68 ( 648) hydrogen bonds : angle 9.29597 / 6.32 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 414 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 478 TYR cc_start: 0.8254 (m-80) cc_final: 0.7956 (m-80) REVERT: L 89 TYR cc_start: 0.8283 (m-80) cc_final: 0.7775 (m-80) REVERT: B 31 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7412 (mt-10) REVERT: B 35 SER cc_start: 0.8436 (p) cc_final: 0.8184 (m) REVERT: B 85 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7736 (mtmt) REVERT: B 377 SER cc_start: 0.7613 (t) cc_final: 0.7294 (t) REVERT: B 380 ASN cc_start: 0.7180 (t0) cc_final: 0.6966 (t0) REVERT: B 431 ILE cc_start: 0.8344 (pt) cc_final: 0.8112 (pt) REVERT: B 433 LYS cc_start: 0.8553 (tttp) cc_final: 0.8268 (tttm) REVERT: F 21 SER cc_start: 0.7529 (m) cc_final: 0.7049 (t) REVERT: C 449 THR cc_start: 0.8200 (m) cc_final: 0.7657 (p) REVERT: C 455 THR cc_start: 0.8403 (m) cc_final: 0.8182 (p) REVERT: G 89 TYR cc_start: 0.8432 (m-80) cc_final: 0.8210 (m-80) outliers start: 3 outliers final: 3 residues processed: 417 average time/residue: 0.1176 time to fit residues: 73.6586 Evaluate side-chains 391 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 388 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 197 ASN A 227 ASN A 277 ASN A 361 GLN A 363 ASN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 159 HIS B 183 ASN B 197 ASN B 277 ASN B 361 GLN B 460 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 197 ASN C 277 ASN C 361 GLN G 38 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106440 restraints weight = 23231.197| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.18 r_work: 0.3237 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15546 Z= 0.229 Angle : 0.647 8.706 21090 Z= 0.345 Chirality : 0.046 0.167 2454 Planarity : 0.005 0.053 2676 Dihedral : 5.130 22.035 2112 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.58 % Allowed : 19.30 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.19), residues: 1965 helix: -0.40 (0.26), residues: 435 sheet: -1.03 (0.22), residues: 570 loop : -1.73 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 56 TYR 0.021 0.002 TYR C 417 PHE 0.012 0.002 PHE F 64 TRP 0.025 0.002 TRP F 37 HIS 0.007 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (15513) covalent geometry : angle 0.64323 / 0.34 (21024) SS BOND : bond 0.00408 / 0.25 ( 33) SS BOND : angle 1.39803 / 1.07 ( 66) hydrogen bonds : bond 0.04797 / 3.13 ( 648) hydrogen bonds : angle 6.00957 / 4.06 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 391 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8206 (mttp) REVERT: A 250 TYR cc_start: 0.8627 (m-80) cc_final: 0.8116 (m-80) REVERT: A 427 LYS cc_start: 0.7846 (tptt) cc_final: 0.7614 (tptt) REVERT: A 440 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8199 (t0) REVERT: L 48 LEU cc_start: 0.9052 (tp) cc_final: 0.8822 (tp) REVERT: B 80 LYS cc_start: 0.8644 (mttt) cc_final: 0.8296 (mttt) REVERT: B 166 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8157 (mttp) REVERT: B 191 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8386 (ttmt) REVERT: B 228 ASN cc_start: 0.8784 (t0) cc_final: 0.8513 (t0) REVERT: B 377 SER cc_start: 0.7829 (t) cc_final: 0.7542 (t) REVERT: B 380 ASN cc_start: 0.7596 (t0) cc_final: 0.7350 (t0) REVERT: B 433 LYS cc_start: 0.8488 (tttp) cc_final: 0.8204 (tttm) REVERT: B 472 GLU cc_start: 0.7614 (tp30) cc_final: 0.7261 (tp30) REVERT: F 21 SER cc_start: 0.7834 (m) cc_final: 0.7276 (t) REVERT: F 37 TRP cc_start: 0.8381 (m100) cc_final: 0.8154 (m100) REVERT: C 262 ASN cc_start: 0.8275 (t0) cc_final: 0.8043 (t0) REVERT: C 377 SER cc_start: 0.7755 (t) cc_final: 0.7390 (p) outliers start: 80 outliers final: 50 residues processed: 429 average time/residue: 0.1249 time to fit residues: 78.5666 Evaluate side-chains 419 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 366 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 454 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN B 227 ASN B 240 ASN B 454 ASN B 460 ASN D 74 ASN C 159 HIS C 183 ASN C 197 ASN C 454 ASN E 32 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106709 restraints weight = 23393.568| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.23 r_work: 0.3250 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15546 Z= 0.170 Angle : 0.573 6.922 21090 Z= 0.306 Chirality : 0.044 0.154 2454 Planarity : 0.005 0.055 2676 Dihedral : 4.838 19.381 2109 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.61 % Allowed : 19.24 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.19), residues: 1965 helix: -0.07 (0.26), residues: 435 sheet: -0.89 (0.21), residues: 585 loop : -1.68 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 56 TYR 0.020 0.002 TYR A 457 PHE 0.011 0.001 PHE B 190 TRP 0.012 0.002 TRP G 37 HIS 0.006 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15513) covalent geometry : angle 0.57177 / 0.31 (21024) SS BOND : bond 0.00313 / 0.20 ( 33) SS BOND : angle 0.88271 / 0.64 ( 66) hydrogen bonds : bond 0.04081 / 2.68 ( 648) hydrogen bonds : angle 5.56369 / 3.75 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 369 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 166 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: A 222 GLU cc_start: 0.7638 (tt0) cc_final: 0.7338 (tm-30) REVERT: A 226 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8092 (ttmm) REVERT: A 250 TYR cc_start: 0.8560 (m-80) cc_final: 0.7997 (m-80) REVERT: A 323 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.5748 (m) REVERT: A 427 LYS cc_start: 0.7843 (tptt) cc_final: 0.7603 (tptt) REVERT: A 478 TYR cc_start: 0.8473 (m-80) cc_final: 0.8140 (m-80) REVERT: L 48 LEU cc_start: 0.9043 (tp) cc_final: 0.8821 (tp) REVERT: B 80 LYS cc_start: 0.8697 (mttt) cc_final: 0.8326 (mttt) REVERT: B 166 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8153 (mttp) REVERT: B 191 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8359 (ttmt) REVERT: B 228 ASN cc_start: 0.8797 (t0) cc_final: 0.8531 (t0) REVERT: B 377 SER cc_start: 0.7857 (t) cc_final: 0.7561 (t) REVERT: B 380 ASN cc_start: 0.7537 (t0) cc_final: 0.7323 (t0) REVERT: B 433 LYS cc_start: 0.8460 (tttp) cc_final: 0.8186 (tttm) REVERT: F 37 TRP cc_start: 0.8417 (m100) cc_final: 0.8005 (m100) REVERT: C 84 ASP cc_start: 0.6884 (t0) cc_final: 0.6467 (t0) REVERT: C 262 ASN cc_start: 0.8303 (t0) cc_final: 0.8058 (t0) REVERT: C 377 SER cc_start: 0.7802 (t) cc_final: 0.7400 (p) REVERT: C 433 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8208 (ttpp) REVERT: E 79 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7983 (tp) outliers start: 98 outliers final: 64 residues processed: 416 average time/residue: 0.1146 time to fit residues: 70.0116 Evaluate side-chains 433 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 364 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 150 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 124 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 363 ASN A 454 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 227 ASN C 159 HIS C 183 ASN C 317 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107969 restraints weight = 23356.077| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.20 r_work: 0.3267 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15546 Z= 0.123 Angle : 0.525 6.018 21090 Z= 0.281 Chirality : 0.043 0.141 2454 Planarity : 0.004 0.051 2676 Dihedral : 4.589 17.942 2109 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.95 % Allowed : 21.13 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 1965 helix: 0.42 (0.26), residues: 420 sheet: -0.72 (0.22), residues: 588 loop : -1.67 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 56 TYR 0.018 0.001 TYR A 417 PHE 0.013 0.001 PHE B 190 TRP 0.010 0.001 TRP B 52 HIS 0.008 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15513) covalent geometry : angle 0.52443 / 0.28 (21024) SS BOND : bond 0.00241 / 0.16 ( 33) SS BOND : angle 0.62629 / 0.43 ( 66) hydrogen bonds : bond 0.03479 / 2.28 ( 648) hydrogen bonds : angle 5.20005 / 3.49 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 361 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8078 (mttp) REVERT: A 222 GLU cc_start: 0.7586 (tt0) cc_final: 0.7335 (tt0) REVERT: A 226 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8120 (ttmm) REVERT: A 250 TYR cc_start: 0.8526 (m-80) cc_final: 0.7964 (m-80) REVERT: A 427 LYS cc_start: 0.7830 (tptt) cc_final: 0.7591 (tptt) REVERT: A 478 TYR cc_start: 0.8411 (m-80) cc_final: 0.8059 (m-80) REVERT: L 63 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7166 (ptp-170) REVERT: B 30 GLU cc_start: 0.7973 (tt0) cc_final: 0.7608 (tt0) REVERT: B 161 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6765 (mm-30) REVERT: B 166 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8114 (mttp) REVERT: B 191 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8349 (ttmt) REVERT: B 222 GLU cc_start: 0.7876 (tt0) cc_final: 0.7564 (tm-30) REVERT: B 228 ASN cc_start: 0.8759 (t0) cc_final: 0.8498 (t0) REVERT: B 380 ASN cc_start: 0.7456 (t0) cc_final: 0.7253 (t0) REVERT: B 433 LYS cc_start: 0.8422 (tttp) cc_final: 0.8202 (tttm) REVERT: F 37 TRP cc_start: 0.8386 (m100) cc_final: 0.8119 (m100) REVERT: F 63 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7281 (ptp-170) REVERT: C 84 ASP cc_start: 0.6869 (t0) cc_final: 0.6461 (t0) REVERT: C 222 GLU cc_start: 0.7686 (tt0) cc_final: 0.7203 (tt0) REVERT: C 227 ASN cc_start: 0.8287 (t0) cc_final: 0.8056 (t0) REVERT: C 262 ASN cc_start: 0.8299 (t0) cc_final: 0.8047 (t0) REVERT: C 323 THR cc_start: 0.6589 (OUTLIER) cc_final: 0.5476 (m) REVERT: C 377 SER cc_start: 0.7795 (t) cc_final: 0.7340 (p) REVERT: C 399 LYS cc_start: 0.8152 (mttt) cc_final: 0.7685 (mttt) outliers start: 69 outliers final: 48 residues processed: 390 average time/residue: 0.1148 time to fit residues: 65.1689 Evaluate side-chains 399 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN B 227 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 ASN C 240 ASN C 454 ASN C 460 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107551 restraints weight = 23287.030| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.20 r_work: 0.3258 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15546 Z= 0.144 Angle : 0.542 10.850 21090 Z= 0.289 Chirality : 0.043 0.145 2454 Planarity : 0.004 0.048 2676 Dihedral : 4.606 18.734 2109 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.81 % Allowed : 20.10 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1965 helix: 0.61 (0.26), residues: 429 sheet: -0.51 (0.22), residues: 573 loop : -1.59 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 56 TYR 0.017 0.002 TYR A 457 PHE 0.011 0.001 PHE C 505 TRP 0.009 0.001 TRP A 52 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15513) covalent geometry : angle 0.54107 / 0.29 (21024) SS BOND : bond 0.00266 / 0.17 ( 33) SS BOND : angle 0.67549 / 0.45 ( 66) hydrogen bonds : bond 0.03566 / 2.34 ( 648) hydrogen bonds : angle 5.14687 / 3.46 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 362 time to evaluate : 0.466 Fit side-chains REVERT: A 29 THR cc_start: 0.8408 (p) cc_final: 0.8182 (t) REVERT: A 166 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: A 222 GLU cc_start: 0.7650 (tt0) cc_final: 0.7401 (tt0) REVERT: A 226 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8132 (ttmm) REVERT: A 227 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8114 (t0) REVERT: A 250 TYR cc_start: 0.8546 (m-80) cc_final: 0.8000 (m-80) REVERT: A 323 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.5682 (m) REVERT: A 427 LYS cc_start: 0.7809 (tptt) cc_final: 0.7583 (tptt) REVERT: A 478 TYR cc_start: 0.8420 (m-80) cc_final: 0.8099 (m-80) REVERT: L 63 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7196 (ptp-170) REVERT: B 30 GLU cc_start: 0.8013 (tt0) cc_final: 0.7595 (tt0) REVERT: B 161 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6765 (mm-30) REVERT: B 166 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8092 (mttp) REVERT: B 168 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8493 (mtpp) REVERT: B 222 GLU cc_start: 0.7917 (tt0) cc_final: 0.7586 (tt0) REVERT: B 226 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8432 (ttmm) REVERT: B 228 ASN cc_start: 0.8762 (t0) cc_final: 0.8496 (t0) REVERT: B 294 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 433 LYS cc_start: 0.8421 (tttp) cc_final: 0.8197 (tttm) REVERT: F 63 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7257 (ptp-170) REVERT: C 84 ASP cc_start: 0.6885 (t0) cc_final: 0.6468 (t0) REVERT: C 222 GLU cc_start: 0.7683 (tt0) cc_final: 0.7431 (tt0) REVERT: C 262 ASN cc_start: 0.8310 (t0) cc_final: 0.8050 (t0) REVERT: C 323 THR cc_start: 0.6579 (OUTLIER) cc_final: 0.5434 (m) REVERT: C 377 SER cc_start: 0.7776 (t) cc_final: 0.7357 (p) REVERT: C 399 LYS cc_start: 0.8149 (mttt) cc_final: 0.7668 (mttt) outliers start: 84 outliers final: 56 residues processed: 400 average time/residue: 0.1107 time to fit residues: 65.1346 Evaluate side-chains 421 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 358 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 94 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN B 227 ASN B 380 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 ASN C 460 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106197 restraints weight = 23112.595| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.22 r_work: 0.3233 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15546 Z= 0.204 Angle : 0.595 10.341 21090 Z= 0.316 Chirality : 0.045 0.153 2454 Planarity : 0.005 0.052 2676 Dihedral : 4.861 19.393 2109 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.15 % Allowed : 20.96 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1965 helix: 0.54 (0.26), residues: 429 sheet: -0.74 (0.21), residues: 627 loop : -1.59 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 56 TYR 0.021 0.002 TYR A 457 PHE 0.012 0.001 PHE F 64 TRP 0.023 0.002 TRP F 37 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (15513) covalent geometry : angle 0.59401 / 0.32 (21024) SS BOND : bond 0.00337 / 0.22 ( 33) SS BOND : angle 0.84302 / 0.57 ( 66) hydrogen bonds : bond 0.03977 / 2.58 ( 648) hydrogen bonds : angle 5.31873 / 3.58 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 365 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.8441 (p) cc_final: 0.8189 (t) REVERT: A 166 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8128 (mttp) REVERT: A 222 GLU cc_start: 0.7705 (tt0) cc_final: 0.7430 (tt0) REVERT: A 226 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8136 (ttmm) REVERT: A 227 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7963 (t160) REVERT: A 250 TYR cc_start: 0.8549 (m-80) cc_final: 0.8049 (m-80) REVERT: A 323 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.5765 (m) REVERT: A 392 ASP cc_start: 0.7868 (t0) cc_final: 0.7573 (t0) REVERT: A 427 LYS cc_start: 0.7824 (tptt) cc_final: 0.7596 (tptt) REVERT: A 478 TYR cc_start: 0.8497 (m-80) cc_final: 0.8165 (m-80) REVERT: A 491 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7557 (t) REVERT: B 166 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8108 (mttp) REVERT: B 204 LEU cc_start: 0.8143 (mt) cc_final: 0.7879 (mp) REVERT: B 222 GLU cc_start: 0.7954 (tt0) cc_final: 0.7639 (tt0) REVERT: B 226 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8475 (ttmm) REVERT: B 228 ASN cc_start: 0.8791 (t0) cc_final: 0.8525 (t0) REVERT: B 289 MET cc_start: 0.7782 (tpt) cc_final: 0.7456 (tpt) REVERT: B 433 LYS cc_start: 0.8448 (tttp) cc_final: 0.8183 (tttm) REVERT: C 84 ASP cc_start: 0.6940 (t0) cc_final: 0.6504 (t0) REVERT: C 227 ASN cc_start: 0.8361 (t0) cc_final: 0.8134 (t0) REVERT: C 262 ASN cc_start: 0.8324 (t0) cc_final: 0.8058 (t0) REVERT: C 323 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.5408 (m) REVERT: C 377 SER cc_start: 0.7795 (t) cc_final: 0.7417 (p) outliers start: 90 outliers final: 63 residues processed: 409 average time/residue: 0.1067 time to fit residues: 64.5255 Evaluate side-chains 429 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 360 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 134 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN A 460 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN B 227 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 ASN C 454 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108105 restraints weight = 23174.933| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.20 r_work: 0.3259 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15546 Z= 0.126 Angle : 0.535 9.607 21090 Z= 0.285 Chirality : 0.043 0.182 2454 Planarity : 0.004 0.047 2676 Dihedral : 4.570 18.458 2109 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.52 % Allowed : 21.76 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1965 helix: 0.79 (0.27), residues: 420 sheet: -0.57 (0.22), residues: 606 loop : -1.54 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 56 TYR 0.018 0.001 TYR A 417 PHE 0.012 0.001 PHE C 505 TRP 0.011 0.001 TRP F 37 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15513) covalent geometry : angle 0.53445 / 0.28 (21024) SS BOND : bond 0.00251 / 0.16 ( 33) SS BOND : angle 0.62713 / 0.44 ( 66) hydrogen bonds : bond 0.03331 / 2.18 ( 648) hydrogen bonds : angle 5.01449 / 3.36 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 0.568 Fit side-chains REVERT: A 29 THR cc_start: 0.8408 (p) cc_final: 0.8177 (t) REVERT: A 166 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8092 (mttp) REVERT: A 222 GLU cc_start: 0.7645 (tt0) cc_final: 0.7381 (tt0) REVERT: A 227 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7909 (t160) REVERT: A 250 TYR cc_start: 0.8519 (m-80) cc_final: 0.7942 (m-80) REVERT: A 323 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.5753 (m) REVERT: A 427 LYS cc_start: 0.7795 (tptt) cc_final: 0.7569 (tptt) REVERT: A 478 TYR cc_start: 0.8423 (m-80) cc_final: 0.8097 (m-80) REVERT: L 63 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7186 (ptp-170) REVERT: B 30 GLU cc_start: 0.8043 (tt0) cc_final: 0.7683 (tt0) REVERT: B 166 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8100 (mttp) REVERT: B 168 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8401 (mtmt) REVERT: B 222 GLU cc_start: 0.7873 (tt0) cc_final: 0.7577 (tt0) REVERT: B 226 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8466 (ttmm) REVERT: B 228 ASN cc_start: 0.8747 (t0) cc_final: 0.8474 (t0) REVERT: B 289 MET cc_start: 0.7669 (tpt) cc_final: 0.7455 (tpt) REVERT: B 295 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6899 (mt-10) REVERT: B 392 ASP cc_start: 0.7705 (t0) cc_final: 0.7489 (t0) REVERT: B 491 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7378 (t) REVERT: F 63 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7267 (ptp-170) REVERT: C 84 ASP cc_start: 0.6913 (t0) cc_final: 0.6491 (t0) REVERT: C 227 ASN cc_start: 0.8326 (t0) cc_final: 0.8102 (t0) REVERT: C 262 ASN cc_start: 0.8294 (t0) cc_final: 0.8026 (t0) REVERT: C 323 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.5316 (m) REVERT: E 51 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8119 (pt) outliers start: 79 outliers final: 56 residues processed: 394 average time/residue: 0.1110 time to fit residues: 64.7091 Evaluate side-chains 415 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 350 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 ASN C 454 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107125 restraints weight = 23242.221| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.18 r_work: 0.3248 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15546 Z= 0.177 Angle : 0.574 9.100 21090 Z= 0.305 Chirality : 0.044 0.197 2454 Planarity : 0.005 0.051 2676 Dihedral : 4.738 19.196 2109 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.75 % Allowed : 21.53 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1965 helix: 0.74 (0.27), residues: 420 sheet: -0.53 (0.21), residues: 612 loop : -1.64 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 56 TYR 0.019 0.002 TYR A 457 PHE 0.017 0.001 PHE A 505 TRP 0.013 0.001 TRP F 37 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (15513) covalent geometry : angle 0.57266 / 0.30 (21024) SS BOND : bond 0.00315 / 0.20 ( 33) SS BOND : angle 0.80054 / 0.53 ( 66) hydrogen bonds : bond 0.03699 / 2.40 ( 648) hydrogen bonds : angle 5.14726 / 3.45 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 365 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.8460 (p) cc_final: 0.8227 (t) REVERT: A 166 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: A 222 GLU cc_start: 0.7659 (tt0) cc_final: 0.7430 (tt0) REVERT: A 227 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7964 (t160) REVERT: A 250 TYR cc_start: 0.8558 (m-80) cc_final: 0.8075 (m-80) REVERT: A 289 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7621 (tpt) REVERT: A 323 THR cc_start: 0.6862 (OUTLIER) cc_final: 0.5707 (m) REVERT: A 392 ASP cc_start: 0.7827 (t0) cc_final: 0.7474 (t0) REVERT: A 427 LYS cc_start: 0.7781 (tptt) cc_final: 0.7561 (tptt) REVERT: A 440 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: A 478 TYR cc_start: 0.8467 (m-80) cc_final: 0.8130 (m-80) REVERT: A 491 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7392 (t) REVERT: L 63 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7224 (ptp-170) REVERT: B 30 GLU cc_start: 0.8042 (tt0) cc_final: 0.7702 (tt0) REVERT: B 166 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: B 222 GLU cc_start: 0.7876 (tt0) cc_final: 0.7584 (tt0) REVERT: B 226 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8463 (ttmm) REVERT: B 228 ASN cc_start: 0.8788 (t0) cc_final: 0.8522 (t0) REVERT: B 289 MET cc_start: 0.7733 (tpt) cc_final: 0.7461 (tpt) REVERT: B 295 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 491 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7421 (t) REVERT: C 84 ASP cc_start: 0.6936 (t0) cc_final: 0.6515 (t0) REVERT: C 227 ASN cc_start: 0.8345 (t0) cc_final: 0.8124 (t0) REVERT: C 262 ASN cc_start: 0.8268 (t0) cc_final: 0.7995 (t0) REVERT: C 323 THR cc_start: 0.6500 (OUTLIER) cc_final: 0.5334 (m) REVERT: C 377 SER cc_start: 0.7774 (t) cc_final: 0.7399 (p) REVERT: E 51 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8113 (pt) outliers start: 83 outliers final: 59 residues processed: 405 average time/residue: 0.1110 time to fit residues: 66.4347 Evaluate side-chains 431 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 361 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 363 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN B 225 GLN D 32 HIS C 159 HIS C 183 ASN C 454 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106272 restraints weight = 23119.055| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.20 r_work: 0.3231 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15546 Z= 0.202 Angle : 0.600 10.387 21090 Z= 0.317 Chirality : 0.045 0.203 2454 Planarity : 0.005 0.052 2676 Dihedral : 4.865 20.035 2109 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.81 % Allowed : 21.71 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.19), residues: 1965 helix: 0.64 (0.27), residues: 423 sheet: -0.75 (0.21), residues: 636 loop : -1.65 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 56 TYR 0.020 0.002 TYR A 457 PHE 0.023 0.002 PHE C 435 TRP 0.012 0.002 TRP F 37 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (15513) covalent geometry : angle 0.59915 / 0.32 (21024) SS BOND : bond 0.00350 / 0.22 ( 33) SS BOND : angle 0.85607 / 0.58 ( 66) hydrogen bonds : bond 0.03842 / 2.48 ( 648) hydrogen bonds : angle 5.22018 / 3.50 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 374 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.8460 (p) cc_final: 0.8216 (t) REVERT: A 166 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8159 (mttp) REVERT: A 250 TYR cc_start: 0.8543 (m-80) cc_final: 0.8057 (m-80) REVERT: A 256 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 289 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7625 (tpt) REVERT: A 323 THR cc_start: 0.6853 (OUTLIER) cc_final: 0.5829 (m) REVERT: A 427 LYS cc_start: 0.7747 (tptt) cc_final: 0.7536 (tptt) REVERT: A 478 TYR cc_start: 0.8484 (m-80) cc_final: 0.8138 (m-80) REVERT: B 30 GLU cc_start: 0.8045 (tt0) cc_final: 0.7723 (tt0) REVERT: B 166 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8133 (mttp) REVERT: B 222 GLU cc_start: 0.7907 (tt0) cc_final: 0.7613 (tt0) REVERT: B 226 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8457 (ttmm) REVERT: B 228 ASN cc_start: 0.8773 (t0) cc_final: 0.8506 (t0) REVERT: B 289 MET cc_start: 0.7794 (tpt) cc_final: 0.7480 (tpt) REVERT: B 295 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 478 TYR cc_start: 0.8421 (m-80) cc_final: 0.7993 (m-80) REVERT: B 491 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7521 (t) REVERT: C 84 ASP cc_start: 0.6907 (t0) cc_final: 0.6482 (t0) REVERT: C 227 ASN cc_start: 0.8382 (t0) cc_final: 0.8161 (t0) REVERT: C 262 ASN cc_start: 0.8295 (t0) cc_final: 0.8026 (t0) REVERT: C 293 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8115 (tttt) REVERT: C 323 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.5305 (m) REVERT: C 377 SER cc_start: 0.7775 (t) cc_final: 0.7407 (p) outliers start: 84 outliers final: 65 residues processed: 412 average time/residue: 0.1313 time to fit residues: 79.5866 Evaluate side-chains 441 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 369 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 0.9980 chunk 139 optimal weight: 0.0060 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN B 317 HIS ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 ASN C 363 ASN C 454 ASN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107948 restraints weight = 23308.422| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.20 r_work: 0.3255 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15546 Z= 0.133 Angle : 0.558 10.230 21090 Z= 0.294 Chirality : 0.044 0.189 2454 Planarity : 0.004 0.048 2676 Dihedral : 4.646 18.915 2109 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.01 % Allowed : 22.45 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.19), residues: 1965 helix: 0.86 (0.27), residues: 423 sheet: -0.52 (0.22), residues: 576 loop : -1.63 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 56 TYR 0.021 0.001 TYR A 417 PHE 0.017 0.001 PHE C 435 TRP 0.012 0.001 TRP E 33 HIS 0.009 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15513) covalent geometry : angle 0.55751 / 0.29 (21024) SS BOND : bond 0.00255 / 0.16 ( 33) SS BOND : angle 0.77815 / 0.55 ( 66) hydrogen bonds : bond 0.03378 / 2.20 ( 648) hydrogen bonds : angle 4.99277 / 3.35 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 361 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 29 THR cc_start: 0.8436 (p) cc_final: 0.8208 (t) REVERT: A 166 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8117 (mttp) REVERT: A 222 GLU cc_start: 0.7700 (tt0) cc_final: 0.7213 (tt0) REVERT: A 227 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7938 (t160) REVERT: A 250 TYR cc_start: 0.8530 (m-80) cc_final: 0.8003 (m-80) REVERT: A 289 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7649 (tpt) REVERT: A 323 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.5741 (m) REVERT: A 427 LYS cc_start: 0.7730 (tptt) cc_final: 0.7516 (tptt) REVERT: A 478 TYR cc_start: 0.8432 (m-80) cc_final: 0.8105 (m-80) REVERT: L 63 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7208 (ptp-170) REVERT: B 30 GLU cc_start: 0.8035 (tt0) cc_final: 0.7698 (tt0) REVERT: B 166 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8108 (mttp) REVERT: B 168 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8416 (mtmt) REVERT: B 222 GLU cc_start: 0.7887 (tt0) cc_final: 0.7590 (tt0) REVERT: B 228 ASN cc_start: 0.8742 (t0) cc_final: 0.8475 (t0) REVERT: B 289 MET cc_start: 0.7663 (tpt) cc_final: 0.7419 (tpt) REVERT: B 478 TYR cc_start: 0.8386 (m-80) cc_final: 0.7955 (m-80) REVERT: B 491 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7325 (t) REVERT: F 63 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7297 (ptp-170) REVERT: C 84 ASP cc_start: 0.6919 (t0) cc_final: 0.6497 (t0) REVERT: C 227 ASN cc_start: 0.8352 (t0) cc_final: 0.8131 (t0) REVERT: C 256 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7850 (mt-10) REVERT: C 262 ASN cc_start: 0.8276 (t0) cc_final: 0.8004 (t0) REVERT: E 51 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8114 (pt) outliers start: 70 outliers final: 49 residues processed: 395 average time/residue: 0.1238 time to fit residues: 72.0121 Evaluate side-chains 412 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 363 ASN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 183 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 ASN C 284 GLN C 363 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106704 restraints weight = 23180.593| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.19 r_work: 0.3240 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15546 Z= 0.185 Angle : 0.601 11.238 21090 Z= 0.316 Chirality : 0.045 0.197 2454 Planarity : 0.005 0.051 2676 Dihedral : 4.813 19.863 2109 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.12 % Allowed : 22.39 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1965 helix: 0.86 (0.27), residues: 429 sheet: -0.63 (0.21), residues: 615 loop : -1.68 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 56 TYR 0.023 0.002 TYR A 417 PHE 0.023 0.002 PHE C 435 TRP 0.012 0.002 TRP F 37 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (15513) covalent geometry : angle 0.59944 / 0.32 (21024) SS BOND : bond 0.00307 / 0.20 ( 33) SS BOND : angle 0.94458 / 0.65 ( 66) hydrogen bonds : bond 0.03714 / 2.41 ( 648) hydrogen bonds : angle 5.14051 / 3.45 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4305.74 seconds wall clock time: 74 minutes 20.81 seconds (4460.81 seconds total)