Starting phenix.real_space_refine on Thu Sep 18 05:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pls_13499/09_2025/7pls_13499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pls_13499/09_2025/7pls_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pls_13499/09_2025/7pls_13499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pls_13499/09_2025/7pls_13499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pls_13499/09_2025/7pls_13499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pls_13499/09_2025/7pls_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 dihedrals: 3 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: 2.48, per 1000 atoms: 0.17 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: 0.90 Conformation dependent library (CDL) restraints added in 465.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.39 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: 2.06 Time building geometry restraints manager: 1.15 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: 7372 17.16 - 34.32: 668 34.32 - 51.48: 264 51.48 - 68.64: 48 68.64 - 85.80: 28 Dihedral angle restraints: 8380 sinusoidal: 3384 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 8377 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: 0.03 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 16.349 85.803 5168 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 aren 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 covalent geometry : bond 0.00322 (14724) covalent geometry : angle 0.57844 (20148) SS BOND : bond 0.00810 ( 4) SS BOND : angle 2.26948 ( 8) hydrogen bonds : bond 0.12984 ( 488) hydrogen bonds : angle 5.34946 ( 1320) link_NAG-ASN : bond 0.00322 ( 4) link_NAG-ASN : angle 1.50784 ( 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 : 0.504 Fit side-chains REVERT: A 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6973 (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: 0.7682 (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: 0.6109 time to fit residues: 88.7703 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 : 0.566 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.085658 restraints weight = 14985.335| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.45 r_work: 0.2738 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14732 Z= 0.139 Angle : 0.546 5.722 20168 Z= 0.284 Chirality : 0.045 0.142 2036 Planarity : 0.005 0.037 2548 Dihedral : 5.662 50.473 1976 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.60 % Allowed : 10.93 % 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 aren not related in a simple way. whole: 0.48 (0.21), residues: 1716 helix: 1.55 (0.23), residues: 532 sheet: 0.05 (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 259 TYR 0.010 0.001 TYR A 126 PHE 0.013 0.002 PHE A 240 TRP 0.009 0.001 TRP A 243 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00330 (14724) covalent geometry : angle 0.54221 (20148) SS BOND : bond 0.00934 ( 4) SS BOND : angle 2.72932 ( 8) hydrogen bonds : bond 0.04135 ( 488) hydrogen bonds : angle 4.79292 ( 1320) link_NAG-ASN : bond 0.00042 ( 4) link_NAG-ASN : angle 1.57581 ( 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 140 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.532 Fit side-chains REVERT: A 402 VAL cc_start: 0.7863 (t) cc_final: 0.7578 (t) REVERT: A 411 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6312 (p) REVERT: B 402 VAL cc_start: 0.7839 (t) cc_final: 0.7556 (t) REVERT: B 411 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6308 (p) REVERT: C 402 VAL cc_start: 0.7846 (t) cc_final: 0.7561 (t) REVERT: C 411 THR cc_start: 0.6522 (OUTLIER) cc_final: 0.6314 (p) REVERT: D 402 VAL cc_start: 0.7850 (t) cc_final: 0.7564 (t) REVERT: D 411 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.6305 (p) outliers start: 24 outliers final: 12 residues processed: 132 average time/residue: 0.6117 time to fit residues: 88.7491 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 : 0.560 ------------------------------------------------------------------------------- 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: 5.9990 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.084403 restraints weight = 15001.127| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.44 r_work: 0.2719 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14732 Z= 0.174 Angle : 0.581 5.893 20168 Z= 0.303 Chirality : 0.047 0.144 2036 Planarity : 0.005 0.040 2548 Dihedral : 4.770 22.728 1956 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.33 % Allowed : 11.20 % 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 aren not related in a simple way. whole: 0.39 (0.21), residues: 1716 helix: 1.48 (0.23), residues: 532 sheet: -0.03 (0.29), residues: 292 loop : -0.33 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.012 0.002 TYR D 126 PHE 0.016 0.002 PHE C 137 TRP 0.010 0.001 TRP B 243 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00418 (14724) covalent geometry : angle 0.57741 (20148) SS BOND : bond 0.01625 ( 4) SS BOND : angle 2.50407 ( 8) hydrogen bonds : bond 0.04485 ( 488) hydrogen bonds : angle 4.91031 ( 1320) link_NAG-ASN : bond 0.00048 ( 4) link_NAG-ASN : angle 1.71887 ( 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 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.589 Fit side-chains REVERT: A 312 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: A 402 VAL cc_start: 0.7784 (t) cc_final: 0.7509 (t) REVERT: A 411 THR cc_start: 0.6581 (OUTLIER) cc_final: 0.6333 (p) REVERT: B 312 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: B 402 VAL cc_start: 0.7759 (t) cc_final: 0.7486 (t) REVERT: B 411 THR cc_start: 0.6579 (OUTLIER) cc_final: 0.6324 (p) REVERT: C 312 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: C 402 VAL cc_start: 0.7758 (t) cc_final: 0.7482 (t) REVERT: C 411 THR cc_start: 0.6579 (OUTLIER) cc_final: 0.6325 (p) REVERT: D 312 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: D 402 VAL cc_start: 0.7774 (t) cc_final: 0.7498 (t) REVERT: D 411 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6322 (p) outliers start: 20 outliers final: 8 residues processed: 124 average time/residue: 0.6506 time to fit residues: 88.6929 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 : 0.541 ------------------------------------------------------------------------------- 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 411 THR 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 411 THR 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 411 THR 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 411 THR Chi-restraints excluded: chain D residue 429 THR 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: 2.9990 chunk 79 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.084525 restraints weight = 15012.263| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.44 r_work: 0.2718 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14732 Z= 0.167 Angle : 0.580 5.949 20168 Z= 0.302 Chirality : 0.046 0.142 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.573 21.396 1944 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.87 % Allowed : 11.47 % 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 aren not related in a simple way. whole: 0.31 (0.20), residues: 1716 helix: 1.50 (0.23), residues: 532 sheet: -0.27 (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 0.012 0.002 TYR C 126 PHE 0.016 0.002 PHE A 137 TRP 0.010 0.001 TRP B 243 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00400 (14724) covalent geometry : angle 0.57582 (20148) SS BOND : bond 0.01302 ( 4) SS BOND : angle 2.72432 ( 8) hydrogen bonds : bond 0.04313 ( 488) hydrogen bonds : angle 4.89405 ( 1320) link_NAG-ASN : bond 0.00031 ( 4) link_NAG-ASN : angle 1.66903 ( 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 144 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.530 Fit side-chains REVERT: A 312 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: A 402 VAL cc_start: 0.7803 (t) cc_final: 0.7535 (t) REVERT: B 312 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: B 402 VAL cc_start: 0.7777 (t) cc_final: 0.7513 (t) REVERT: C 312 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: C 402 VAL cc_start: 0.7773 (t) cc_final: 0.7505 (t) REVERT: D 77 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: D 312 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: D 402 VAL cc_start: 0.7786 (t) cc_final: 0.7518 (t) outliers start: 28 outliers final: 12 residues processed: 140 average time/residue: 0.6019 time to fit residues: 92.9721 Evaluate side-chains 129 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.084853 restraints weight = 15150.575| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.42 r_work: 0.2724 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0829 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 6.579 20168 Z= 0.299 Chirality : 0.046 0.141 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.591 21.337 1944 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.13 % Allowed : 12.20 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1716 helix: 1.52 (0.23), residues: 532 sheet: -0.34 (0.28), residues: 292 loop : -0.38 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.011 0.001 TYR C 126 PHE 0.014 0.002 PHE D 137 TRP 0.010 0.001 TRP B 243 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00371 (14724) covalent geometry : angle 0.57320 (20148) SS BOND : bond 0.01752 ( 4) SS BOND : angle 2.44492 ( 8) hydrogen bonds : bond 0.04173 ( 488) hydrogen bonds : angle 4.85284 ( 1320) link_NAG-ASN : bond 0.00039 ( 4) link_NAG-ASN : angle 1.63366 ( 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 129 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.408 Fit side-chains REVERT: A 312 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: A 402 VAL cc_start: 0.7812 (t) cc_final: 0.7521 (t) REVERT: B 312 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 402 VAL cc_start: 0.7780 (t) cc_final: 0.7491 (t) REVERT: C 312 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: C 402 VAL cc_start: 0.7790 (t) cc_final: 0.7499 (t) REVERT: D 77 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: D 312 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: D 402 VAL cc_start: 0.7801 (t) cc_final: 0.7510 (t) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.6605 time to fit residues: 90.2278 Evaluate side-chains 125 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 161 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.084302 restraints weight = 15077.869| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.43 r_work: 0.2714 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14732 Z= 0.171 Angle : 0.583 5.987 20168 Z= 0.304 Chirality : 0.046 0.141 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.642 21.345 1944 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.40 % Allowed : 11.93 % 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 aren not related in a simple way. whole: 0.23 (0.20), residues: 1716 helix: 1.46 (0.23), residues: 532 sheet: -0.43 (0.28), residues: 292 loop : -0.39 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 259 TYR 0.013 0.002 TYR B 126 PHE 0.016 0.002 PHE D 137 TRP 0.011 0.001 TRP B 243 HIS 0.003 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00409 (14724) covalent geometry : angle 0.57956 (20148) SS BOND : bond 0.01585 ( 4) SS BOND : angle 2.48297 ( 8) hydrogen bonds : bond 0.04363 ( 488) hydrogen bonds : angle 4.90102 ( 1320) link_NAG-ASN : bond 0.00023 ( 4) link_NAG-ASN : angle 1.68169 ( 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 125 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.607 Fit side-chains REVERT: A 312 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 312 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: C 312 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: D 77 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: D 312 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7977 (mt-10) outliers start: 21 outliers final: 12 residues processed: 121 average time/residue: 0.6390 time to fit residues: 85.1218 Evaluate side-chains 121 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 3 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.085695 restraints weight = 14920.937| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.43 r_work: 0.2737 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14732 Z= 0.126 Angle : 0.539 5.765 20168 Z= 0.279 Chirality : 0.044 0.139 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.434 21.713 1944 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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 aren not related in a simple way. whole: 0.35 (0.21), residues: 1716 helix: 1.54 (0.23), residues: 540 sheet: -0.30 (0.28), residues: 288 loop : -0.34 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 259 TYR 0.009 0.001 TYR D 126 PHE 0.011 0.002 PHE D 137 TRP 0.010 0.001 TRP A 243 HIS 0.002 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00296 (14724) covalent geometry : angle 0.53523 (20148) SS BOND : bond 0.01213 ( 4) SS BOND : angle 2.54589 ( 8) hydrogen bonds : bond 0.03793 ( 488) hydrogen bonds : angle 4.74314 ( 1320) link_NAG-ASN : bond 0.00046 ( 4) link_NAG-ASN : angle 1.52548 ( 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: 16 poor density : 116 time to evaluate : 0.562 Fit side-chains REVERT: A 312 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 312 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: C 312 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: D 312 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7897 (mt-10) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 0.6304 time to fit residues: 88.7003 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 : 0.531 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.084845 restraints weight = 15011.853| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.43 r_work: 0.2723 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14732 Z= 0.147 Angle : 0.557 5.829 20168 Z= 0.289 Chirality : 0.045 0.140 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.530 21.798 1944 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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 aren not related in a simple way. whole: 0.30 (0.21), residues: 1716 helix: 1.55 (0.23), residues: 532 sheet: -0.35 (0.28), residues: 288 loop : -0.39 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.012 0.001 TYR D 126 PHE 0.014 0.002 PHE C 137 TRP 0.011 0.001 TRP B 243 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00349 (14724) covalent geometry : angle 0.55315 (20148) SS BOND : bond 0.01245 ( 4) SS BOND : angle 2.55625 ( 8) hydrogen bonds : bond 0.04107 ( 488) hydrogen bonds : angle 4.80997 ( 1320) link_NAG-ASN : bond 0.00052 ( 4) link_NAG-ASN : angle 1.60221 ( 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 : 0.491 Fit side-chains REVERT: A 312 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: B 312 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: C 312 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: D 312 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7939 (mt-10) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.5538 time to fit residues: 75.9389 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 : 0.531 ------------------------------------------------------------------------------- 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: 1.9990 chunk 113 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.084471 restraints weight = 15048.174| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.43 r_work: 0.2715 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14732 Z= 0.170 Angle : 0.598 8.857 20168 Z= 0.310 Chirality : 0.046 0.142 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.666 21.584 1944 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.86 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1716 helix: 1.50 (0.23), residues: 532 sheet: -0.39 (0.28), residues: 288 loop : -0.43 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.012 0.002 TYR D 126 PHE 0.016 0.002 PHE C 137 TRP 0.011 0.001 TRP A 243 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00407 (14724) covalent geometry : angle 0.59413 (20148) SS BOND : bond 0.01852 ( 4) SS BOND : angle 2.83321 ( 8) hydrogen bonds : bond 0.04288 ( 488) hydrogen bonds : angle 4.87485 ( 1320) link_NAG-ASN : bond 0.00037 ( 4) link_NAG-ASN : angle 1.63143 ( 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 : 0.540 Fit side-chains REVERT: A 312 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: B 312 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: C 312 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: D 312 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7968 (mt-10) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.6263 time to fit residues: 85.6775 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 : 0.642 ------------------------------------------------------------------------------- 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: 0.0870 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 81 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.087757 restraints weight = 15074.022| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.42 r_work: 0.2769 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0867 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= 0.101 Angle : 0.529 7.811 20168 Z= 0.271 Chirality : 0.043 0.138 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.278 21.666 1944 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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 aren not related in a simple way. whole: 0.48 (0.21), residues: 1716 helix: 1.69 (0.23), residues: 540 sheet: -0.26 (0.28), residues: 288 loop : -0.27 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 371 TYR 0.006 0.001 TYR D 126 PHE 0.009 0.001 PHE D 394 TRP 0.009 0.001 TRP B 183 HIS 0.001 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00234 (14724) covalent geometry : angle 0.52603 (20148) SS BOND : bond 0.01418 ( 4) SS BOND : angle 2.42694 ( 8) hydrogen bonds : bond 0.03267 ( 488) hydrogen bonds : angle 4.57141 ( 1320) link_NAG-ASN : bond 0.00078 ( 4) link_NAG-ASN : angle 1.33626 ( 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 140 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.449 Fit side-chains REVERT: A 312 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: A 400 ASN cc_start: 0.8373 (p0) cc_final: 0.7986 (p0) REVERT: A 402 VAL cc_start: 0.7781 (t) cc_final: 0.7311 (t) REVERT: B 312 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: B 400 ASN cc_start: 0.8367 (p0) cc_final: 0.7979 (p0) REVERT: B 402 VAL cc_start: 0.7765 (t) cc_final: 0.7296 (t) REVERT: C 312 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: C 400 ASN cc_start: 0.8360 (p0) cc_final: 0.7975 (p0) REVERT: C 402 VAL cc_start: 0.7761 (t) cc_final: 0.7292 (t) REVERT: D 312 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: D 400 ASN cc_start: 0.8363 (p0) cc_final: 0.7973 (p0) REVERT: D 402 VAL cc_start: 0.7762 (t) cc_final: 0.7287 (t) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 0.6006 time to fit residues: 87.2317 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 : 0.604 ------------------------------------------------------------------------------- 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: 1.9990 chunk 101 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.085213 restraints weight = 15035.896| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.44 r_work: 0.2728 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14732 Z= 0.146 Angle : 0.577 7.606 20168 Z= 0.297 Chirality : 0.045 0.142 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.521 21.948 1944 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.07 % Allowed : 12.53 % Favored : 86.40 % 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 aren not related in a simple way. whole: 0.42 (0.21), residues: 1716 helix: 1.69 (0.23), residues: 532 sheet: -0.29 (0.28), residues: 288 loop : -0.34 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 259 TYR 0.011 0.001 TYR C 126 PHE 0.013 0.002 PHE A 240 TRP 0.011 0.001 TRP A 243 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00346 (14724) covalent geometry : angle 0.57396 (20148) SS BOND : bond 0.01649 ( 4) SS BOND : angle 2.56804 ( 8) hydrogen bonds : bond 0.04013 ( 488) hydrogen bonds : angle 4.73604 ( 1320) link_NAG-ASN : bond 0.00092 ( 4) link_NAG-ASN : angle 1.57881 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4428.66 seconds wall clock time: 76 minutes 27.93 seconds (4587.93 seconds total)