Starting phenix.real_space_refine on Fri Jul 3 12:55:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pls_13499/07_2026/7pls_13499.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 40 5.16 5 C 9240 2.51 5 N 2332 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14224 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Restraints were copied for chains: B, C, D Time building chain proxies: 3.46, per 1000 atoms: 0.24 Number of scatterers: 14224 At special positions: 0 Unit cell: (159.714, 114.882, 59.776, 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 40 16.00 O 2612 8.00 N 2332 7.00 C 9240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.04 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 274 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 236 " " NAG B 501 " - " ASN B 236 " " NAG C 501 " - " ASN C 236 " " NAG D 501 " - " ASN D 236 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 722.9 milliseconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 37.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 97 through 105 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 97 through 105 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 97 through 105 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 35 through 40 Processing helix chain 'D' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 97 through 105 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR A 174 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP A 223 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 176 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 225 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS A 178 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 127 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 129 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER A 179 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR A 131 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 53 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL A 128 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 55 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 130 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 57 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS A 132 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP A 370 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR A 383 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL A 372 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL A 381 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE A 455 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS A 415 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 457 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR A 413 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY A 459 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 411 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR B 174 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP B 223 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 176 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP B 225 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS B 178 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 127 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 129 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER B 179 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR B 131 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE B 53 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL B 128 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 55 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B 130 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 57 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 132 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP B 370 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR B 383 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL B 372 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL B 381 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE B 455 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS B 415 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU B 457 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR B 413 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY B 459 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 411 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 405 Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR C 174 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP C 223 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 176 " --> pdb=" O TRP C 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP C 225 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS C 178 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 127 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 177 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 129 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER C 179 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR C 131 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE C 53 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL C 128 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 55 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 130 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 57 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS C 132 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP C 370 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR C 383 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL C 372 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL C 381 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE C 455 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS C 415 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU C 457 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR C 413 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY C 459 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 411 " --> pdb=" O GLY C 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 405 Processing sheet with id=AB1, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR D 174 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP D 223 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU D 176 " --> pdb=" O TRP D 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP D 225 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS D 178 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 127 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 177 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 129 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER D 179 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR D 131 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE D 53 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL D 128 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 55 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 130 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE D 57 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS D 132 " --> pdb=" O ILE D 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP D 370 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR D 383 " --> pdb=" O TRP D 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL D 372 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL D 381 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE D 455 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS D 415 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU D 457 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR D 413 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY D 459 " --> pdb=" O THR D 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D 411 " --> pdb=" O GLY D 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 405 488 hydrogen bonds defined for protein. 1320 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: 2.35 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4104 1.34 - 1.46: 3588 1.46 - 1.58: 6972 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 14724 Sorted by residual: bond pdb=" N ILE D 317 " pdb=" CA ILE D 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE B 317 " pdb=" CA ILE B 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE C 317 " pdb=" CA ILE C 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE A 317 " pdb=" CA ILE A 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE C 316 " pdb=" CA ILE C 316 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.67e+00 ... (remaining 14719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 19012 1.08 - 2.16: 804 2.16 - 3.24: 268 3.24 - 4.32: 40 4.32 - 5.40: 24 Bond angle restraints: 20148 Sorted by residual: angle pdb=" CA VAL B 321 " pdb=" C VAL B 321 " pdb=" O VAL B 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL A 321 " pdb=" C VAL A 321 " pdb=" O VAL A 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL C 321 " pdb=" C VAL C 321 " pdb=" O VAL C 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL D 321 " pdb=" C VAL D 321 " pdb=" O VAL D 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" O ILE D 317 " pdb=" C ILE D 317 " pdb=" N SER D 318 " ideal model delta sigma weight residual 121.87 124.66 -2.79 9.70e-01 1.06e+00 8.29e+00 ... (remaining 20143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 7288 17.16 - 34.32: 668 34.32 - 51.48: 264 51.48 - 68.64: 48 68.64 - 85.80: 28 Dihedral angle restraints: 8296 sinusoidal: 3300 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1232 0.033 - 0.066: 492 0.066 - 0.099: 184 0.099 - 0.132: 100 0.132 - 0.165: 28 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CA ILE B 316 " pdb=" N ILE B 316 " pdb=" C ILE B 316 " pdb=" CB ILE B 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE C 316 " pdb=" N ILE C 316 " pdb=" C ILE C 316 " pdb=" CB ILE C 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2033 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG B 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG D 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG A 501 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " 0.045 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " -0.012 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3614 2.80 - 3.33: 12958 3.33 - 3.85: 26466 3.85 - 4.38: 32558 4.38 - 4.90: 52340 Nonbonded interactions: 127936 Sorted by model distance: nonbonded pdb=" OE2 GLU B 362 " pdb=" OH TYR B 391 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU C 362 " pdb=" OH TYR C 391 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU D 362 " pdb=" OH TYR D 391 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU A 362 " pdb=" OH TYR A 391 " model vdw 2.275 3.040 nonbonded pdb=" O PHE A 137 " pdb=" O HOH A 601 " model vdw 2.294 3.040 ... (remaining 127931 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.003 0.033 14732 Z= 0.193 Angle : 0.581 5.397 20168 Z= 0.342 Chirality : 0.047 0.165 2036 Planarity : 0.005 0.048 2548 Dihedral : 16.458 85.803 5084 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.33 % Allowed : 12.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1716 helix: 0.95 (0.22), residues: 544 sheet: 0.21 (0.28), residues: 284 loop : -0.11 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 89 TYR 0.008 0.001 TYR A 126 PHE 0.012 0.001 PHE C 137 TRP 0.007 0.001 TRP A 183 HIS 0.002 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.19 (14724) covalent geometry : angle 0.57844 / 0.34 (20148) SS BOND : bond 0.00810 / 0.41 ( 4) SS BOND : angle 2.26948 / 1.54 ( 8) hydrogen bonds : bond 0.12984 / 8.54 ( 488) hydrogen bonds : angle 5.34946 / 3.84 ( 1320) link_NAG-ASN : bond 0.00322 / 0.16 ( 4) link_NAG-ASN : angle 1.50784 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.654 Fit side-chains REVERT: A 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: A 315 GLU cc_start: 0.7375 (tp30) cc_final: 0.7040 (tp30) REVERT: B 312 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: B 315 GLU cc_start: 0.7374 (tp30) cc_final: 0.7041 (tp30) REVERT: C 312 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: C 315 GLU cc_start: 0.7379 (tp30) cc_final: 0.7046 (tp30) REVERT: D 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: D 315 GLU cc_start: 0.7373 (tp30) cc_final: 0.7038 (tp30) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.6023 time to fit residues: 87.8709 Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.115960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.085662 restraints weight = 14959.876| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.45 r_work: 0.2740 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14732 Z= 0.140 Angle : 0.546 5.712 20168 Z= 0.284 Chirality : 0.045 0.141 2036 Planarity : 0.005 0.037 2548 Dihedral : 5.810 50.684 1892 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.73 % Allowed : 10.80 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1716 helix: 1.55 (0.23), residues: 532 sheet: 0.06 (0.28), residues: 292 loop : -0.28 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 42 TYR 0.010 0.001 TYR D 126 PHE 0.013 0.002 PHE B 240 TRP 0.009 0.001 TRP D 243 HIS 0.002 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (14724) covalent geometry : angle 0.54180 / 0.28 (20148) SS BOND : bond 0.00934 / 0.47 ( 4) SS BOND : angle 2.73945 / 1.80 ( 8) hydrogen bonds : bond 0.04133 / 2.74 ( 488) hydrogen bonds : angle 4.78843 / 3.40 ( 1320) link_NAG-ASN : bond 0.00003 / 0.00 ( 4) link_NAG-ASN : angle 1.63652 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.569 Fit side-chains REVERT: A 402 VAL cc_start: 0.7831 (t) cc_final: 0.7555 (t) REVERT: A 411 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6352 (p) REVERT: B 402 VAL cc_start: 0.7807 (t) cc_final: 0.7534 (t) REVERT: B 411 THR cc_start: 0.6634 (OUTLIER) cc_final: 0.6347 (p) REVERT: C 402 VAL cc_start: 0.7814 (t) cc_final: 0.7539 (t) REVERT: C 411 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.6353 (p) REVERT: D 402 VAL cc_start: 0.7818 (t) cc_final: 0.7542 (t) REVERT: D 411 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6341 (p) outliers start: 26 outliers final: 12 residues processed: 134 average time/residue: 0.6018 time to fit residues: 88.9180 Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.083713 restraints weight = 15030.085| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.44 r_work: 0.2706 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14732 Z= 0.208 Angle : 0.611 5.960 20168 Z= 0.320 Chirality : 0.048 0.145 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.971 22.383 1872 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.60 % Allowed : 10.67 % Favored : 87.73 % 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: 0.36 (0.20), residues: 1716 helix: 1.46 (0.23), residues: 524 sheet: -0.06 (0.29), residues: 292 loop : -0.33 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 259 TYR 0.014 0.002 TYR A 126 PHE 0.019 0.002 PHE A 137 TRP 0.011 0.002 TRP C 223 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (14724) covalent geometry : angle 0.60739 / 0.32 (20148) SS BOND : bond 0.01766 / 0.88 ( 4) SS BOND : angle 2.71891 / 1.91 ( 8) hydrogen bonds : bond 0.04796 / 3.20 ( 488) hydrogen bonds : angle 5.00425 / 3.54 ( 1320) link_NAG-ASN : bond 0.00021 / 0.01 ( 4) link_NAG-ASN : angle 1.83859 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.584 Fit side-chains REVERT: A 77 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: A 312 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: A 402 VAL cc_start: 0.7811 (t) cc_final: 0.7539 (t) REVERT: A 411 THR cc_start: 0.6513 (OUTLIER) cc_final: 0.6293 (p) REVERT: B 312 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: B 402 VAL cc_start: 0.7792 (t) cc_final: 0.7519 (t) REVERT: B 411 THR cc_start: 0.6506 (OUTLIER) cc_final: 0.6281 (p) REVERT: C 312 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: C 402 VAL cc_start: 0.7790 (t) cc_final: 0.7514 (t) REVERT: C 411 THR cc_start: 0.6512 (OUTLIER) cc_final: 0.6288 (p) REVERT: D 77 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: D 312 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: D 402 VAL cc_start: 0.7795 (t) cc_final: 0.7518 (t) REVERT: D 411 THR cc_start: 0.6504 (OUTLIER) cc_final: 0.6284 (p) outliers start: 24 outliers final: 12 residues processed: 128 average time/residue: 0.6038 time to fit residues: 85.3985 Evaluate side-chains 134 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.084699 restraints weight = 15089.536| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.43 r_work: 0.2722 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14732 Z= 0.157 Angle : 0.570 5.903 20168 Z= 0.297 Chirality : 0.046 0.142 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.650 21.332 1860 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.73 % Allowed : 11.07 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1716 helix: 1.48 (0.23), residues: 532 sheet: -0.26 (0.28), residues: 292 loop : -0.37 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.011 0.001 TYR C 126 PHE 0.014 0.002 PHE B 137 TRP 0.011 0.001 TRP A 243 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (14724) covalent geometry : angle 0.56570 / 0.30 (20148) SS BOND : bond 0.01255 / 0.63 ( 4) SS BOND : angle 2.74651 / 1.89 ( 8) hydrogen bonds : bond 0.04201 / 2.79 ( 488) hydrogen bonds : angle 4.87120 / 3.44 ( 1320) link_NAG-ASN : bond 0.00037 / 0.02 ( 4) link_NAG-ASN : angle 1.69127 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.545 Fit side-chains REVERT: A 77 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: A 312 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: A 402 VAL cc_start: 0.7768 (t) cc_final: 0.7497 (t) REVERT: B 312 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 402 VAL cc_start: 0.7761 (t) cc_final: 0.7496 (t) REVERT: C 312 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: C 402 VAL cc_start: 0.7749 (t) cc_final: 0.7478 (t) REVERT: D 77 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: D 312 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: D 402 VAL cc_start: 0.7771 (t) cc_final: 0.7502 (t) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.5892 time to fit residues: 89.9086 Evaluate side-chains 134 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 123 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.084743 restraints weight = 15097.472| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.43 r_work: 0.2721 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14732 Z= 0.156 Angle : 0.576 6.513 20168 Z= 0.299 Chirality : 0.045 0.141 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.692 21.316 1860 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.20 % Allowed : 11.87 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1716 helix: 1.49 (0.23), residues: 532 sheet: -0.36 (0.28), residues: 292 loop : -0.37 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 259 TYR 0.012 0.001 TYR C 126 PHE 0.015 0.002 PHE C 137 TRP 0.011 0.001 TRP D 243 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (14724) covalent geometry : angle 0.57280 / 0.30 (20148) SS BOND : bond 0.01752 / 0.88 ( 4) SS BOND : angle 2.44930 / 1.74 ( 8) hydrogen bonds : bond 0.04189 / 2.79 ( 488) hydrogen bonds : angle 4.85267 / 3.43 ( 1320) link_NAG-ASN : bond 0.00040 / 0.02 ( 4) link_NAG-ASN : angle 1.68881 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.505 Fit side-chains REVERT: A 77 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: A 312 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: B 312 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: C 312 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: D 77 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: D 312 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (mt-10) outliers start: 18 outliers final: 12 residues processed: 122 average time/residue: 0.6414 time to fit residues: 85.8487 Evaluate side-chains 134 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 42 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.084727 restraints weight = 15070.968| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.44 r_work: 0.2719 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14732 Z= 0.155 Angle : 0.567 5.915 20168 Z= 0.295 Chirality : 0.045 0.141 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.674 21.306 1860 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.47 % Allowed : 11.60 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1716 helix: 1.49 (0.23), residues: 532 sheet: -0.40 (0.28), residues: 292 loop : -0.36 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 259 TYR 0.012 0.001 TYR A 126 PHE 0.015 0.002 PHE D 137 TRP 0.011 0.001 TRP B 243 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (14724) covalent geometry : angle 0.56358 / 0.29 (20148) SS BOND : bond 0.01493 / 0.75 ( 4) SS BOND : angle 2.38953 / 1.70 ( 8) hydrogen bonds : bond 0.04164 / 2.77 ( 488) hydrogen bonds : angle 4.85166 / 3.43 ( 1320) link_NAG-ASN : bond 0.00040 / 0.02 ( 4) link_NAG-ASN : angle 1.68442 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.594 Fit side-chains REVERT: A 77 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: A 312 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: B 312 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: C 312 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: D 77 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: D 312 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7956 (mt-10) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.6062 time to fit residues: 84.5596 Evaluate side-chains 130 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 116 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.086573 restraints weight = 14945.666| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.43 r_work: 0.2752 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14732 Z= 0.108 Angle : 0.518 5.589 20168 Z= 0.267 Chirality : 0.043 0.137 2036 Planarity : 0.005 0.042 2548 Dihedral : 4.424 21.608 1860 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.80 % Allowed : 12.53 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1716 helix: 1.59 (0.23), residues: 540 sheet: -0.24 (0.29), residues: 288 loop : -0.29 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.008 0.001 TYR C 126 PHE 0.009 0.001 PHE C 96 TRP 0.009 0.001 TRP C 243 HIS 0.002 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (14724) covalent geometry : angle 0.51459 / 0.27 (20148) SS BOND : bond 0.01122 / 0.56 ( 4) SS BOND : angle 2.32185 / 1.64 ( 8) hydrogen bonds : bond 0.03525 / 2.33 ( 488) hydrogen bonds : angle 4.65538 / 3.28 ( 1320) link_NAG-ASN : bond 0.00047 / 0.02 ( 4) link_NAG-ASN : angle 1.52259 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.388 Fit side-chains REVERT: A 312 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: B 312 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: C 312 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: D 312 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7906 (mt-10) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.5493 time to fit residues: 75.1215 Evaluate side-chains 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.084043 restraints weight = 15031.512| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.44 r_work: 0.2709 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14732 Z= 0.186 Angle : 0.589 5.963 20168 Z= 0.307 Chirality : 0.047 0.144 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.741 21.537 1860 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.07 % Allowed : 12.00 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1716 helix: 1.47 (0.23), residues: 532 sheet: -0.41 (0.28), residues: 292 loop : -0.37 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.014 0.002 TYR A 126 PHE 0.018 0.002 PHE B 137 TRP 0.011 0.002 TRP C 243 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (14724) covalent geometry : angle 0.58552 / 0.31 (20148) SS BOND : bond 0.01424 / 0.71 ( 4) SS BOND : angle 2.77381 / 1.94 ( 8) hydrogen bonds : bond 0.04485 / 2.98 ( 488) hydrogen bonds : angle 4.90368 / 3.46 ( 1320) link_NAG-ASN : bond 0.00047 / 0.02 ( 4) link_NAG-ASN : angle 1.75066 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.552 Fit side-chains REVERT: A 312 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: B 312 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: C 312 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: D 312 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7966 (mt-10) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.5828 time to fit residues: 77.5590 Evaluate side-chains 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 165 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.085635 restraints weight = 15145.809| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.42 r_work: 0.2736 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14732 Z= 0.129 Angle : 0.561 8.633 20168 Z= 0.288 Chirality : 0.044 0.140 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.611 21.714 1860 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.07 % Allowed : 12.27 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1716 helix: 1.51 (0.23), residues: 540 sheet: -0.42 (0.28), residues: 292 loop : -0.30 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.010 0.001 TYR C 126 PHE 0.012 0.002 PHE A 240 TRP 0.010 0.001 TRP C 243 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14724) covalent geometry : angle 0.55751 / 0.29 (20148) SS BOND : bond 0.01718 / 0.86 ( 4) SS BOND : angle 2.73642 / 1.88 ( 8) hydrogen bonds : bond 0.03801 / 2.52 ( 488) hydrogen bonds : angle 4.74968 / 3.35 ( 1320) link_NAG-ASN : bond 0.00071 / 0.04 ( 4) link_NAG-ASN : angle 1.58812 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.608 Fit side-chains REVERT: A 312 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: B 312 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: C 312 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: D 312 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7924 (mt-10) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.4928 time to fit residues: 65.6839 Evaluate side-chains 124 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.084821 restraints weight = 14984.460| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.44 r_work: 0.2721 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14732 Z= 0.151 Angle : 0.586 8.379 20168 Z= 0.302 Chirality : 0.045 0.141 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.678 21.687 1860 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.07 % Allowed : 12.00 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1716 helix: 1.45 (0.23), residues: 540 sheet: -0.44 (0.28), residues: 292 loop : -0.34 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.012 0.001 TYR A 126 PHE 0.014 0.002 PHE A 137 TRP 0.010 0.001 TRP C 243 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (14724) covalent geometry : angle 0.58201 / 0.30 (20148) SS BOND : bond 0.01765 / 0.88 ( 4) SS BOND : angle 2.68129 / 1.84 ( 8) hydrogen bonds : bond 0.04099 / 2.73 ( 488) hydrogen bonds : angle 4.82576 / 3.41 ( 1320) link_NAG-ASN : bond 0.00049 / 0.02 ( 4) link_NAG-ASN : angle 1.65025 / 1.18 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.520 Fit side-chains REVERT: A 312 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: B 312 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: C 312 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: D 312 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7937 (mt-10) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.5197 time to fit residues: 67.7957 Evaluate side-chains 124 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 chunk 136 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.088067 restraints weight = 15086.640| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.44 r_work: 0.2777 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14732 Z= 0.096 Angle : 0.521 7.490 20168 Z= 0.266 Chirality : 0.043 0.137 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.313 21.614 1860 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.07 % Allowed : 12.13 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1716 helix: 1.73 (0.23), residues: 540 sheet: -0.21 (0.29), residues: 288 loop : -0.21 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.006 0.001 TYR D 177 PHE 0.009 0.001 PHE B 394 TRP 0.009 0.001 TRP A 243 HIS 0.001 0.000 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (14724) covalent geometry : angle 0.51819 / 0.27 (20148) SS BOND : bond 0.01314 / 0.66 ( 4) SS BOND : angle 2.41580 / 1.69 ( 8) hydrogen bonds : bond 0.03169 / 2.09 ( 488) hydrogen bonds : angle 4.52960 / 3.19 ( 1320) link_NAG-ASN : bond 0.00072 / 0.04 ( 4) link_NAG-ASN : angle 1.34674 / 0.98 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4186.87 seconds wall clock time: 72 minutes 26.73 seconds (4346.73 seconds total)